From e6c692a85b1d6673ff3c3189a23def3c40ed86f0 Mon Sep 17 00:00:00 2001 From: matentzn Date: Mon, 9 Sep 2019 15:17:43 +0100 Subject: [PATCH 01/11] First push ODK --- .gitignore | 22 ++ .travis.yml | 27 ++ src/metadata/README.md | 23 ++ src/metadata/geno.md | 46 +++ src/metadata/geno.yml | 27 ++ src/ontology/Dockerfile | 3 + src/ontology/Makefile | 348 ++++++++++++++++++ src/ontology/README-editors.md | 193 ++++++++++ src/ontology/build.sh | 2 + src/ontology/geno-edit.owl | 39 ++ src/ontology/geno-idranges.owl | 53 +++ src/ontology/geno.Makefile | 5 + src/ontology/imports/iao_import.owl | 14 + src/ontology/imports/iao_terms.txt | 2 + src/ontology/imports/ro_import.owl | 14 + src/ontology/imports/ro_terms.txt | 3 + src/ontology/imports/so_import.owl | 14 + src/ontology/imports/so_terms.txt | 4 + src/ontology/keeprelations.txt | 1 + src/ontology/ontologyterms.txt | 0 src/ontology/patterns.sh | 2 + src/ontology/prepare_release.sh | 2 + src/ontology/reports/README.md | 3 + src/ontology/run.bat | 1 + src/ontology/run.sh | 12 + src/ontology/test.sh | 2 + src/ontology/tmp/README.md | 1 + src/patterns/README.md | 0 src/patterns/definitions.owl | 11 + src/patterns/dosdp-patterns/external.txt | 1 + src/patterns/pattern.owl | 11 + src/sparql/README.md | 32 ++ src/sparql/basic-report.sparql | 12 + src/sparql/class-count-by-prefix.sparql | 10 + src/sparql/def-lacks-xref-violation.sparql | 12 + src/sparql/edges.sparql | 19 + .../equivalent-classes-violation.sparql | 14 + src/sparql/geno_terms.sparql | 7 + src/sparql/inject-subset-declaration.ru | 9 + src/sparql/labels.sparql | 9 + src/sparql/nolabels-violation.sparql | 13 + src/sparql/obsolete-violation.sparql | 24 ++ src/sparql/obsoletes.sparql | 14 + .../owldef-self-reference-violation.sparql | 11 + src/sparql/owldef-violation.sparql | 9 + .../redundant-subClassOf-violation.sparql | 15 + src/sparql/simple-seed.sparql | 12 + src/sparql/subsets-labeled.sparql | 14 + src/sparql/synonyms.sparql | 26 ++ src/sparql/terms.sparql | 7 + .../trailing-whitespace-violation.sparql | 11 + src/sparql/xref-syntax-violation.sparql | 13 + src/sparql/xrefs.sparql | 8 + 53 files changed, 1187 insertions(+) create mode 100644 .gitignore create mode 100644 .travis.yml create mode 100644 src/metadata/README.md create mode 100644 src/metadata/geno.md create mode 100644 src/metadata/geno.yml create mode 100644 src/ontology/Dockerfile create mode 100644 src/ontology/Makefile create mode 100644 src/ontology/README-editors.md create mode 100644 src/ontology/build.sh create mode 100644 src/ontology/geno-edit.owl create mode 100644 src/ontology/geno-idranges.owl create mode 100644 src/ontology/geno.Makefile create mode 100644 src/ontology/imports/iao_import.owl create mode 100644 src/ontology/imports/iao_terms.txt create mode 100644 src/ontology/imports/ro_import.owl create mode 100644 src/ontology/imports/ro_terms.txt create mode 100644 src/ontology/imports/so_import.owl create mode 100644 src/ontology/imports/so_terms.txt create mode 100644 src/ontology/keeprelations.txt create mode 100644 src/ontology/ontologyterms.txt create mode 100644 src/ontology/patterns.sh create mode 100644 src/ontology/prepare_release.sh create mode 100644 src/ontology/reports/README.md create mode 100644 src/ontology/run.bat create mode 100644 src/ontology/run.sh create mode 100644 src/ontology/test.sh create mode 100644 src/ontology/tmp/README.md create mode 100644 src/patterns/README.md create mode 100644 src/patterns/definitions.owl create mode 100644 src/patterns/dosdp-patterns/external.txt create mode 100644 src/patterns/pattern.owl create mode 100644 src/sparql/README.md create mode 100644 src/sparql/basic-report.sparql create mode 100644 src/sparql/class-count-by-prefix.sparql create mode 100644 src/sparql/def-lacks-xref-violation.sparql create mode 100644 src/sparql/edges.sparql create mode 100644 src/sparql/equivalent-classes-violation.sparql create mode 100644 src/sparql/geno_terms.sparql create mode 100644 src/sparql/inject-subset-declaration.ru create mode 100644 src/sparql/labels.sparql create mode 100644 src/sparql/nolabels-violation.sparql create mode 100644 src/sparql/obsolete-violation.sparql create mode 100644 src/sparql/obsoletes.sparql create mode 100644 src/sparql/owldef-self-reference-violation.sparql create mode 100644 src/sparql/owldef-violation.sparql create mode 100644 src/sparql/redundant-subClassOf-violation.sparql create mode 100644 src/sparql/simple-seed.sparql create mode 100644 src/sparql/subsets-labeled.sparql create mode 100644 src/sparql/synonyms.sparql create mode 100644 src/sparql/terms.sparql create mode 100644 src/sparql/trailing-whitespace-violation.sparql create mode 100644 src/sparql/xref-syntax-violation.sparql create mode 100644 src/sparql/xrefs.sparql diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..6af8efa --- /dev/null +++ b/.gitignore @@ -0,0 +1,22 @@ +.DS_Store +*.tmp +src/ontology/mirror +src/ontology/mirror/* +src/ontology/geno.owl +src/ontology/geno.obo +src/ontology/geno.json +src/ontology/geno-base.* +src/ontology/geno-basic.* +src/ontology/geno-full.* +src/ontology/geno-simple.* +src/ontology/geno-simple-non-classified.* +semantic.cache +bin/ +src/ontology/seed.txt +src/ontology/target/ +src/ontology/dosdp-tools.log +src/patterns/imports/seed_sorted.txt +src/ontology/ed_definitions_merged.owl +src/ontology/patterns +*.tmp.obo +*.tmp.owl \ No newline at end of file diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..6c19a18 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,27 @@ +## REMEMBER TO SET UP YOUR GIT REPO FOR TRAVIS +## Go to: https://travis-ci.org/monarch-initiative for details +sudo: required + +services: + - docker + +before_install: + - docker pull obolibrary/odkfull + +# command to run tests +script: cd src/ontology && sh run.sh make test + +#after_success: +# coveralls + +# whitelist +branches: + only: + - master + - test-travis + +### Add your own lists here +### See https://github.com/INCATools/ontology-development-kit/issues/35 +notifications: + email: + - obo-ci-reports-all@groups.io \ No newline at end of file diff --git a/src/metadata/README.md b/src/metadata/README.md new file mode 100644 index 0000000..dca52da --- /dev/null +++ b/src/metadata/README.md @@ -0,0 +1,23 @@ +Metadata files for the OBO Library + + * [geno.yml](geno.yml) + * Determines how your purl.obolibrary.org/obo/geno/ redirects will be handled + * Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config + * Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config) + * Paste in the contents of [geno.yml](geno.yml) + * Click "Commit new file" + * IMPORTANT: remember to make a pull request + * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library* + * [geno.md](geno.md) + * Determines how your metadata is shown on OBO Library, OLS and AberOWL + * Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology + * Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology) + * Paste in the contents of [geno.md](geno.md) + * Click "Commit new file" + * IMPORTANT: remember to make a pull request + * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library* + +For more background see: + + * http://obofoundry.org/ + * http://obofoundry.org/faq/how-do-i-edit-metadata.html \ No newline at end of file diff --git a/src/metadata/geno.md b/src/metadata/geno.md new file mode 100644 index 0000000..e7ebcd0 --- /dev/null +++ b/src/metadata/geno.md @@ -0,0 +1,46 @@ +--- +layout: ontology_detail +id: geno +title: GENO ontology +jobs: + - id: https://travis-ci.org/monarch-initiative/GENO-ontology + type: travis-ci +build: + checkout: git clone https://github.com/monarch-initiative/GENO-ontology.git + system: git + path: "." +contact: + email: + label: + github: +description: GENO ontology is an ontology... +domain: stuff +homepage: https://github.com/monarch-initiative/GENO-ontology +products: + - id: geno.owl + name: "GENO ontology main release in OWL format" + - id: geno.obo + name: "GENO ontology additional release in OBO format" + - id: geno.json + name: "GENO ontology additional release in OBOJSon format" + - id: geno/geno-base.owl + name: "GENO ontology main release in OWL format" + - id: geno/geno-base.obo + name: "GENO ontology additional release in OBO format" + - id: geno/geno-base.json + name: "GENO ontology additional release in OBOJSon format" +dependencies: +- id: ro +- id: iao +- id: so + +tracker: https://github.com/monarch-initiative/GENO-ontology/issues +license: + url: http://creativecommons.org/licenses/by/3.0/ + label: CC-BY +activity_status: active +--- + +Enter a detailed description of your ontology here. You can use arbitrary markdown and HTML. +You can also embed images too. + diff --git a/src/metadata/geno.yml b/src/metadata/geno.yml new file mode 100644 index 0000000..c86715b --- /dev/null +++ b/src/metadata/geno.yml @@ -0,0 +1,27 @@ +# PURL configuration for http://purl.obolibrary.org/obo/geno + +idspace: GENO +base_url: /obo/geno + +products: +- geno.owl: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/master/geno.owl +- geno.obo: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/master/geno.obo + +term_browser: ontobee +example_terms: +- geno_0000000 + +entries: + +- prefix: /releases/ + replacement: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/v + +- prefix: /tracker/ + replacement: https://github.com/monarch-initiative/GENO-ontology/issues + +- prefix: /about/ + replacement: http://www.ontobee.org/ontology/GENO?iri=http://purl.obolibrary.org/obo/ + +## generic fall-through, serve direct from github by default +- prefix: / + replacement: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/master/ diff --git a/src/ontology/Dockerfile b/src/ontology/Dockerfile new file mode 100644 index 0000000..661e66d --- /dev/null +++ b/src/ontology/Dockerfile @@ -0,0 +1,3 @@ +FROM cmungall/osk + +CMD make test diff --git a/src/ontology/Makefile b/src/ontology/Makefile new file mode 100644 index 0000000..2bb52e5 --- /dev/null +++ b/src/ontology/Makefile @@ -0,0 +1,348 @@ +# ---------------------------------------- +# Makefile for geno +# Generated using ontology-starter-kit +# ODK Version: v1.2.17 +# ---------------------------------------- +# + +# ---------------------------------------- +# Standard Constants +# ---------------------------------------- +# these can be overwritten on the command line + +URIBASE= http://purl.obolibrary.org/obo +ONT= geno +ONTBASE= $(URIBASE)/$(ONT) +EDIT_FORMAT= owl +SRC = $(ONT)-edit.$(EDIT_FORMAT) +CATALOG= catalog-v001.xml +ROBOT= robot --catalog $(CATALOG) +RELEASEDIR= ../.. +PATTERNDIR= ../patterns +REPORTDIR= reports +SPARQLDIR = ../sparql +REPORT_FAIL_ON = None +OBO_FORMAT_OPTIONS = +SPARQL_VALIDATION_CHECKS = equivalent-classes trailing-whitespace owldef-self-reference xref-syntax nolabels +SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms +ODK_VERSION = v1.2.17 + +TODAY ?= $(shell date +%Y-%m-%d) +OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') + + +FORMATS = $(sort owl obo json owl) +FORMATS_INCL_TSV = $(sort $(FORMAT) tsv) +RELEASE_ARTEFACTS = $(sort base full base full) + +# ---------------------------------------- +# Top-level targets +# ---------------------------------------- + +.PHONY: .FORCE +all: odkversion all_imports all_main all_subsets sparql_test all_reports all_assets +test: odkversion sparql_test all_reports + $(ROBOT) reason --input $(SRC) --reasoner ELK --equivalent-classes-allowed all --output test.owl && rm test.owl && echo "Success" + +odkversion: + echo "ODK Makefile version: $(ODK_VERSION) (this is the version of the ODK with which this Makefile was generated, not the version of the ODK you are running)" &&\ + echo "ROBOT version (ODK): " && $(ROBOT) --version + +## -- main targets -- +## +## By default this is the cross-product of {ont, ont-base} x FORMATS + +MAIN_PRODUCTS = $(sort $(foreach r,$(RELEASE_ARTEFACTS), $(ONT)-$(r)) $(ONT)) +MAIN_GZIPPED = +MAIN_FILES = $(foreach n,$(MAIN_PRODUCTS), $(foreach f,$(FORMATS), $(n).$(f))) $(MAIN_GZIPPED) + +all_main: $(MAIN_FILES) + +## -- import targets -- +## +## By default this is the cross-product of IMPORT_MODULES x FORMATS + + +IMPORTS = ro iao so + +IMPORT_ROOTS = $(patsubst %, imports/%_import, $(IMPORTS)) +IMPORT_FILES = $(foreach n,$(IMPORT_ROOTS), $(foreach f,$(FORMATS), $(n).$(f))) +IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) + +all_imports: $(IMPORT_FILES) + +all_imports_owl: $(foreach n,$(IMPORT_ROOTS), $(n).owl) + +all_imports_obo: $(foreach n,$(IMPORT_ROOTS), $(n).obo) + +all_imports_json: $(foreach n,$(IMPORT_ROOTS), $(n).json) + + +## -- subset targets -- +## +## By default this is the cross-product of SUBSETS x FORMATS +## Note we also include TSV as a format + + +SUBSETS = + +SUBSET_ROOTS = $(patsubst %, subsets/%, $(SUBSETS)) +SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f))) + +all_subsets: $(SUBSET_FILES) + +## -- dosdp pattern targets -- +## + + +PATTERNS = + +PATTERN_ROOTS = $(patsubst %, $(PATTERNDIR)/%, $(PATTERNS)) +PATTERN_FILES = $(foreach n,$(PATTERN_ROOTS), $(n).owl) + +all_patterns: $(PATTERN_FILES) + +## -- dosdp pattern targets -- +## + +OBO_REPORT = $(SRC)-obo-report +REPORTS = $(OBO_REPORT) +REPORT_FILES = $(patsubst %, $(REPORTDIR)/%.tsv, $(REPORTS)) + +all_reports: all_reports_onestep $(REPORT_FILES) + +## -- all files/assets -- + +ASSETS = \ + $(IMPORT_FILES) \ + $(MAIN_FILES) \ + $(REPORT_FILES) \ + $(SUBSET_FILES) + +all_assets: $(ASSETS) + +show_assets: + echo $(ASSETS) + du -sh $(ASSETS) + + +# ---------------------------------------- +# Release Management +# ---------------------------------------- + +KEEPRELATIONS=keeprelations.txt +ONTOLOGYTERMS=ontologyterms.txt +SIMPLESEED=simple_seed.txt + +# This should be executed by the release manager whenever time comes to make a release. +# It will ensure that all assets/files are fresh, and will copy to release folder +prepare_release: $(ASSETS) $(PATTERN_RELEASE_FILES) + rsync -R $(ASSETS) $(RELEASEDIR) &&\ + echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab" + +prepare_initial_release: prepare_release + cd $(RELEASEDIR) && git add $(ASSETS) + +# ---------------------------------------- +# Export formats +# ---------------------------------------- + + +$(ONT)-base.obo: $(ONT)-base.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo +$(ONT)-base.json: $(ONT)-base.owl + $(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ \ + convert --check false -f json -o $@.tmp.json && mv $@.tmp.json $@ +$(ONT)-full.obo: $(ONT)-full.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo +$(ONT)-full.json: $(ONT)-full.owl + $(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ \ + convert --check false -f json -o $@.tmp.json && mv $@.tmp.json $@ +# Main release artefacts +$(ONT).owl: $(ONT)-full.owl + $(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ \ + convert -o $@.tmp.owl && mv $@.tmp.owl $@ + +$(ONT).obo: $(ONT).owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo +$(ONT).json: $(ONT)-full.owl + $(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY) \ + convert --check false -f json -o $@.tmp.json && mv $@.tmp.json $@ +# ---------------------------------------- +# Initiating Step: Reason over source +# ---------------------------------------- + +ANNOTATE_VERSION_IRI = annotate -V $(ONTBASE)/releases/$(TODAY)/$@.owl + +# by default we use ELK to perform a reason-relax-reduce chain +# after that we annotate the ontology with the release versionInfo + +OTHER_SRC = + + +$(ONTOLOGYTERMS): $(SRC) $(OTHER_SRC) + $(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/geno_terms.sparql $@ + + + + + + + + + + + +# base: OTHER sources of interest, such as definitions owl +$(ONT)-base.owl: $(SRC) $(OTHER_SRC) + $(ROBOT) remove --input $< --select imports --trim false \ + merge $(patsubst %, -i %, $(OTHER_SRC)) \ + annotate --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ --output $@.tmp.owl && mv $@.tmp.owl $@ + +# Full: The full artefacts with imports merged, reasoned +$(ONT)-full.owl: $(SRC) $(OTHER_SRC) + $(ROBOT) merge --input $< \ + reason --reasoner ELK --equivalent-classes-allowed all \ + relax \ + reduce -r ELK \ + annotate --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ --output $@.tmp.owl && mv $@.tmp.owl $@ + +# ---------------------------------------- +# Import modules +# ---------------------------------------- +# Most ontologies are modularly constructed using portions of other ontologies +# These live in the imports/ folder + +# seed.txt contains all referenced entities + + +seed.txt: $(SRC) + @if [ $(IMP) = true ]; then $(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/terms.sparql $@; fi + + +# Generate terms.txt for each import. (Assume OBO-style Possibly hacky step?) +# Should be able to drop this if robot can just take a big messy list of terms as input. + +imports/%_terms_combined.txt: seed.txt imports/%_terms.txt + @if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi + +# -- Generate Import Modules -- +# +# This pattern uses ROBOT to generate an import module +imports/%_import.owl: mirror/%.owl imports/%_terms_combined.txt + @if [ $(IMP) = true ]; then $(ROBOT) extract -i $< -T imports/$*_terms_combined.txt --force true --method BOT \ + query --update ../sparql/inject-subset-declaration.ru \ + annotate --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ --output $@.tmp.owl && mv $@.tmp.owl $@; fi +.PRECIOUS: imports/%_import.owl + +# convert imports to obo. +# this can be useful for spot-checks and diffs. +# we set strict mode to false by default. For discussion see https://github.com/owlcs/owlapi/issues/752 +imports/%_import.obo: imports/%_import.owl + @if [ $(IMP) = true ]; then $(ROBOT) convert --check false -i $< -f obo -o $@.tmp.obo && mv $@.tmp.obo $@; fi +imports/%_import.json: imports/%_import.owl + @if [ $(IMP) = true ]; then $(ROBOT) convert --check false -i $< -f json -o $@.tmp.json && mv $@.tmp.json $@; fi + + +# ---------------------------------------- +# Mirroring upstream ontologies +# ---------------------------------------- +# + +IMP=true # Global parameter to bypass import generation +MIR=true # Global parameter to bypass mirror generation + + + +## ONTOLOGY: ro +## Copy of ro is re-downloaded whenever source changes +mirror/ro.trigger: $(SRC) + +mirror/ro.owl: mirror/ro.trigger + @if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I $(URIBASE)/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi + +.PRECIOUS: mirror/%.owl + + +## ONTOLOGY: iao +## Copy of iao is re-downloaded whenever source changes +mirror/iao.trigger: $(SRC) + +mirror/iao.owl: mirror/iao.trigger + @if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I $(URIBASE)/iao.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi + +.PRECIOUS: mirror/%.owl + + +## ONTOLOGY: so +## Copy of so is re-downloaded whenever source changes +mirror/so.trigger: $(SRC) + +mirror/so.owl: mirror/so.trigger + @if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I $(URIBASE)/so.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi + +.PRECIOUS: mirror/%.owl + + + +# ---------------------------------------- +# Subsets +# ---------------------------------------- +subsets/%.tsv: subsets/%.owl + $(ROBOT) query -f tsv -i $< -s ../sparql/labels.sparql $@ +subsets/%.owl: $(ONT).owl + owltools --use-catalog $< --extract-ontology-subset --fill-gaps --subset $* -o $@.tmp.owl && mv $@.tmp.owl $@ + + +# ---------------------------------------- +# Release +# ---------------------------------------- +# copy from staging area (this directory) to top-level +release: $(ONT).owl $(ONT).obo + cp $^ $(RELEASEDIR) && cp imports/* $(RELEASEDIR)/imports + +# ---------------------------------------- +# Sparql queries: Q/C +# ---------------------------------------- + +# these live in the ../sparql directory, and have suffix -violation.sparql +# adding the name here will make the violation check live. +# NOTE: these will soon be phased out and replaced by robot-report + +# run all violation checks +SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$V-violation.sparql) +sparql_test: $(SRC) + $(ROBOT) verify --catalog catalog-v001.xml -i $< --queries $(SPARQL_VALIDATION_QUERIES) -O reports/ + +# ---------------------------------------- +# ROBOT report +# ---------------------------------------- +reports/%-obo-report.tsv: % + $(ROBOT) report -i $< --fail-on $(REPORT_FAIL_ON) -o $@ + +# ---------------------------------------- +# Sparql queries: Exports +# ---------------------------------------- + +SPARQL_EXPORTS_ARGS = $(foreach V,$(SPARQL_EXPORTS),-s $(SPARQLDIR)/$V.sparql reports/$V.tsv) +# This combines all into one single command +all_reports_onestep: $(SRC) + $(ROBOT) query -f tsv -i $< $(SPARQL_EXPORTS_ARGS) + + +# ---------------------------------------- +# Docker (experimental) +# ---------------------------------------- +IM=build-$(ONT) +build-docker: + docker build -t $(ONT) . + + + + + + + + + +include geno.Makefile \ No newline at end of file diff --git a/src/ontology/README-editors.md b/src/ontology/README-editors.md new file mode 100644 index 0000000..f4333a5 --- /dev/null +++ b/src/ontology/README-editors.md @@ -0,0 +1,193 @@ +These notes are for the EDITORS of geno + +This project was created using the [ontology development kit](https://github.com/INCATools/ontology-development-kit). See the site for details. + +For more details on ontology management, please see the [OBO tutorial](https://github.com/jamesaoverton/obo-tutorial) or the [Gene Ontology Editors Tutorial](https://go-protege-tutorial.readthedocs.io/en/latest/) + +You may also want to read the [GO ontology editors guide](http://go-ontology.readthedocs.org/) + +## Requirements + + 1. Protege (for editing) + 2. A git client (we assume command line git) + 3. [docker](https://www.docker.com/get-docker) (for managing releases) + +## Editors Version + +Make sure you have an ID range in the [idranges file](geno-idranges.owl) + +If you do not have one, get one from the maintainer of this repo. + +The editors version is [geno-edit.owl](geno-edit.owl) + +** DO NOT EDIT geno.obo OR geno.owl in the top level directory ** + +[../../geno.owl](../../geno.owl) is the release version + +To edit, open the file in Protege. First make sure you have the repository cloned, see [the GitHub project](https://github.com/monarch-initiative/GENO-ontology) for details. + +You should discuss the git workflow you should use with the maintainer +of this repo, who should document it here. If you are the maintainer, +you can contact the odk developers for assistance. You may want to +copy the flow an existing project, for example GO: [Gene Ontology +Editors Tutorial](https://go-protege-tutorial.readthedocs.io/en/latest/). + +In general, it is bad practice to commit changes to master. It is +better to make changes on a branch, and make Pull Requests. + +## ID Ranges + +These are stored in the file + + * [geno-idranges.owl](geno-idranges.owl) + +** ONLY USE IDs WITHIN YOUR RANGE!! ** + +If you have only just set up this repository, modify the idranges file + and add yourself or other editors. Note Protege does not read the file +- it is up to you to ensure correct Protege configuration. + + +### Setting ID ranges in Protege + +We aim to put this up on the technical docs for OBO on http://obofoundry.org/ + +For now, consult the [GO Tutorial on configuring Protege](http://go-protege-tutorial.readthedocs.io/en/latest/Entities.html#new-entities) + +## Imports + +All import modules are in the [imports/](imports/) folder. + +There are two ways to include new classes in an import module + + 1. Reference an external ontology class in the edit ontology. In Protege: "add new entity", then paste in the PURL + 2. Add to the imports/geno_terms.txt file + +After doing this, you can run + +`./run.sh make all_imports` + +to regenerate imports. + +Note: the geno_terms.txt file may include 'starter' classes seeded from +the ontology starter kit. It is safe to remove these. + +## Design patterns + +You can automate (class) term generation from design patterns by placing DOSDP +yaml file and tsv files under src/patterns. Any pair of files in this +folder that share a name (apart from the extension) are assumed to be +a DOSDP design pattern and a corresponding tsv specifying terms to +add. + +Design patterns can be used to maintain and generate complete terms +(names, definitions, synonyms etc) or to generate logical axioms +only, with other axioms being maintained in editors file. This can be +specified on a per-term basis in the TSV file. + +Design pattern docs are checked for validity via Travis, but can be +tested locally using + +`./run.sh make patterns` + +In addition to running standard tests, this command generates an owl +file (`src/patterns/pattern.owl`), which demonstrates the relationships +between design patterns. + +(At the time of writing, the following import statements need to be +added to `src/patterns/pattern.owl` for all imports generated in +`src/imports/*_import.owl`. This will be automated in a future release.') + +To compile design patterns to terms run: + +`./run.sh make ../patterns/definitions.owl` + +This generates a file (`src/patterns/definitions.owl`). You then need +to add an import statement to the editor's file to import the +definitions file. + + +## Release Manager notes + +You should only attempt to make a release AFTER the edit version is +committed and pushed, AND the travis build passes. + +These instructions assume you have +[docker](https://www.docker.com/get-docker). This folder has a script +[run.sh](run.sh) that wraps docker commands. + +to release: + +first type + + git branch + +to make sure you are on master + + cd src/ontology + ./build.sh + +If this looks good type: + + ./prepare_release.sh + +This generates derived files such as geno.owl and geno.obo and places +them in the top level (../..). + +Note that the versionIRI value automatically will be added, and will +end with YYYY-MM-DD, as per OBO guidelines. + +Commit and push these files. + + git commit -a + +And type a brief description of the release in the editor window + +Finally type: + + git push origin master + +IMMEDIATELY AFTERWARDS (do *not* make further modifications) go here: + + * https://github.com/monarch-initiative/GENO-ontology/releases + * https://github.com/monarch-initiative/GENO-ontology/releases/new + +__IMPORTANT__: The value of the "Tag version" field MUST be + + vYYYY-MM-DD + +The initial lowercase "v" is REQUIRED. The YYYY-MM-DD *must* match +what is in the `owl:versionIRI` of the derived geno.owl (`data-version` in +geno.obo). This will be today's date. + +This cannot be changed after the fact, be sure to get this right! + +Release title should be YYYY-MM-DD, optionally followed by a title (e.g. "january release") + +You can also add release notes (this can also be done after the fact). These are in markdown format. +In future we will have better tools for auto-generating release notes. + +Then click "publish release" + +__IMPORTANT__: NO MORE THAN ONE RELEASE PER DAY. + +The PURLs are already configured to pull from github. This means that +BOTH ontology purls and versioned ontology purls will resolve to the +correct ontologies. Try it! + + * http://purl.obolibrary.org/obo/geno.owl <-- current ontology PURL + * http://purl.obolibrary.org/obo/geno/releases/YYYY-MM-DD.owl <-- change to the release you just made + +For questions on this contact Chris Mungall or email obo-admin AT obofoundry.org + +# Travis Continuous Integration System + +Check the build status here: [![Build Status](https://travis-ci.org/monarch-initiative/GENO-ontology.svg?branch=master)](https://travis-ci.org/monarch-initiative/GENO-ontology) + +Note: if you have only just created this project you will need to authorize travis for this repo. + + 1. Go to [https://travis-ci.org/profile/monarch-initiative](https://travis-ci.org/profile/monarch-initiative) + 2. click the "Sync account" button + 3. Click the tick symbol next to GENO-ontology + +Travis builds should now be activated \ No newline at end of file diff --git a/src/ontology/build.sh b/src/ontology/build.sh new file mode 100644 index 0000000..22add54 --- /dev/null +++ b/src/ontology/build.sh @@ -0,0 +1,2 @@ +#!/bin/sh +./run.sh make all diff --git a/src/ontology/geno-edit.owl b/src/ontology/geno-edit.owl new file mode 100644 index 0000000..52f0f7b --- /dev/null +++ b/src/ontology/geno-edit.owl @@ -0,0 +1,39 @@ + +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) +Prefix(dce:=) +Prefix(dcterms:=) + + +Ontology( + +Import() + +Import() + +Import() + + + +Annotation(dce:title "GENO ontology") +Annotation(dcterms:license "Unspecified") +Annotation(dce:description "None") + +Declaration(Class()) + + +############################ +# Classes +############################ + +# Class: + +AnnotationAssertion(rdfs:label "root node"@en) + + +) + diff --git a/src/ontology/geno-idranges.owl b/src/ontology/geno-idranges.owl new file mode 100644 index 0000000..55796a8 --- /dev/null +++ b/src/ontology/geno-idranges.owl @@ -0,0 +1,53 @@ +## ID Ranges File +Prefix: rdf: +Prefix: idsfor: +Prefix: dc: +Prefix: xsd: +Prefix: allocatedto: +Prefix: xml: +Prefix: idprefix: +Prefix: iddigits: +Prefix: rdfs: +Prefix: idrange: +Prefix: owl: + +Ontology: + + +Annotations: + idsfor: "GENO", + idprefix: "http://purl.obolibrary.org/obo/GENO_", + iddigits: 7 + +AnnotationProperty: idprefix: + + +AnnotationProperty: iddigits: + + +AnnotationProperty: idsfor: + + +AnnotationProperty: allocatedto: + +Datatype: idrange:1 + + Annotations: + allocatedto: "ONTOLOGY-CREATOR" + + EquivalentTo: + xsd:integer[>= 0 , <= 999999] + + +Datatype: idrange:2 + + Annotations: + allocatedto: "ADDITIONAL EDITOR" + + EquivalentTo: + xsd:integer[>= 1000000 , <= 1999999] + + +Datatype: xsd:integer +Datatype: rdf:PlainLiteral + diff --git a/src/ontology/geno.Makefile b/src/ontology/geno.Makefile new file mode 100644 index 0000000..e4e87b4 --- /dev/null +++ b/src/ontology/geno.Makefile @@ -0,0 +1,5 @@ +## Customize Makefile settings for geno +## +## If you need to customize your Makefile, make +## changes here rather than in the main Makefile + diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl new file mode 100644 index 0000000..38752b0 --- /dev/null +++ b/src/ontology/imports/iao_import.owl @@ -0,0 +1,14 @@ + + + + + + diff --git a/src/ontology/imports/iao_terms.txt b/src/ontology/imports/iao_terms.txt new file mode 100644 index 0000000..b6d1a4e --- /dev/null +++ b/src/ontology/imports/iao_terms.txt @@ -0,0 +1,2 @@ +IAO:0000577 + diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl new file mode 100644 index 0000000..263fa34 --- /dev/null +++ b/src/ontology/imports/ro_import.owl @@ -0,0 +1,14 @@ + + + + + + diff --git a/src/ontology/imports/ro_terms.txt b/src/ontology/imports/ro_terms.txt new file mode 100644 index 0000000..ad63866 --- /dev/null +++ b/src/ontology/imports/ro_terms.txt @@ -0,0 +1,3 @@ +BFO:0000050 +RO:0002202 + diff --git a/src/ontology/imports/so_import.owl b/src/ontology/imports/so_import.owl new file mode 100644 index 0000000..e27f414 --- /dev/null +++ b/src/ontology/imports/so_import.owl @@ -0,0 +1,14 @@ + + + + + + diff --git a/src/ontology/imports/so_terms.txt b/src/ontology/imports/so_terms.txt new file mode 100644 index 0000000..65725e0 --- /dev/null +++ b/src/ontology/imports/so_terms.txt @@ -0,0 +1,4 @@ +SO:0000000 +SO:0000001 +SO:0000002 + diff --git a/src/ontology/keeprelations.txt b/src/ontology/keeprelations.txt new file mode 100644 index 0000000..f55fc52 --- /dev/null +++ b/src/ontology/keeprelations.txt @@ -0,0 +1 @@ +BFO:0000050 \ No newline at end of file diff --git a/src/ontology/ontologyterms.txt b/src/ontology/ontologyterms.txt new file mode 100644 index 0000000..e69de29 diff --git a/src/ontology/patterns.sh b/src/ontology/patterns.sh new file mode 100644 index 0000000..e2fb401 --- /dev/null +++ b/src/ontology/patterns.sh @@ -0,0 +1,2 @@ +#!/bin/sh +./run.sh make patterns diff --git a/src/ontology/prepare_release.sh b/src/ontology/prepare_release.sh new file mode 100644 index 0000000..6aefd94 --- /dev/null +++ b/src/ontology/prepare_release.sh @@ -0,0 +1,2 @@ +#!/bin/sh +./run.sh make prepare_release diff --git a/src/ontology/reports/README.md b/src/ontology/reports/README.md new file mode 100644 index 0000000..933492c --- /dev/null +++ b/src/ontology/reports/README.md @@ -0,0 +1,3 @@ +# Reports folder + +Files are added to this during the release process diff --git a/src/ontology/run.bat b/src/ontology/run.bat new file mode 100644 index 0000000..717ca49 --- /dev/null +++ b/src/ontology/run.bat @@ -0,0 +1 @@ +docker run -v %cd%\..\..\:/work -w /work/src/ontology --rm -ti obolibrary/odkfull %* diff --git a/src/ontology/run.sh b/src/ontology/run.sh new file mode 100644 index 0000000..24126d2 --- /dev/null +++ b/src/ontology/run.sh @@ -0,0 +1,12 @@ +#!/bin/sh +# Wrapper script for docker. +# +# This is used primarily for wrapping the GNU Make workflow. +# Instead of typing "make TARGET", type "./run.sh make TARGET". +# This will run the make workflow within a docker container. +# +# The assumption is that you are working in the src/ontology folder; +# we therefore map the whole repo (../..) to a docker volume. +# +# See README-editors.md for more details. +docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx8G' --rm -ti obolibrary/odkfull "$@" \ No newline at end of file diff --git a/src/ontology/test.sh b/src/ontology/test.sh new file mode 100644 index 0000000..dfd54a7 --- /dev/null +++ b/src/ontology/test.sh @@ -0,0 +1,2 @@ +#!/bin/sh +./run.sh make test diff --git a/src/ontology/tmp/README.md b/src/ontology/tmp/README.md new file mode 100644 index 0000000..1ad5315 --- /dev/null +++ b/src/ontology/tmp/README.md @@ -0,0 +1 @@ +# This folder contains files that are regenerated with every release to keep the src/ontology folder clean \ No newline at end of file diff --git a/src/patterns/README.md b/src/patterns/README.md new file mode 100644 index 0000000..e69de29 diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl new file mode 100644 index 0000000..64d9ab8 --- /dev/null +++ b/src/patterns/definitions.owl @@ -0,0 +1,11 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +) \ No newline at end of file diff --git a/src/patterns/dosdp-patterns/external.txt b/src/patterns/dosdp-patterns/external.txt new file mode 100644 index 0000000..09e32e0 --- /dev/null +++ b/src/patterns/dosdp-patterns/external.txt @@ -0,0 +1 @@ +http://purl.obolibrary.org/obo/upheno/patterns/abnormalAnatomicalEntity.yaml \ No newline at end of file diff --git a/src/patterns/pattern.owl b/src/patterns/pattern.owl new file mode 100644 index 0000000..b9e4ae3 --- /dev/null +++ b/src/patterns/pattern.owl @@ -0,0 +1,11 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +) \ No newline at end of file diff --git a/src/sparql/README.md b/src/sparql/README.md new file mode 100644 index 0000000..93582ca --- /dev/null +++ b/src/sparql/README.md @@ -0,0 +1,32 @@ +# Sparql checks + +[SPARQL](https://www.w3.org/TR/rdf-sparql-query/) is a W3C standard +query language for RDF. This directory contains useful SPARQL queries +for perfoming over the ontology. + +SPARQL can be executed on a triplestore or directly on any OWL +file. The queries here are all executed on either geno-edit.obo or +downstream products in the [ontology](../ontology/) folder. We use +`robot` as this allows easy execution over any Obo-format or OWL file. + +We break the queries into 3 categories: + +## Constraint Violation checks + +These are all named `*violation.sparql`. A subset of these are +configured to be executed via travis. If these return any results, +then the build will fail. + +Consult the individual sparql files to see the intent of the check + +## Construct queries + +These are named `construct*.sparql`, and always have the form `CONSTRUCT ...`. + +These are used to generate new OWL axioms that can be inserted back +into the ontology. + +## Reports + +The remaining SPARQL queries are for informative purposes. A subset +may be executed with each release. \ No newline at end of file diff --git a/src/sparql/basic-report.sparql b/src/sparql/basic-report.sparql new file mode 100644 index 0000000..cff9773 --- /dev/null +++ b/src/sparql/basic-report.sparql @@ -0,0 +1,12 @@ +prefix oio: +prefix def: +prefix owl: + +SELECT ?cls ?def (group_concat(?xref) as ?xrefs) WHERE +{ + ?cls a owl:Class . + OPTIONAL { ?cls oio:hasDbXref ?xref } . + OPTIONAL { ?cls def: ?def } . + FILTER (!isBlank(?cls)) +} +GROUP BY ?cls ?def diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql new file mode 100644 index 0000000..0c4d284 --- /dev/null +++ b/src/sparql/class-count-by-prefix.sparql @@ -0,0 +1,10 @@ +prefix owl: +prefix obo: + +SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE +{ + ?cls a owl:Class . + FILTER (!isBlank(?cls)) + BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix) +} +GROUP BY ?prefix diff --git a/src/sparql/def-lacks-xref-violation.sparql b/src/sparql/def-lacks-xref-violation.sparql new file mode 100644 index 0000000..cff9773 --- /dev/null +++ b/src/sparql/def-lacks-xref-violation.sparql @@ -0,0 +1,12 @@ +prefix oio: +prefix def: +prefix owl: + +SELECT ?cls ?def (group_concat(?xref) as ?xrefs) WHERE +{ + ?cls a owl:Class . + OPTIONAL { ?cls oio:hasDbXref ?xref } . + OPTIONAL { ?cls def: ?def } . + FILTER (!isBlank(?cls)) +} +GROUP BY ?cls ?def diff --git a/src/sparql/edges.sparql b/src/sparql/edges.sparql new file mode 100644 index 0000000..5fec04e --- /dev/null +++ b/src/sparql/edges.sparql @@ -0,0 +1,19 @@ +prefix obo: +prefix owl: +prefix rdfs: +prefix rdf: + +SELECT ?x ?p ?y +WHERE { + {?x rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty ?p ; + owl:someValuesFrom ?y ] + } + UNION { + ?x rdfs:subClassOf ?y . + BIND(rdfs:subClassOf AS ?p) + } + ?x a owl:Class . + ?y a owl:Class . +} diff --git a/src/sparql/equivalent-classes-violation.sparql b/src/sparql/equivalent-classes-violation.sparql new file mode 100644 index 0000000..ed5ccdd --- /dev/null +++ b/src/sparql/equivalent-classes-violation.sparql @@ -0,0 +1,14 @@ +prefix oio: +prefix owl: +prefix rdfs: + +SELECT ?baseClass ?baseLabel ?equivalentClass ?equivalentLabel WHERE +{ + ?baseClass owl:equivalentClass ?equivalentClass . + ?baseClass rdfs:label ?baseLabel . + ?equivalentClass rdfs:label ?equivalentLabel . + + FILTER (!isBlank(?baseClass)) . + FILTER (!isBlank(?equivalentClass)) + +} diff --git a/src/sparql/geno_terms.sparql b/src/sparql/geno_terms.sparql new file mode 100644 index 0000000..de9b8a2 --- /dev/null +++ b/src/sparql/geno_terms.sparql @@ -0,0 +1,7 @@ +SELECT DISTINCT ?term +WHERE { + { ?s1 ?p1 ?term . } + UNION + { ?term ?p2 ?o2 . } + FILTER(isIRI(?term) && (regex(str(?term), UCASE("geno_")))) +} diff --git a/src/sparql/inject-subset-declaration.ru b/src/sparql/inject-subset-declaration.ru new file mode 100644 index 0000000..d7368cb --- /dev/null +++ b/src/sparql/inject-subset-declaration.ru @@ -0,0 +1,9 @@ +PREFIX : +PREFIX rdf: +PREFIX rdfs: + +INSERT { ?y rdfs:subPropertyOf . } + +WHERE { + ?x ?y . +} \ No newline at end of file diff --git a/src/sparql/labels.sparql b/src/sparql/labels.sparql new file mode 100644 index 0000000..89e9ec7 --- /dev/null +++ b/src/sparql/labels.sparql @@ -0,0 +1,9 @@ +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: + +SELECT ?x (STR(?lab) AS ?label) WHERE { + ?x rdf:type owl:Class . + OPTIONAL {?x rdfs:label ?lab} +} +ORDER BY ?x diff --git a/src/sparql/nolabels-violation.sparql b/src/sparql/nolabels-violation.sparql new file mode 100644 index 0000000..d506a41 --- /dev/null +++ b/src/sparql/nolabels-violation.sparql @@ -0,0 +1,13 @@ +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX replaced_by: + +SELECT ?cls WHERE { + ?cls a owl:Class + FILTER NOT EXISTS {?cls rdfs:label ?lab} + FILTER NOT EXISTS {?cls replaced_by: ?replCls} + FILTER (!isBlank(?cls)) + FILTER ( regex(str(?cls), "^http://purl.obolibrary.org/obo/GO_")) +} +ORDER BY ?cls diff --git a/src/sparql/obsolete-violation.sparql b/src/sparql/obsolete-violation.sparql new file mode 100644 index 0000000..c81bf71 --- /dev/null +++ b/src/sparql/obsolete-violation.sparql @@ -0,0 +1,24 @@ +prefix xsd: +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX replaced_by: +PREFIX consider: + +SELECT ?cls ?clsLabel ?rule WHERE { + ?cls a owl:Class ; + rdfs:label ?clsLabel ; + owl:deprecated "true"^^xsd:boolean + { + { + FILTER ( ! regex(str(?clsLabel), "^obsolete ") ) + BIND ("obsolete label must start with obsolete" AS ?rule) + } + UNION + { + ?cls rdfs:subClassOf ?parent + BIND("no logical axioms for obsolete" AS ?rule) + } + } +} +ORDER BY ?cls diff --git a/src/sparql/obsoletes.sparql b/src/sparql/obsoletes.sparql new file mode 100644 index 0000000..7aff433 --- /dev/null +++ b/src/sparql/obsoletes.sparql @@ -0,0 +1,14 @@ +prefix xsd: +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX replaced_by: +PREFIX consider: + +SELECT ?cls ?replCls ?consCls WHERE { + ?cls a owl:Class ; + owl:deprecated "true"^^xsd:boolean . + OPTIONAL {?cls replaced_by: ?replCls} + OPTIONAL {?cls consider: ?consCls} +} +ORDER BY ?cls diff --git a/src/sparql/owldef-self-reference-violation.sparql b/src/sparql/owldef-self-reference-violation.sparql new file mode 100644 index 0000000..63857fe --- /dev/null +++ b/src/sparql/owldef-self-reference-violation.sparql @@ -0,0 +1,11 @@ +prefix rdf: +prefix oio: +prefix owl: +prefix rdfs: + +SELECT ?c +WHERE { + { ?c owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?c ] ] } + UNION + { ?c owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?c ] ] ] } +} diff --git a/src/sparql/owldef-violation.sparql b/src/sparql/owldef-violation.sparql new file mode 100644 index 0000000..3b59f88 --- /dev/null +++ b/src/sparql/owldef-violation.sparql @@ -0,0 +1,9 @@ +prefix oio: +prefix owl: +prefix rdfs: + +WELECT * +WHERE { + ?c rdfs:subClassOf ?d ; + owl:equivalentClass [ + owl:intersectionOf TODO diff --git a/src/sparql/redundant-subClassOf-violation.sparql b/src/sparql/redundant-subClassOf-violation.sparql new file mode 100644 index 0000000..bed15cd --- /dev/null +++ b/src/sparql/redundant-subClassOf-violation.sparql @@ -0,0 +1,15 @@ +prefix oio: +prefix owl: +prefix rdfs: + +SELECT ?x ?xl ?y ?yl ?z ?zl WHERE +{ + ?x rdfs:subClassOf ?y ; + rdfs:label ?xl . + ?y rdfs:subClassOf+ ?z ; + rdfs:label ?yl . + ?x rdfs:subClassOf ?z . + ?z rdfs:label ?zl . + + +} diff --git a/src/sparql/simple-seed.sparql b/src/sparql/simple-seed.sparql new file mode 100644 index 0000000..e62d216 --- /dev/null +++ b/src/sparql/simple-seed.sparql @@ -0,0 +1,12 @@ +prefix owl: +prefix obo: + +SELECT DISTINCT ?cls WHERE +{ + {?cls a owl:ObjectProperty .} + UNION + {?x ?cls} + UNION + {?x ?cls} + FILTER (!isBlank(?cls)) +} diff --git a/src/sparql/subsets-labeled.sparql b/src/sparql/subsets-labeled.sparql new file mode 100644 index 0000000..9f8aca6 --- /dev/null +++ b/src/sparql/subsets-labeled.sparql @@ -0,0 +1,14 @@ +prefix oio: +prefix def: +prefix owl: +prefix inSubset: +prefix rdfs: + +SELECT ?subset ?clsLabel +WHERE +{ + ?cls a owl:Class . + inSubset: ?subset ; + rdfs:label ?clsLabel +} +ORDER BY ?subset ?cls diff --git a/src/sparql/synonyms.sparql b/src/sparql/synonyms.sparql new file mode 100644 index 0000000..ba6b03a --- /dev/null +++ b/src/sparql/synonyms.sparql @@ -0,0 +1,26 @@ +prefix owl: +prefix oboInOwl: +prefix rdfs: + +SELECT ?cls ?pred ?val ?synType +WHERE + { ?cls ?pred ?val ; + a owl:Class . + FILTER ( + ?pred = rdfs:label || + ?pred = oboInOwl:hasRelatedSynonym || + ?pred = oboInOwl:hasNarrowSynonym || + ?pred = oboInOwl:hasBroadSynonym || + ?pred = oboInOwl:hasExactSynonym + ) + + OPTIONAL { + [ + a owl:Axiom ; + owl:annotatedSource ?cls ; + owl:annotatedProperty ?pred ; + owl:annotatedTarget ?val ; + oboInOwl:hasSynonymType ?synType + ] + } + } diff --git a/src/sparql/terms.sparql b/src/sparql/terms.sparql new file mode 100644 index 0000000..e65a105 --- /dev/null +++ b/src/sparql/terms.sparql @@ -0,0 +1,7 @@ +SELECT DISTINCT ?term +WHERE { + { ?s1 ?p1 ?term . } + UNION + { ?term ?p2 ?o2 . } + FILTER(isIRI(?term)) +} \ No newline at end of file diff --git a/src/sparql/trailing-whitespace-violation.sparql b/src/sparql/trailing-whitespace-violation.sparql new file mode 100644 index 0000000..1d69472 --- /dev/null +++ b/src/sparql/trailing-whitespace-violation.sparql @@ -0,0 +1,11 @@ +# home: hp/sparql/trailing-whitespace-violation.sparql +prefix owl: +prefix rdfs: + +SELECT ?c ?p ?x WHERE +{ + ?c ?p ?x . + + FILTER( regex(STR(?x), "^ ") || regex(STR(?x), " $") ) + FILTER( ?p != owl:annotatedTarget ) +} diff --git a/src/sparql/xref-syntax-violation.sparql b/src/sparql/xref-syntax-violation.sparql new file mode 100644 index 0000000..98a6172 --- /dev/null +++ b/src/sparql/xref-syntax-violation.sparql @@ -0,0 +1,13 @@ +# home: hp +prefix hasDbXref: +prefix oio: +prefix owl: +prefix rdfs: + +SELECT ?c ?x WHERE +{ + ?c hasDbXref: ?x . + + FILTER( regex(STR(?x), " ") || regex(STR(?x), ";") || STR(?x) = "" ) + +} diff --git a/src/sparql/xrefs.sparql b/src/sparql/xrefs.sparql new file mode 100644 index 0000000..bde8fc9 --- /dev/null +++ b/src/sparql/xrefs.sparql @@ -0,0 +1,8 @@ +prefix oio: +prefix owl: + +SELECT ?cls ?xref WHERE +{ + ?cls a owl:Class ; + oio:hasDbXref ?xref +} From 89ccb2e91603489fc12db65fd4ed3c6baa790fd3 Mon Sep 17 00:00:00 2001 From: matentzn Date: Mon, 9 Sep 2019 16:37:05 +0100 Subject: [PATCH 02/11] changes second run --- src/ontology/Makefile | 14 +- src/ontology/catalog-v001.xml | 28 +- src/ontology/geno.owl | 8198 -------------------- src/ontology/imports/iao_import.json | 3550 +++++++++ src/ontology/imports/iao_import.obo | 940 +++ src/ontology/imports/iao_import.owl | 2638 ++++++- src/ontology/imports/ro_import.json | 4812 ++++++++++++ src/ontology/imports/ro_import.obo | 1804 +++++ src/ontology/imports/ro_import.owl | 4541 ++++++++++- src/ontology/imports/so_import.json | 3780 +++++++++ src/ontology/imports/so_import.obo | 1323 ++++ src/ontology/imports/so_import.owl | 3356 +++++++- src/ontology/pre_odk/catalog-v001.xml | 9 + src/ontology/pre_odk/geno_imports.owl | 25 + src/ontology/pre_odk/oboInOwl.owl | 713 ++ src/ontology/pre_odk/ontology-metadata.owl | 881 +++ 16 files changed, 28370 insertions(+), 8242 deletions(-) delete mode 100644 src/ontology/geno.owl create mode 100644 src/ontology/imports/iao_import.json create mode 100644 src/ontology/imports/iao_import.obo create mode 100644 src/ontology/imports/ro_import.json create mode 100644 src/ontology/imports/ro_import.obo create mode 100644 src/ontology/imports/so_import.json create mode 100644 src/ontology/imports/so_import.obo create mode 100644 src/ontology/pre_odk/catalog-v001.xml create mode 100644 src/ontology/pre_odk/geno_imports.owl create mode 100644 src/ontology/pre_odk/oboInOwl.owl create mode 100644 src/ontology/pre_odk/ontology-metadata.owl diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 2bb52e5..16dc59d 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -16,7 +16,7 @@ ONTBASE= $(URIBASE)/$(ONT) EDIT_FORMAT= owl SRC = $(ONT)-edit.$(EDIT_FORMAT) CATALOG= catalog-v001.xml -ROBOT= robot --catalog $(CATALOG) +ROBOT= robot --catalog $(CATALOG) -vvv RELEASEDIR= ../.. PATTERNDIR= ../patterns REPORTDIR= reports @@ -63,7 +63,7 @@ all_main: $(MAIN_FILES) ## By default this is the cross-product of IMPORT_MODULES x FORMATS -IMPORTS = ro iao so +IMPORTS = ro iao IMPORT_ROOTS = $(patsubst %, imports/%_import, $(IMPORTS)) IMPORT_FILES = $(foreach n,$(IMPORT_ROOTS), $(foreach f,$(FORMATS), $(n).$(f))) @@ -274,16 +274,6 @@ mirror/iao.owl: mirror/iao.trigger .PRECIOUS: mirror/%.owl -## ONTOLOGY: so -## Copy of so is re-downloaded whenever source changes -mirror/so.trigger: $(SRC) - -mirror/so.owl: mirror/so.trigger - @if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I $(URIBASE)/so.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi - -.PRECIOUS: mirror/%.owl - - # ---------------------------------------- # Subsets diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 3ef2a96..3e6e2aa 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -1,12 +1,20 @@ - - - - - - - - - - + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/ontology/geno.owl b/src/ontology/geno.owl deleted file mode 100644 index bcec2b8..0000000 --- a/src/ontology/geno.owl +++ /dev/null @@ -1,8198 +0,0 @@ - - - - - - GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. - -Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 - - - - - - - - - - - - - Used to annotation axioms that define identity criteria for instances of a class. - is_identity_criteria - - - - - - - - - proabalistic_quantifier - - - - - - - - Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models. - mixin - - - - - - - - - gene symbol - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - begin - - - - - - - - - end - - - - - - - - - location - - - - - - - - - The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly. - reference - - - - - - - - - - - is part of - - - - - - - - - - has part - - - - - - - - - - - - - - - - - - A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'. - Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants. - http://purl.obolibrary.org/obo/so_has_quality - has_sequence_attribute - - - - - - - - - - - - A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes - materializes - Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence. - bears_concretization_of - - - - - - - - - is_genotype_of - - - - - - - - - - - - - - - - - - - A relationship that holds between a biological entity and some level of genetic variation present in its genome. - This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype. - The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations. - has_genotype - - - - - - - - - - - An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO) - No proper part relation anymore in RO/BFO? - http://semanticscience.org/resource/SIO_000053 - has_proper_part - - - - - - - - - - A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears. - has_sequence_component - has_state - VMC:state - 'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule. - has_sequence - - - - - - - - - - A geno:intrinnsic genotype 'specifies' a SO:genome. -A geno:karyotype 'specifies' a geno:karyotype feature collection. - A relationship between an information content entity representing a specification, and the entity it specifies. - obsolete_specifies - - - - - - - - - Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. - obsolete_approximates_sequence - - - - - - - - - Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. - obsolete_resolves_to_sequence - - - - - - - - - An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole. - http://semanticscience.org/resource/SIO_000093 - is_proper_part_of - - - - - - - - - is_sequence_of - - - - - - - - - is_subject_of - - - - - - - - - obsolete_is_specified_by - - - - - - - - - - shortcut relation used to link a phenotype directly to a genotype of an organism - is_phenotype_of_organism_with_genotype - is_phenotype_with_genotype - phenotype_has_genotype - Might expand to something like: - -phenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype))))))) - obsolete_is_phenotype_of_genotype - - - - - - - - - - A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next. - Exploratory/temporary property, as we formalize our phenotypic inheritance model. - obsolete_participates_in_inheritance_process - - - - - - - - - - - A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression. - has_variant_part - - - - - - - - - - is_variant_part_of - - - - - - - - - - - A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant. - has_reference_sequence_part - has_reference_part - - - - - - - - - is_reference_part_of - - - - - - - - - - - <fgf8a^ti282a> is_allele_of the 'danio rerio fgf8a' gene locus. - A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size. - Domain = allele -Range = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation). - Note that the allele <fgf8a^ti282a> is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the <fgf8a^ti282a> allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product. - is_sequence_variant_of - To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size). - -While conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like "fgf8a<ti282a> is an allele of the Danio rerio fgf8a gene", and we may create data where fgf8a<ti282a> is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene). - -It is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. - -This departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\GAL4 gene. - -At the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'. - is_allele_of - - - - - - - - - - A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level). - is_variant_instance_of - formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus) - Domain = genomic feature instance -Range = punned gene class IRI - obsolete_is_genetic_variant_of - - - - - - - - - A relation linking a gene class to a sequence-varaint or expression-variant of the gene. - has_variant_instance - formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by) - Domain = punned gene class -Range = genomic feature - obsolete_has_genetic_variant - - - - - - - - - A relation linking a gene class to one of its sequence-variant alleles. - Domain = punned gene class -Range = allele - has_sequence_variant - has_allele - - - - - - - - - - A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets. - This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets. - targets_gene - - - - - - - - - - - - - - - - - A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression. - This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset. - has_affected_feature - - - - - - - - - - A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents. - Domain = expression variant feature. -Range = punned gene class - This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class. - is_expression_variant_of - - - - - - - - A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature. - class_to_feature_relation - This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases) - is_feature_affected_by - - - - - - - - - A relation between a gene class and a gene targeting reagent that targets it. - is_target_of - Domain = punned gene class -Range = gene knockdown reagent - is_gene_target_of - - - - - - - - - A relation linking a gene class to one of an expression-variant of that gene.. - Domain = punned gene class -Range = expression variant feature - has_expression_variant_instance - has_expression_variant - - - - - - - - - A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression. - Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property. - This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of. - obsolete_is_variant_with - - - - - - - - - A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways). - obsolete_is_expression_variant_with - - - - - - - - A relation used to describe a context or conditions that define and/or identify an entity. - Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association. - -Used in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features. - has_qualifying_context - has_qualifier - - - - - - - - - - - a relation to link a single locus complement to its zygosity. - has_zygosity - - - - - - - - - - A relationship between a reference locus/allele and the gene class it is an allele of. - is_reference_allele_of - - - - - - - - - Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed. - has_color_value - Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized. - has_staining_intensity - - - - - - - - Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant. - relation between an molecular agent and its molecular target - is_targeted_by - - - - - - - - - - - - - 1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. - -2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds. - -3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC) - Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence. - sequence_derives_from - - - - - - - - - - A relationship between a variant allele and the gene class it is an allele of. - is_variant_allele_of - - - - - - - - - - Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases. - has_sex_agnostic_part - - - - - - - - - - A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of. - is_mutant_allele_of - - - - - - - - - - A relationship between a polymorphic allele and the gene class it is an allele of. - is_polymorphic_allele_of - - - - - - - - - - A relationship between a wild-type allele and the gene class it is an allele of. - is_wild_type_allele_of - - - - - - - - - - An organizational class to hold relations of parthood between sequences/features. - has_sequence_part - - - - - - - - - is_sequence_part_of - - - - - - - - - Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases. - is_sex_agnostic_part_of - - - - - - - - - A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part). - This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of) - varies_with - - - - - - - - organizational property to hold imports from faldo. - faldo properties - - - - - - - - - - - - - - - - - A relation linking a qualified sequence feature to its component sequence feature. - has_sequence_feature_component - In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism. - has_sequence_feature - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - has_inferred_phenotype - - - - - - - - - Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype. - - - - - - - - - - Property chain to propagate inferred phenotype associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. - - - - - - - - - Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration. - - - - - - - - - - Property chain to propagate inferred phenotype associations from an intrinsic genotype component (e.g. a (sequence-)variant locus instance) to a gene class. - - - - - - - - - Property chain to propagate inferred phenotype associations from a (sequence-)variant locus instance to a gene class (to support cases where the phenotype association is made at the level of the variant gene locus). - - - - - - - - - - Property chain to propagate inferred phenotype associations from an extrinnsic genotype component (e.g. a expression-variant gene instance) to a gene class. - - - - - - - - - Property chain to propagate inferred phenotype associations from an expression-variant gene instance to a gene class (to support cases where the phenotype association is made at the level of the expression-variant gene). - - - - - - - - - Property chain to propagate inferred phenotype associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components) - - - - - - - - - Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes. - obsolete_has_regulatory_part - - - - - - - - - - - - - - A relation linking a sequence_alteration to the gene it alters. - is_within_allele_of - obsolete_is_alteration_within - - - - - - - - - has_asserted_phenotype - - - - - - - - - Proposal for a property linking regulatory elements to larger features of which they are a part. - is_regulatory_part_of - - - - - - - - - A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances. - For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them. - obsolete_has_position_component - - - - - - - - - A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues) - has_sequence_unit - - - - - - - - - - A relation between two seqeunces or features that are considered variant with each other along their entire extents. - completely_varies_with - - - - - - - - related_condition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene) - The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains. - -Below are the different kinds/paths of propagation we desire: -1. Propagation 'down' a genotype (from larger components to smaller ones) -2. Propagation 'up' a genotype (from smaller components to larger ones) -3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype). -4. From an effective genotype to its intrinsic and extrinsic components. -5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele). -6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this. - -Note that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha<tbx392>/shha<tbx392> [AB] to shha<tbx392>/shha<tbx392> [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition') - inferred_to_cause_condition - - - - - - - - - - This is a case of inter-gneotype phenotype propagation, requiring propagation down oen genotype and then up another. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to have this chain. - -This property chain propagates a phenotype asserted on a sex-qualified intrinsic genotype, down to its sex-agnostic genotype part, and then up to a parent effective genotype that has it as a variant part. I think this is OK in all cases, so we can implement this as the one case where we can have inter-genotype pheno propagation. But as noted, there will likely be no data that actually meets criteria to use this chain, so we can probably leave it out. - - - - - - - - - Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype. - - - - - - - - - - - Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, to the coompnent variant parts of this sex-agnostic genotype. - - - - - - - - - - Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to move past the sex-agnostic genotype and down to its parts. - -The following shorter chain would also suffice here: -is_variant_part_of o inferred_to_cause_condition - - - - - - - - - Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration. - - - - - - - - - - - - Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, through the coompnent variant parts of this sex-agnostic genotype, and to the affected gene. - - - - - - - - - - - Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to propagate to genes. - -The shorter chain below would also suffice for this propagation: -has_allele o inferred_to_cause_condition - - - - - - - - - - Property chain to propagate inferred condition associations from an sequence alteration through the variant locus to a gene class. (separate chains are needed to propagate from the variant locus to the gene class, and another to propagate from a genotype, GVC, or VSLC to the gene class). - - -NOTE that i dont need this property chain if I have a property chain to infer a has_affected_locus link from a sequence alteration to a gene when the link is asserted from the variant locus to the gene: - -is_variant_part_of o has_affected_locus --> has_affected_locus - - - - - - - - - - Obsolete comment: Property chain to propagate inferred condition associations from an intrinsic genotype, GC, or VLSC to a gene class. (a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class). - -The following, shorter chain, would also suffice here: -has_allele o inferred_to_cause_condition -> inferred_to_cause_condition - Property chain to propagate inferred condition associations from an intrinsic genotype, GVC, or VLSC to an affected gene class, or from an extrinsic gneotype or component to an affected gene class. - -The following, shorter chain, would also suffice here: -has_affected_locus o inferred_to_cause_condition -> inferred_to_cause_condition - -Note that a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class in cases where the link to gene is through the variant locus rather than the seq alteration). - - - - - - - - - Property chain to propagate inferred condition associations from a variant locus instance to a gene class (to support cases where the phenotype association is made directly at the level of the variant locus/allele). - - - - - - - - - - Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype to a sex-agnostic intrinsic genotype. - - - - - - - - - Property chain to propagate inferred condition associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components) - - - - - - - - - inferred_to_contribute_to_condition - - - - - - - - - inferred_to_correlate_with_condition - - - - - - - - - LOINC:LA6668-3 - pathogenic_for_condition - - - - - - - - - LOINC:LA26332-9 - likely_pathogenic_for_condition - - - - - - - - - Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to. - non-causal_for_condition - - - - - - - - - LOINC:LA6675-8 - benign_for_condition - - - - - - - - - LOINC:LA26334-5 - likely_benign_for_condition - - - - - - - - - LOINC:LA26333-7 - has_uncertain_significance_for_condition - - - - - - - - - A relation used to describe a process contextualizing the identity of an entity. - has_qualifying_process - - - - - - - - - A relation used to describe an environment contextualizing the identity of an entity. - has_qualifying_environment - - - - - - - - - is_candidate_variant_for - - - - - - - - - - A relation linking a sequence feature to the location it occupies on some reference sequence. - occupies - has_location - - - - - - - - Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from. - on strand - - - - - - - - - - - - - - - - - Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement. - Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location. - -For copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. - has_defining_location - - - - - - - - - - - - - - - - - Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement. - Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement. - has_defining_sequence - - - - - - - - - - - - - - - - - Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement. - Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference. - -For copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. - has_defining_feature - - - - - - - - - Relates a sequence feature location to an interval that defines its start and end position. - Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects. - has_interval - - - - - - - - Relates a 'sequence feature location' to a sequence that it is anchored to. - has_reference_sequence - - - - - - - - is_about is a (currently) primitive relation that relates an information artifact to an entity. - is about - - - - - - - - - Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of. - denotes - - - - - - - - - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. - has_specified_input - - - - - - - - - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - has_specified_output - - - - - - - - a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence - inheres_in - - - - - - - - a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence - bearer of - - - - - - - - - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates in - - - - - - - - a relation between a process and a continuant, in which the continuant is somehow involved in the process - has participant - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - - - - - - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - has quality - - - - - - - - - has_role - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - derives from - - - - - - - - - starts during - - - - - - - - - ends during - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - overlaps - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - in taxon - - - - - - - - - - A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - has phenotype - - - - - - - - - phenotype of - - - - - - - - temporally related to - - - - - - - - - p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - has input - - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. - has output - - - - - - - - - - is member of - - - - - - - - - Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes - -Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component - has member is a mereological relation between a collection and an item. - has member - - - - - - - - - input of - - - - - - - - - output of - - - - - - - - - obsolete_formed as result of - - - - - - - - Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b - molecularly controls - - - - - - - - - x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall - bounds sequence of - - - - - - - - - - x has subsequence y iff all of the sequence parts of x are sequence parts of y - has subsequence - - - - - - - - - is subsequence of - - - - - - - - - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - http://biorxiv.org/content/early/2014/06/27/006650.abstract - overlaps sequence of - - - - - - - - inverse of downstream of sequence of - is upstream of sequence of - - - - - - - - x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - is downstream of sequence of - - - - - - - - Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? - Matthew Brush - The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. - is model of - - - - - - - - - The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. - -An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. - A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition. - Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. - causes or contributes to condition - - - - - - - - - A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition. - causes condition - - - - - - - - - A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition. - contributes to condition - - - - - - - - - A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual. - contributes to expressivity of condition - contributes to severity of condition - - - - - - - - - A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population. - contributes to penetrance of condition - contributes to frequency of condition - - - - - - - - - A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition. - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. - is preventative for condition - - - - - - - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - correlated with condition - - - - - - - - association has object - - - - - - - - association has predicate - - - - - - - - association has subject - - - - - - - - - - - - - The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is. - position - - - - - - - - - Property linking a sequence or sequence feature to an integer representing its length in terms of the number of units in the sequence. - has_extent - - - - - - - - - - Shortcut relation linking a sequence feature directly to a string representing the 'state' of its sequence - i.e. the ordering of units that comprise it (e.g. 'atgcagctagctaccgtcgatcg'). - has_sequence_string - - - - - - - - ObsoleteDataProperty - - - - - - - - The 'rank' quantifier in Bgee gene-anatomy associations, that indicates the imporatnace/specificity of a gene expression in a given anatommy relative to expressionin other anatomies for the same gene. - Property to link an assertion or association with some value quantifying its relevance or ranking. - has_quantifier - - - - - - - - The starting position of a sequence feature or interval. - start_position - - - - - - - - The ending position of a sequence feature or interval. - end_position - - - - - - - - - - Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg'). - has_string - - - - - - - - Describes the number of members in some set. - has_count - In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'. - has_member_count - - - - - - - - - - - - - - Both strands - - - - - - - - - A position that is exactly known. - Exact position - - - - - - - - - Positive strand - - - - - - - - - Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate. - We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region). - FALDO - Position - - - - - - - - - - - - - - 1 - - - - - 1 - - - - - - A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene. - From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence. - Region - - - - - - - - - Negative strand - - - - - - - - - Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'. - Stranded position - - - - - - - - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - - - - - - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - continuant - continuant - - - - - - - - - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - occurrent - occurrent - - - - - - - - - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - independent continuant - independent continuant - - - - - - - - - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - - process - process - - - - - - - - - - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocitosis and exocitosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89 - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - disposition - disposition - - - - - - - - - - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - realizable entity - realizable entity - - - - - - - - - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - quality - quality - - - - - - - - - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - specifically dependent continuant - specifically dependent continuant - - - - - - - - - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - role - role - - - - - - - - - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - generically dependent continuant - generically dependent continuant - - - - - - - - - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - function - - - - - - - - - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - material entity - material entity - - - - - - - - - Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology. - molecular entity - - - - - - - - - nucleic acid - - - - - - - - - - - - - - - A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). - cell line - - - - - - - - - Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies. - cell - - - - - - - - - 1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions. - -2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity). - In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. - environmental system - - - - - - - - - A technique is a planned process used to accomplish a specific activity or task. - technique - - - - - - - - - A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo. - embryonic stem cell line - - - - - - - - - A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types. - stem cell line - - - - - - - - - Example zebrafish intrinsic genotype: - -Genotype = fgf8a<ti282a/+>; shha<tb392/tb392> (AB) -reference component (genomic background) = AB -variant component ('genomic variation complement') = fgf8a<ti282a/+>; shha<tb392/tb392> - -. . . and within this variant component, there are two 'variant single locus complements' represented: - -allele complement 1 = fgf8a<ti282a/+> -allele complement 2 = shha<tb392/tb392> - -and within each of these 'variant single locus complements' there is one or more variant gene locus member: - -in complement 1: fgf8a<ti282a> -in complement 2: shha<ttb392> - A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement) - This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). - -Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. - genotype - organismal genotype - sex-agnostic intrinsic genotype - In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances). - genomic genotype (sex-agnostic) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An allele that varies in it sequence from what is considered the reference or canonical sequence at that location. - The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles. - alternate allele - sequence-variant feature - variant feature - Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another. - -A variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence. - variant allele - - - - - - - - - - - - - - - - - - - A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype. - Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases. - A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation. - -In model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a<t1282a/+>(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)). - genomic variation complement - - - - - - - - - The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB) - A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). - Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it. - genomic background - OBI:genetic population background information - background genome - - - - - - - - - - - - - - - The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The "mn004Gt" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome. - -http://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722 - -http://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8 - A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene) - Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment). - -This design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not. - http://purl.obolibrary.org/obo/SO_0001023 ! allele - In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion. - -A genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene. - gene allele - - - - - - - - - - - - - - - - - - - A sequence that serves as a standard against which other sequences at the same location are compared. - The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant. - reference sequence - A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence. - reference sequence - - - - - - - - - a collection more than one sequence features (ie a collection of discontinuous sequence features) - perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one) - 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. - obsolete_sequence feature collection - - - - - - - - - A sequence feature collection comprised of discontiguous sequences from a single genome - Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system. - genomic feature collection - Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. - obsolete_genomic feature collection - - - - - - - - - A single locus complement that serves as a standard against which 'variant' sequences are compared - reference allelic complement - reference single locus feature complement - Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. - -Eq Class axiom: -'single locus complement' - and (has_sequence_attribute some reference) - -SC axioms: -'has member' exactly 0 'variant allele' -'has member' only 'reference genomic feature' -'has member' some 'reference genomic feature' - obsolete_reference single locus complement - - - - - - - - - - - - - - - - - - - A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13). - variant allelic complement - Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members. - -Note that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant. - variant single locus complement - - - - - - - - - - - - - - - - - - - - - - - - - A genome that varies at one or more loci from the sequence of some reference genome. - http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here) - variant genome - - - - - - - - - - - - - - - - - - - An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome. - Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population. - -In model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared. - reference allele - - - - - - - - - - A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus). - Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '. - Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. - -Eq Class def: 'genomic feature' - and (has_sequence_attribute some unspecified) - An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). - obsolete_unspecified feature - - - - - - - - - A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature. - hemizygous reference junction - Eliminating unecessary defined/organizational classes. Former logical def: - -junction - and (has_sequence_attribute some reference) - -Subclass axiom: -is_variant_with some insertion - In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. - -The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. - obsolete_reference junction - - - - - - - - - - - - - - - - - - - A gene that originates from the genome of a danio rerio. - danio rerio gene - - - - - - - - - - - - - - - - - - - A gene that originates from the genome of a homo sapiens. - homo sapiens gene - - - - - - - - - - - - - - - - - - - A gene that originates from the genome of a mus musculus. - mus musculus gene - - - - - - - - - A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development. -http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690 - -Note that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469 - A version/allele of a gene that serves as a standard against which variant genes are compared. - reference gene - Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. - -Eq Class axiom: -'gene allele' - and (has_sequence_attribute some reference) - -SC axioms: -is_variant_with some 'gene allele' -is_reference_allele_of some gene - Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. - -In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. - obsolete_reference gene allele - - - - - - - - - obsolete_experimental insertion - - - - - - - - - - - - - - - gene trap insertion - - - - - - - - - - - - - - - A transgene that has been integrated into a chrromosome in the host genome. - An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion. - -An 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome. - integrated transgene - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny. - 1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. - -2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way. - 1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. - -2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms. - genomic material - - - - - - - - - A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion. - physical genome - A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements. - -Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome. - material genome - - - - - - - - - a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role) - Consider http://semanticscience.org/resource/SIO_001062 ! human population ("A human population refers to a collection of human beings"). - homo sapiens population - human population - - - - - - - - - - - - - - - A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical. - organism strain or breed - Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR) - strain or breed - - - - - - - - - A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon) - taxonomic group - - - - - - - - - mus musculus strain - - - - - - - - - - - - - - - - - - - - - danio rerio strain - - - - - - - - - sequence attribute that can inhere only in a collection of more than one sequence features - obsolete_sequence feature collection attribute - - - - - - - - - A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes). - in cis - - - - - - - - - A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes). - in trans - - - - - - - - - - - - - - - An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different). - allelic state - derived from https://en.wikipedia.org/wiki/Zygosity - http://semanticscience.org/resource/SIO_001263 - zygosity - - - - - - - - - hemizygous - - - - - - - - - heterozygous - - - - - - - - - homozygous - - - - - - - - - indeterminite zygosity - no-call zygosity - unknown zygosity - unspecified zygosity - - - - - indeterminite zygosity - MGI uses this term when zygosity is not known. - - - - - no-call zygosity - (this is how the GVF10 format/standard refers to loci without enough data to make an accurate call . . . see http://www.sequenceontology.org/resources/gvf.html#quick_gvf_examples) - - - - - - - - - The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event. - We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells). - -We can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms. - heritabililty - - - - - - - - - heritable - - - - - - - - - non-heritable - - - - - - - - - The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment. - The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family. - mode of inheritance - phenotypic inheritance pattern - http://purl.obolibrary.org/obo/HP_0000005 - http://purl.obolibrary.org/obo/NCIT_C45827 - An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, "genetic context" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. - -These genetic and environmental "interactions" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y. - inheritance pattern - - - - - - - - - disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes - Triage until decide if want to define this as grouping class that would result in multiple-inheritance. - obsolete_dominant inheritance - - - - - - - - - An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. - co-dominant autosomal inheritance - - - - - - - - - An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. - pure dominant inheritance - complete autosomal dominant inheritance - - - - - - - - - An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. - intermediate dominant autosomal inheritance - semi-dominant autosomal inheritance - incomplete autosomal dominant inheritance - - - - - - - - - An X-linked inheritance pattern wherein the trait manifests in heterozygotes. - http://purl.obolibrary.org/obo/HP_0001423 - X-linked dominant inheritance - - - - - - - - - An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes. - vertical inheritance - http://purl.obolibrary.org/obo/HP_0000006 - autosomal dominant inheritance - - - - - - - - - An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals. - autosomal recessive inheritance - - - - - - - - - An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals. - http://purl.obolibrary.org/obo/HP_0001419 - X-linked recessive inheritance - - - - - - - - - duplicate term, use GENO:0000148 - obsolete_autosomal recessive inheritance - - - - - - - - - An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared. - Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another. - reference - - - - - - - - - unspecified life cycle stage - - - - - - - - - objective is to insert some specified sequence into the genome of a cell or virus - genetic insertion technique - - - - - - - - - mutagen treatment technique - - - - - - - - - - - - - - - a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). - This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. - targeted gene mutation technique - - - - - - - - - Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. - random genetic insertion technique - - - - - - - - - - - - - - - targeted genetic insertion technique - - - - - - - - - - - - - - - enhancer trapping technique - - - - - - - - - - - - - - - gene trapping technique - - - - - - - - - - - - - - - promoter trapping technique - - - - - - - - - - - - - - - targeted knock-in technique - - - - - - - - - random transgene insertion technique - - - - - - - - - A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome - obsolete_chromosome complement - - - - - - - - - - - - - - - - A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation - duplicate chromosome - This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome. - gained aneusomic chromosome - - - - - - - - - - - - 0 - - - - A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation. - This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as "the point at which one or more contiguous nucleotides were excised". - absent aneusomic chromosome - lost aneusomic chromosome - - - - - - - - - - - - - - - - - - - - - - A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation. - Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism. - aneuploid chromosomal segment - aneusomic chromosomal subregion/segment - partial aneusomic chromosomal element - Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome." - aneusomic chromosomal part - - - - - - - - - - A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event. - duplicate partial aneuploid chromosomal element - translocated duplicate chromosomal element - translocated duplicate chromosomal segment - Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location. - gained aneusomic chromosomal segment - - - - - - - - - - - - 0 - - - - A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome. - In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement - dropped partial anneuploid chromosomal element - translocated absent chromosomal segment - truncated chromosome terminus - This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome. - -Loss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus. - lost aneusomic chromosomal segment - - - - - - - - - - - - - - - - - A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation - complete aneusomic chromosome - Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism. - -Similarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication. - aneusomic chromosome - - - - - - - - - Stub class to serve as root of hierarchy for imports of biological processes from GO-BP. - biological process - - - - - - - - - disomic zygosity - - - - - - - - - aneusomic zygosity - - - - - - - - - trisomic homozygous - - - - - - - - - trisomic heterozygous - - - - - - - - - A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a<ti282a>/fgf8a<x15>) - trans-heterozygous - compound heterozygous - - - - - - - - - A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe) - replaced with SO:engineered_region - extra-genomic sequence - obsolete_reagent sequence feature - - - - - - - - - a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a<ti282a/+>) - simple heterozygous - - - - - - - - - - - - - - - - - - - A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc) - transgene part - - - - - - - - - An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level - variant - - - - - - - - - An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant. - polymorphic - - - - - - - - - An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence. - mutant - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism) - This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology. - 1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. - -2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). - -3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome. - genomic feature - - - - - - - - - - A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion). - This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material. - genetic material - - - - - - - - - - An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain. - Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines - Not required for any specific use case at this point so removed for simplicity. -Formely asserted as allele and inferred as varaint allele. -Eq class definition: -allele - and (mutation or ('has subsequence' some mutation)) - 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. - obsolete_mutant allele - - - - - - - - - - - - - - - A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain. - mutation - - - - - - - - - - - - - - - - - - - - - - - - - - - A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon) - Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element - episomal replicon - Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. - extrachromosomal replicon - - - - - - - - - expression construct feature - expression construct - - - - - - - - - An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population. - PMID: 25741868 ACMG Guidelines - Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%). - polymorphic allele - - - - - - - - - A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location. - major allele - major polymorphic allele - - - - - - - - - A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location). - minor allele - minor polymorphic allele - - - - - - - - - A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree. - ancestral allele - ancestral polymorphic allele - - - - - - - - - - - - - - - An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared. - wild-type allele - 'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain. - -The notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis. - wild-type allele - - - - - - - - - - wild-type gene allele - A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation. - wild-type gene - - - - - - - - - - - - - - - - - - - - - A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi. - The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position. - reagent targeted gene - - - - - - - - - A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome). - experimentally-expressed transgene - extrinsic transgene - transiently-expressed transgene - - - - - - - - - An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared. - wild-type - - - - - - - - - - - - - - - - - - - One of a set of sequence features known to exist at a particular genomic location. - A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene. - -To be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene. - -[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17) -[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17) -[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17) -[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17) -[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17) -[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17) -[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483 -[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17) -[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17) -[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17) -[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17) -[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17) - variable feature - An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). - -Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence). - allele - - - - - - - - - - a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation. - aneusomic - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An allele of a gene that contains some sequence alteration. - A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset. - variant gene allele - - - - - - - - - The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a<ti282a/+>. - -The collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome. - A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism. - TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label. - allelic complement - homologous allele complement - single locus feature complement - A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes. - -The fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. - single locus complement - - - - - - - - - In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as: - - shha<MO1-1ng/ul>; shhb<pFLAG-mmusShhb> - -This notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct. - A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state. - We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. - -Our rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. - -Finally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." - experimental genotype - expression genotype - An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment. - -The 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations. - extrinsic genotype - - - - - - - - - - - - - - - - - - - - - A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs). - Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." - An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment. - effective genotype - - - - - - - - - - - - - - - A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes). - A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment. - reagent-targeted gene complement - - - - - - - - - - - - - - - The set of all transgenes trransiently expressed in a biological system in the context of a given experiment. - experimental transgene complement - transiently-expressed transgene complement - - - - - - - - - - - - - - - Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes). - A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism). - See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself. - expression allele - Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism). - -The identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system. - expression-variant gene - - - - - - - - - gene targeting reagent - sequence targeting reagent - gene knockdown reagent - - - - - - - - - A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent. - targeted gene segment - reagent-targeted gene subregion - - - - - - - - - - - - - - - - - - - - - - A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference. - As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh<tbx292>, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above. - Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). -Note however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO. - 1. Scope of 'Genetic State': -'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs. - -2. Genotype Subtypes: -In GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. - -Two more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features. - -3. The Genotype Partonomy: -'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a<ti282a/ti282a>; fgf3<t24149/+>[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements: - - - GVC: fgf8a<ti282a/ti282a>; fgf3<t24149/+> (total intrinsic variation in the genome) - - Genomic Background: AB (the reference against which the GVC is variant) - - VSLC1: fgf8a<ti282a/ti282a> (homozygous complement of gene alleles at one known variant locus) - - VSLC2: fgf3<t24149/+> (heterozygous complement of gene alleles at another known variant locus) - - Allele 1: fgf8a<ti282a> (variant version of the fgf8a gene, present in two copies) - - Allele 2: fgf3<t24149> (variant version of the fgf3 gene, present in one copy) - - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy) - - Sequence Alteration1: <ti282a> (the specific mutation within the fgf8a gene that makes it variant) - - Sequence Alteration2: <t24149> (the specific mutation within the fgf3 gene that makes it variant) - -A graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md - -One reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data. - genotype - - - - - - - - - ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl -This ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes. - zebrafish phenotype - - - - - - - - - an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. - homoplasmic - - - - - - - - - an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. - heteroplasmic - - - - - - - - - hemizygous X-linked - - - - - - - - - hemizygous Y-linked - - - - - - - - - hemizygous insertion-linked - - - - - - - - - - - - - - - - - - - - - - - - - A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). - Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it. - background genotype - genomic background - - - - - - - - - - - - - - - The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". - An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. - New term request for SO. - http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: -chromosome > arm > region > band > sub-band - -Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): -chromosome > arm > band > sub-band > sub-sub-band - chromosomal region - - - - - - - - - - - - - - - - - - - - - The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". - http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: -chromosome > arm > region > band > sub-band - -Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): -chromosome > arm > band > sub-band > sub-sub-band - chromosome sub-band - - - - - - - - - chromosomal band brightness - chromosomal band intensity - - - - - - - - - gpos - - - - - - - - - gneg - - - - - - - - - gvar - - - - - - - - - gpos100 - - - - - - - - - gpos75 - - - - - - - - - gpos50 - - - - - - - - - gpos25 - - - - - - - - - A chromosome arm that is the shorter of the two arms of a given chromosome. - p-arm - stalk - short chromosome arm - - - - - - - - - A chromosome arm that is the longer of the two arms of a given chromosome. - q-arm - long chromosome arm - - - - - - - - - gpos66 - - - - - - - - - gpos33 - - - - - - - - - - - - - - - A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed. - regulatory transgene region - - - - - - - - - - - - - - - A transgene part whose sequence is expressed in a gene product through transcription and/or translation. - coding transgene feature - expressed transgene region - - - - - - - - - reporter region - - - - - - - - - - - - - - - - - - - - - - - - - A transgene whose product is used as a selectable marker. - selectable marker transgene - - - - - - - - - - - - - - - A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell. - Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28) - Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). - -A base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation). - karyotype - - - - - - - - - - - - - - - A genomic genotype where the genomic background specifies a male or female sex chromosome complement. - This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). - -In the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former. - intrinsic genotype (sex-specific) - sex-qualified genotype - sex-qualified intrinsic genotype - We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances. - -Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. - genomic genotype (sex-qualified) - - - - - - - - - A genomic genotype here the genomic background specifies a male sex chromosome complement. - male intrinsic genotype - - - - - - - - - A genomic genotype here the genomic background specifies a female sex chromosome complement. - female intrinsic genotype - - - - - - - - - A background genotype whose sequence or identity is not known or specified. - unspecified background genotype - unspecified genomic background - - - - - - - - - - - - - - - - - - - - - 1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus - -2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele. - -3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y} - A set of sequence features. - 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature). - -The notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3]. - -[1] https://www.snpedia.com/index.php/APOE-%CE%B54 -[2] https://www.snpedia.com/index.php/APOE-%CE%B52 -[3] https://www.snpedia.com/index.php/Gs270 - sequence feature set - - - - - - - - - - - - - - - - - - - - - A set of genomic features (i.e. sequence features that are of genomic origin). - In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member. - genomic locus complement - A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature. - -The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. - genomic feature set - - - - - - - - - - - - - - - - - - - A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc). - defined gene part - SO:0000831 (gene member region) - gene part - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A transgene that codes for a product used as a reporter of gene expression or activity. - reporter transgene - - - - - - - - - A junction between bases, a deletion variant, a terminus at the end of a chromosome. - A genomic feature that has an extent of zero. - Former logical def: -'genomic feature' - and (has_extent value 0) - obsolete_null feature - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found. - aberrant extrachromosomal replicon - exogenous extrachromosomal replicon - transgenic extrachromosomal replicon - Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. - novel extrachromosomal replicon - - - - - - - - - - - - - - - - A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome. - This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature. - Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles. - novel replicon - - - - - - - - - An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome. - novel - - - - - - - - - A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide). - terminus - - - - - - - - - - - - - - - - - A sequence feature or a set of such features. - sequence feature or collection - GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. -1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. -2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology). -3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location. - sequence feature or set - - - - - - - - - - - - - - - - - A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides). - GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. -1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. -2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). -3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). - biomacromolecular sequence - state - VMC:State - 'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome. - biological sequence - - - - - - - - - - - true - - - - - state - In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele. - - - - - - - - - A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification. - qualified sequence feature or collection - - - - - - - - - - - - - - - - - - - - - - - - - - - Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes). - A qualified sequence feature that carries sequence derived from the genome of a cell or organism. - qualified genomic feature - - - - - - - - - - - true - This axiom is an initial attempt to formalize the identity criteria of an extrinnsic context that separates qualified sequence features from sequence features (i.e. the context of its material bearer). As we further develop our efforts here this will get refined and more precise. - - - - - - - - - - - true - Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position). - - - - - - - - - - - - - - - - - - - - - - - - - - - A set of qualified sequence features that carry genomic sequence. - Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member. - A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele. - -A complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome. - qualified genomic feature set - - - - - - - - - - - - - - - - - - - - - - A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. - Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome. - 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. - -2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. - intrinsic genotype - - - - - - - - - - - - - - - - - - - - - - - DNA sequence - - - - - - - - - - - - - - - - - - - - - - - RNA sequence - - - - - - - - - - - - - - - - - - - - - - - amino acid sequence - - - - - - - - - obsolete_biological sequence or collection - - - - - - - - - obsolete_biological sequence collection - - - - - - - - - - A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature. - As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell). - location-qualified sequence feature - - - - - - - - - A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct) - expression-qualified sequence feature - - - - - - - - - A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence. - This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature. - genomic coordinates - remodeling notion of sequence feature position around the idea of a 'genomic locus' - obsolete_genomic position - - - - - - - - - phenotypic inheritance process - - - - - - - - - A sequence attribute inhering in a feature whose identity is not specified. - obsolete_unspecified - - - - - - - - - An attribute describing a type of variation inhering in a sequence feature or collection. - allele attribute - variation attribute - - - - - - - - - - - - - - - - - - - An intrinsic genotype that specifies variation from a defined reference genome. - variant genomic genotype - - - - - - - - - An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities. - eliminating classes that are not necessary or add uneeded complexity. - obsolete_sequence information entity - - - - - - - - - - - - - - 1 - - - - - biological sequence residue - monomeric residue - biological sequence unit - - - - - - - - - deoxyribonucleic acid residue - DNA residue - - - - - - - - - ribonucleic acid residue - RNA residue - - - - - - - - - amino acid residue - - - - - - - - - An attribute, quality, or state of a sequence feature or collection. - http://purl.obolibrary.org/obo/SO_0000400 - Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity. - sequence feature attribute - - - - - - - - - - The location of a sequence feature as defined by its start and end position on some reference coordinate system. - 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). - -2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there. - sequence feature location - - - - - - - - - - A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature) - modification-qualified sequence feature - - - - - - - - - - - - - - - - - - - 1. The zebrafish "fgf8a<ti282a>/fgf8a<+>" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state). - -2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308. - - ##fileformat=VCFv4.2 - ##FORMAT=<ID=GT, Description="Genotype, 0=REF, 1=ALT"> - #CHROM POS REF ALT FILTER FORMAT SAMP001 - 20 2300608 C T PASS GT 0/1 - 20 2301308 T G PASS GT 1/1 - (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html) - -3. Some allelic genotype formats encode the genotype as a single string - e.g. "GRCh38 Chr12:258635(A;T)" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12. - A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes. - single locus genotype - An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location. - -This contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background. - allelic genotype - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each. - genotype-phenotype association - - - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - - - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - true - - - - - - - - - - - - - - - knockdown reagent targeted gene complement - - - - - - - - - - A sequence alteration within the coding sequence of a gene. - Not required at this poitn, so marked exploratory and obsoleted. -Asserted under sequence_alteration. - obsolete_coding sequence alteration - - - - - - - - - A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome. - P-element construct - - - - - - - - - An engineered region that is used to transfer foreign genetic material into a host cell. - engineered_genetic_vector - Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. - -Constructs are typically packaged as part of delivery systems such as plasmids or viral vectors. - engineered genetic construct - - - - - - - - - A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct. - non-integrated transgene - extra-chromosomal transgene - - - - - - - - - A collection of more than one sequence feature. - http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection - obsolete_sequence feature collection - - - - - - - - - - - - - - - A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block. - Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block. - -Instead, we can create an 'allele set' class as the haplotype parent? - Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype. - A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. - -As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': - -1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. - -2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). "Star alleles" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/). - -3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. - -Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. - haplotype - - - - - - - - - A set of genomic sequences (a biological sequence that is of genomic origin). - copy number complement - A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. - genomic sequence set - - - - - - - - - A relation used to describe an environment contextualizing the identity of an entity. - microsatellite alteration - - - - - - - - - A relation used to describe a process contextualizing the identity of an entity. - repeat region alteration - - - - - - - - - A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism - allelic state - - - - - - - - - allelic dosage - an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome. - gene dosage - Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute. - Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. - -Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. - obsolete_genetic dosage - - - - - - - - - A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent. - genetic origin - variant origin - allele origin - - - - - - - - - Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg. - maternally inherited - maternal allele origin - - - - - - - - - Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm. - paternally inherited - paternal allele origin - - - - - - - - - Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis. - Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation - We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. - -De novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder. - de novo allele origin - - - - - - - - - Describes an allele whose origin is not known. - unknown allele origin - - - - - - - - - Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body. - acquired - Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation - We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells. - -These acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations. - somatic allele origin - - - - - - - - - a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells). - germ-line - replaced by GENO:0000900 ! 'germline' - obsolete_gametic - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement') - -Alt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome. - "Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes." -From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/ -https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/ - diplotype - - - - - - - - - A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes. - allelic phase - - - - - - - - - - - - - - - - - - - - - oryzias latipes strain - - - - - - - - - Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg). - hereditary - parental origin - parentally inherited - Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation - We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells. - germline allele origin - - - - - - - - - An inheritance pattern that is not determined or not known. - unknown inheritance - undetermined inheritance - - - - - - - - - The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”. - One of a set of sequence features or haplotypes that exist at a particular genetic locus. <see ClinGen Allele Model> - The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. - http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/ - No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. - ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) - As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. - -In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) - obsolete_canonical allele - - - - - - - - - An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence. - The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. - http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ - No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. - -Former axiom: denotes some 'obsolete_canonical allele' - ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) - The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. - obsolete_contextual allele - - - - - - - - - A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not. - heteroplasmic mitochondrial inheritance - - - - - - - - - A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited. - homoplasmic mitochondrial inheritance - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - An generically dependent continuant that carries biological sequence that is part of or derived from a genome. - An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities. - genomic entity - - - - - - - - - A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations. - Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as -"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations." Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location. - -Current definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele. - Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424. - A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. - haplotype block - - - - - - - - - - - - - - - - - - - - - - - - - A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. - 'Genomic Genotype' vs 'Genome' in GENO: -A genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome. - complete genotype - 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. - -2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. - genomic genotype - - - - - - - - - A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells) - decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin - Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. - obsolete_allele cellular context - - - - - - - - - The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system - In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. - -We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences. - In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. - -For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus). - genomic location - genomic locus - VMC:Location - 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. - -2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. - -3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there. - genomic feature location - - - - - - - - - - - - - - - - - - - - - - - - true - A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc). - useful organizational term to collect entities that have genomes/genotypes. - organismal entity - - - - - - - - - The molecular product resulting from transcription of a single gene (either a protein or RNA molecule) - gene product - - - - - - - - - reporter role - - - - - - - - - selectable marker role - - - - - - - - - selectable marker region - - - - - - - - - - - - - - - A genome whose sequence is identical to that of a genome sequence considered to be the reference. - reference genome - - - - - - - - - A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it. - Former comment: "Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project." - Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype. - Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. - -Former SC axioms: -- is_allele_of some 'haplotype block' -- 'has part' some sequence_alteration - 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene). - -2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. - -GENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. - -3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': - -a. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. -b. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. -c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. - -The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. - obsolete_haplotype - - - - - - - - - A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations. - Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block. - Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. - A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. - -The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. - ------------------------ - -* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. - obsolete_haplotype block - - - - - - - - - An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell. - Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene. - organellar plasmy - - - - - - - - - Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes). - A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification. - GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. -1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. -2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). -3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). - Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes. - qualified sequence feature - - - - - - - - - - - - - - - - - - - - - A set of qualified seqeunce features. - 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'. - qualified sequence feature set - - - - - - - - - A biolocical sequence, or set of such sequences. - biological sequence or collection - biological sequence or set - - - - - - - - - A set of biological sequences. - 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. - -A set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence. - biological sequence set - - - - - - - - - A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome. - Formerly considered modeling this as an informational entity, defined as "An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome." - functional feature complement - genetic dosage - Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963. - As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). - The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. - obsolete_functional copy number complement - - - - - - - - - A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form. - obsolete_intrinsic sequence feature attribute - - - - - - - - - A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.) - obsolete_extrinsic sequence feature attribute - - - - - - - - - A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism). - allelic cellular distribution - - - - - - - - - A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin. - constitutional - - - - - - - - - A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin. - clonal - - - - - - - - - An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors. - complex inherritance - multi-factorial inheritance - multi-genic inheritance - multi-locus inheritance - multigenic inheritance - http://purl.obolibrary.org/obo/HP_0001426 - Diseases inherited in this manner are termed 'complex diseases'. - multifactorial inheritance - - - - - - - - - A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes. - http://purl.obolibrary.org/obo/HP_0010984 - digenic inheritance - - - - - - - - - A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes. - http://purl.obolibrary.org/obo/HP_0010983 - It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform. - oligogenic inheritance - - - - - - - - - A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes. - http://purl.obolibrary.org/obo/HP_0010982 - Typically used for traits/conditions governed by more than three gene loci. - polygenic inheritance - - - - - - - - - An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors. - single-gene inheritance - monogenic inheritance - - - - - - - - - An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome. - autosomal inheritance - - - - - - - - - An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome. - gonosomal inheritance - http://purl.obolibrary.org/obo/HP_0010985 - allosomal inheritance - - - - - - - - - An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome. - http://purl.obolibrary.org/obo/HP_0001417 - X-linked inheritance - - - - - - - - - An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. - complete X-linked dominant inheritance - - - - - - - - - An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. - semi-dominant X-linked inheritance - incomplete X-linked dominant inheritance - - - - - - - - - An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. - co-dominant X-linked inheritance - - - - - - - - - An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome. - holandric inheritance - http://purl.obolibrary.org/obo/HP_0001450 - Y-linked inheritance - - - - - - - - - An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome. - Z-linked inheritance - - - - - - - - - A Z-linked inheritance pattern wherein the trait manifests in heterozygotes. - Z-linked dominant inheritance - - - - - - - - - A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. - complete Z-linked dominant inheritance - - - - - - - - - A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. - semi-dominant Z-linked inheritance - incomplete Z-linked dominant inheritance - - - - - - - - - An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. - co-dominant Z-linked inheritance - - - - - - - - - A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals. - Z-linked reccessive inheritance - - - - - - - - - An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome. - W-linked inheritance - - - - - - - - - An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome. - http://purl.obolibrary.org/obo/HP_0001427 - Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy). - mitochondrial inheritance - - - - - An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome. - Human Phenotype Ontology (HPO) - - - - - Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy). - Human Phenotype Ontology (HPO) - - - - - - - - - An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females). - http://purl.obolibrary.org/obo/HP_0001470 - sex-limited autosomal dominant inheritance - - - - - - - - - An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females). - http://purl.obolibrary.org/obo/HP_0031362 - sex-limited autosomal recessive inheritance - - - - - - - - - A set of discrete alleles within a particular genome. - 'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An "Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'. - allele set - - - - - - - - - A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s). - copy number variation - Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. - In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). - -Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. - obsolete_variant copy number complement - - - - - - - - - A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger. - Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961. - 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. - -2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. - -3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. - obsolete_copy number complement - - - - - - - - - - - - - - - A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism). - A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. - genomic sequence - - - - - - - - - A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome. - The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome. - -We represent the notion of copy number at the "sequence level" (as opposed to the "sequence feature level") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The "sequence level" representation here supports this use case. By contrast, a "feature level" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity). - The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result. - -A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. - -The fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. - The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence. - copy number complement - - - - - - - - - A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s). - Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a "sequence feature level" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred). - -For example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains. - 'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome. - variant copy number complement - - - - - - - - - A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome. - functional genetic dosage - A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence. - -'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. - -As we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele. - functional copy complement - - - - - - - - - A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type. - mosaic - - - - - - - - - A pair of integers representing start and end position of a location on a sequence coordinate system. - sequence interval - - - - - - - - - molecular function - - - - - - - - - A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete] - developmental process - - - - - - - - - pulling in HP 'phenotypic abnormality' root here - human phenotypic abnormality - - - - - - - - - Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology. - A spatiotemporal region encompassing some part of the life cycle of an organism. - human life cycle stage - - - - - - - - - information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - - an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert - OBI_0000142 - information content entity - information content entity - - - - - - - - - ontology metadata - data about an ontology part - - - - - - - - - where to place this depends on if we take the organismal view or the quality centric view. - mammalian phenotype - - - - - - - - - Mus musculus - - - - - - - - - Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies. - Viruses - - - - - - - - - Danio rerio - - - - - - - - - Oryzias latipes - - - - - - - - - Homo sapiens - - - - - - - - - A processual entity that realizes a plan which is the concretization of a plan specification. - Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO. - planned process - - - - - - - - - reagent role - - - - - - - - - a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area - population - - - - - - - - - An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. - genotyping assay - - - - - - - - - A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. - A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. - targeted gene knock-out technique - - - - - - - - - targeted gene knock-in technique - - - - - - - - - Stub class to serve as root of hierarchy for imports from NCBI Taxonomy. - organism - - - - - - - - - - - - - - - - - - - - - - - - - the introduction. alteration or integration of genetic material into a cell or organism - genetic modification technique - - - - - - - - - 'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html - Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute. - color value - obsolete_color brightness - - - - - - - - - female - - - - - - - - - male - - - - - - - - - phenotypic sex - - - - - - - - - - - - - - - A material entity that consists of two or more organisms, viruses, or viroids. - A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role). - collection of organisms - - - - - - - - - A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. - family - - - - - - - - - Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. - morpholino_oligo - - - - - - - - - - - - - - - The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". - A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. - Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term. - http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: -chromosome > arm > region > band > sub-band - -Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): -chromosome > arm > band > sub-band > sub-sub-band - chromosome arm - - - - - - - - - - - - - - - - - - - - - Any extent of continuous biological sequence. - GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. -1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. -2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). -3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). - A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome. - sequence_feature - - - - - - - - - - - true - Formalizes the first identity criteria for a sequence feature of its sequence. - - - - - - - - - - - true - Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property). - - - - - - - - - A region of known length which may be used to manufacture a longer region. - obsolete_assembly_component - - - - - - - - - A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. - obsolete_contig - - - - - - - - - - - - 0 - - - The point at which one or more contiguous nucleotides were excised. - deleted_sequence - nucleotide deletion - nucleotide_deletion - - SO:1000033 - SO:0000159 - SOFA - http://en.wikipedia.org/wiki/Nucleotide_deletion - deletion - - - - - - - - - enhancer - - - - - - - - - A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. - promoter - - - - - - - - - A region of nucleotide sequence that has translocated to a new position. - transchr - translocated sequence - - SO:0000199 - DBVAR - translocation - - - - - - - - - SSLP - simple sequence length polymorphism - simple sequence length variation - - SO:0000207 - simple_sequence_length_variation - - - - - - - - - sequence length variation - - SO:0000248 - sequence_length_variation - - - - - - - - - - - - - - - See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25. - -Includes things like loxP sites, inducible promoters, ires elements, etc. - engineered_foreign_gene - - - - - - - - - A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. - http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29 - A defined feature that includes any type of VNTR or SSLP locus. - microsatellite - - - - - - - - - RNAi_reagent - - - - - - - - - Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. - A complete chromosome sequence. - chromosome - - - - - - - - - - - - - - - - - - - - - The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". - A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. - http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: -chromosome > arm > region > band > sub-band - -Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): -chromosome > arm > band > sub-band > sub-sub-band - - "Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. - chromosome band - - - - - - - - - centromere - - - - - - - - - Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct. - obsolete_engineered_plasmid - - - - - - - - - The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. - insertion - nucleotide insertion - nucleotide_insertion - - SO:1000034 - SO:0000667 - DBVAR - SOFA - insertion - - - - - - - - - SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. - single nucleotide polymorphism - - SO:0000694 - SOFA - SNP - - - - - - - - - A junction is a boundary between regions. A boundary has an extent of zero. - junction - - - - - - - - - A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. - Regarding the distinction between a 'gene' and a 'gene allele': -Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment). - A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion. - gene - - - - - - - - - A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. - quantitative trait locus - QTL - - - - - - - - - An attribute to describe a region that was modified in vitro. - engineered - - - - - - - - - - - - - - - - - - - construct - engineered_region - - - - - - - - - - - - - - - - - - - An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'. - chromosomal feature - gross chromosomal part - chromosome part - - - - - - - - - A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome). - On the relationship between 'transgenic insertions', 'transgenes', and 'alleles' -Transgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete. - -In addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. - -For the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach. - Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism). - -Note that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome. - transgene - - - - - - - - - A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. - multiple nucleotide polymorphism - - SO:0001013 - MNP - - - - - - - - - A variation that increases or decreases the copy number of a given region. - CNP - CNV - copy number polymorphism - copy number variation - - SO:0001019 - SOFA - http://en.wikipedia.org/wiki/Copy_number_variation - copy_number_variation - - - - - - - - - - - - - - - A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny) - Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. - 'genome sequence' - A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'. - genome - - - - - - - - - - - - - - - - - - - A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': - -1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871. - -2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112. - -3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112. - A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. - sequence variation - - SO:1000004 - SO:1000007 - SO:0001059 - SOFA - 1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. - -Alleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part. - -2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. - -For a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference. - -3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism. - sequence_alteration - - - - - - - - - - - - - - - An insertion that derives from another organism, via the use of recombinant DNA technology. - transgenic insertion - - SO:0001218 - transgenic_insertion - - - - - - - - - A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. - not currently needed to support modeling use cases. can re-introduce if becomes necessary. - obsolete_experimental_feature - - - - - - - - - A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. - gene_trap_construct - - - - - - - - - A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. - promoter_trap_construct - - - - - - - - - A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. - enhancer_trap_construct - - - - - - - - - SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist. - single nucleotide variant - - kareneilbeck - Thu Oct 08 11:37:49 PDT 2009 - SO:0001483 - SOFA - SNV - - - - - - - - - A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. - heritable_phenotypic_marker - - - - - - - - - - - - - - - 'GRCh37.p10' (a human reference genome build) - A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced. - reference genome sequence - - - - - - - - - A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. - copy number gain - gain - - kareneilbeck - Mon Feb 28 01:54:09 PST 2011 - SO:0001742 - DBVAR - copy_number_gain - - - - - - - - - A sequence alteration whereby the copy number of a given region is less than the reference sequence. - copy number loss - loss - - kareneilbeck - Mon Feb 28 01:55:02 PST 2011 - SO:0001743 - DBVAR - copy_number_loss - - - - - - - - - Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. - UPD - uniparental disomy - - kareneilbeck - Mon Feb 28 02:01:05 PST 2011 - SO:0001744 - DBVAR - http:http\://en.wikipedia.org/wiki/Uniparental_disomy - UPD - - - - - - - - - Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. - maternal uniparental disomy - - kareneilbeck - Mon Feb 28 02:03:01 PST 2011 - SO:0001745 - maternal_uniparental_disomy - - - - - - - - - Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. - paternal uniparental disomy - - kareneilbeck - Mon Feb 28 02:03:30 PST 2011 - SO:0001746 - paternal_uniparental_disomy - - - - - - - - - A structural sequence alteration where there are multiple equally plausible explanations for the change. - complex - - kareneilbeck - Wed Mar 23 03:21:19 PDT 2011 - SO:0001784 - DBVAR - complex_structural_alteration - - - - - - - - - - kareneilbeck - Fri Mar 25 02:27:41 PDT 2011 - SO:0001785 - DBVAR - structural_alteration - - - - - - - - - Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term. - regulatory element - regulatory gene region - regulatory_region - - - - - - - - - Any change in genomic DNA caused by a single event. - - SO:1000002 - SOFA - substitution - - - - - - - - - When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change. - complex substitution - - SO:1000005 - SOFA - complex_substitution - - - - - - - - - A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. - point mutation - - SO:1000008 - SOFA - http://en.wikipedia.org/wiki/Point_mutation - point_mutation - - - - - - - - - Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. - - SO:1000009 - transition - - - - - - - - - A substitution of a pyrimidine, C or T, for another pyrimidine. - pyrimidine transition - - SO:1000010 - pyrimidine_transition - - - - - - - - - A transition of a cytidine to a thymine. - C to T transition - - SO:1000011 - C_to_T_transition - - - - - - - - - The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine. - C to T transition at pCpG site - - SO:1000012 - C_to_T_transition_at_pCpG_site - - - - - - - - - T to C transition - - SO:1000013 - T_to_C_transition - - - - - - - - - A substitution of a purine, A or G, for another purine. - purine transition - - SO:1000014 - purine_transition - - - - - - - - - A transition of an adenine to a guanine. - A to G transition - - SO:1000015 - A_to_G_transition - - - - - - - - - A transition of a guanine to an adenine. - G to A transition - - SO:1000016 - G_to_A_transition - - - - - - - - - Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. - - SO:1000017 - http://en.wikipedia.org/wiki/Transversion - transversion - - - - - - - - - Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. - pyrimidine to purine transversion - - SO:1000018 - pyrimidine_to_purine_transversion - - - - - - - - - A transversion from cytidine to adenine. - C to A transversion - - SO:1000019 - C_to_A_transversion - - - - - - - - - C to G transversion - - SO:1000020 - C_to_G_transversion - - - - - - - - - A transversion from T to A. - T to A transversion - - SO:1000021 - T_to_A_transversion - - - - - - - - - A transversion from T to G. - T to G transversion - - SO:1000022 - T_to_G_transversion - - - - - - - - - Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. - purine to pyrimidine transversion - - SO:1000023 - purine_to_pyrimidine_transversion - - - - - - - - - A transversion from adenine to cytidine. - A to C transversion - - SO:1000024 - A_to_C_transversion - - - - - - - - - A transversion from adenine to thymine. - A to T transversion - - SO:1000025 - A_to_T_transversion - - - - - - - - - A transversion from guanine to cytidine. - G to C transversion - - SO:1000026 - G_to_C_transversion - - - - - - - - - A transversion from guanine to thymine. - G to T transversion - - SO:1000027 - G_to_T_transversion - - - - - - - - - A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. - - SO:1000032 - http://en.wikipedia.org/wiki/Indel - Indels can have a different number of bases than the corresponding reference sequence. - indel - - - - - - - - - One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point. - nucleotide duplication - nucleotide_duplication - - SO:1000035 - duplication - - - - - - - - - A continuous nucleotide sequence is inverted in the same position. - inversion - - SO:1000036 - DBVAR - SOFA - inversion - - - - - - - - - A tandem duplication where the individual regions are in the same orientation. - direct tandem duplication - - SO:1000039 - direct_tandem_duplication - - - - - - - - - A tandem duplication where the individual regions are not in the same orientation. - inverted tandem duplication - mirror duplication - - SO:1000040 - inverted_tandem_duplication - - - - - - - - - A duplication consisting of 2 identical adjacent regions. - erverted - tandem duplication - - SO:1000173 - DBVAR - tandem_duplication - - - - - - - - - Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms) - life cycle stage - - - - - - - - - - - - - - - Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies. - http://purl.obolibrary.org/obo/CARO_0000000 - anatomical entity - - - - - - - - - Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework. - 1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition) - -2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment - Phenotype - - - - - - - - - Animals exhibit variations compared to a given control. - 'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes. - Variant - c. elegans phenotype - worm phenotype - - - - - - - - - abnormal(ly) malformed endocardium cell - - - - - - - - - abnormal(ly) absent dorso-rostral cluster - - - - - - - - - abnormal(ly) disrupted diencephalon development - - - - - - - - - abnormal(ly) disrupted neutrophil aggregation - - - - - - - - - abnormal(ly) absent adaxial cell - - - - - - - - - association - - - - - - - - - - Equivalent to: http://www.informatics.jax.org/marker/MGI:98297 - mus musculus shh gene - - - - - - - - - - http://zfin.org/ZDB-GENE-980526-166 - danio rerio shha gene - - - - - - - - - - http://zfin.org/ZDB-GENE-040123-1 - danio rerio cdkn1ca gene - - - - - - - - - - Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690 - -Codes for: http://www.uniprot.org/uniprot/Q15465 - homo sapiens SHH gene - - - - - - - - - - - - - - exploratory term - - - - - - - - - exemplar term - - - - - - - - - - - - - - - - - Initially created such that integrated transgene infers as child of sequence_alteration. - - - - - - - diff --git a/src/ontology/imports/iao_import.json b/src/ontology/imports/iao_import.json new file mode 100644 index 0000000..ee7a9ee --- /dev/null +++ b/src/ontology/imports/iao_import.json @@ -0,0 +1,3550 @@ +{ + "graphs" : [ { + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "term imported" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "term split" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this cell derives from this parent cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this nucleus derives from this parent nucleus (nuclear division)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "derives from" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent cell derives into this cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent nucleus derives into this nucleus (nuclear division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + } ] + }, + "type" : "PROPERTY", + "lbl" : "derives into" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000230", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We expect to be able to mine these new reasons and add instances as required." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "other" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + } ] + }, + "type" : "PROPERTY", + "lbl" : "part of" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "meta" : { + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor note" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "editor note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "meta" : { + "definition" : { + "val" : "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term editor" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term editor" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000235", + "meta" : { + "definition" : { + "val" : "inverse of the relation 'denotes'", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Mike Conlon" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/206" + } ] + }, + "type" : "PROPERTY", + "lbl" : "denoted by" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000281" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has curation status" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has curation status" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000598", + "meta" : { + "definition" : { + "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID policy for" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000599", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID prefix" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "meta" : { + "definition" : { + "val" : "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "textual definition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has part" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "meta" : { + "definition" : { + "val" : "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + } ] + }, + "type" : "PROPERTY", + "lbl" : "example of usage" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term tracker item" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The 'tracker item' can associate a tracker with a specific ontology term." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term tracker item" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000596", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID digit count" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000597", + "meta" : { + "definition" : { + "val" : "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID range allocated to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000234", + "meta" : { + "definition" : { + "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The 'term requester' can credit the person, organization or project who request the ontology term." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "ontology term requester" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000113", + "meta" : { + "definition" : { + "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "in branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000277" + } ] + }, + "type" : "PROPERTY", + "lbl" : "in branch" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "meta" : { + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has obsolescence reason" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has obsolescence reason" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "meta" : { + "definition" : { + "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term~editor preferred label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term" + } ] + }, + "type" : "PROPERTY", + "lbl" : "editor preferred label" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000078", + "meta" : { + "definition" : { + "val" : "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curation status specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000266" + } ] + }, + "type" : "CLASS", + "lbl" : "curation status specification" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "meta" : { + "definition" : { + "val" : "An administrative note of use for a curator but of no use for a user", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curator note" + } ] + }, + "type" : "PROPERTY", + "lbl" : "curator note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "alternative term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "alternative term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "meta" : { + "definition" : { + "val" : "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition source" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition source" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000312", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is_specified_output_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is_specified_output_of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_specified_output_of" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "metadata complete" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "pending final vetting" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "metadata incomplete" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "meta" : { + "definition" : { + "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the undetached arm of a human being" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a puff of smoke" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an epidemic" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a forest fire" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a hurricane" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a flame" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a sea wave" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "material" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a tornado" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an aggregate of human beings." + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "MaterialEntity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an energy wave" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a human being" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a photon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "material entity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "type" : "INDIVIDUAL", + "lbl" : "example to be eventually removed" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "uncurated" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "meta" : { + "definition" : { + "val" : "term created to ease viewing/sort terms for development purpose, and will not be included in a release", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "organizational term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "ready for release" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000409", + "meta" : { + "definition" : { + "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Barry Smith, Werner Ceusters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "CLASS", + "lbl" : "denotator type" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "type" : "PROPERTY", + "lbl" : "disposition of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000020", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:48Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "EL++ ontology module" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass", + "type" : "CLASS", + "lbl" : "Obsolete Class" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000019", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module subsetted by OWL profile" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000011", + "meta" : { + "definition" : { + "val" : "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:00:14Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "external import" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "external import ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000012", + "meta" : { + "definition" : { + "val" : "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:14:16Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "taxon subset" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + }, + "type" : "CLASS", + "lbl" : "species subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000136", + "meta" : { + "definition" : { + "val" : "is_about is a (currently) primitive relation that relates an information artifact to an entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This document is about information artifacts and their representations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is about" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000015", + "meta" : { + "definition" : { + "val" : "A quality of an information bearer that imparts the information content", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "information carrier" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "CLASS", + "lbl" : "information carrier" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000411", + "meta" : { + "definition" : { + "val" : "relates an class defined in an ontology, to the type of it's denotator", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is denotator type" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is denotator type" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000013", + "meta" : { + "definition" : { + "val" : "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:20:33Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/reason" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "reasoned ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000014", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:21:12Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" + } ] + }, + "type" : "CLASS", + "lbl" : "generated ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000412", + "meta" : { + "definition" : { + "val" : "For external terms/classes, the ontology from which the term was imported", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "imported from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "imported from" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000015", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://doi.org/10.1186/s13326-017-0126-0" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/template" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:21:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "template generated ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "universal" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:28:15Z" + } ] + }, + "type" : "CLASS", + "lbl" : "taxonomic bridge ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000017", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:15:54Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module subsetted by expressivity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000018", + "meta" : { + "definition" : { + "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:10Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" + } ] + }, + "type" : "CLASS", + "lbl" : "obo basic subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000293", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has_specified_input" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Coutot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Larry Hunter" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has_specified_input" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "see is_input_of example_of_usage" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_specified_input" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "meta" : { + "definition" : { + "val" : "Add as annotation triples in the granting ontology", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term replaced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term replaced by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "role of" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000295", + "type" : "PROPERTY", + "lbl" : "is_specified_input_of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + } ] + }, + "type" : "PROPERTY", + "lbl" : "quality of" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000010", + "meta" : { + "definition" : { + "val" : "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:59:57Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "antislim" + } ] + }, + "type" : "CLASS", + "lbl" : "exclusion subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000299", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has_specified_output" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has_specified_output" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Larry Hunter" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_specified_output" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has role" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has quality" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000008", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended for usage in analysis or discovery applications.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:49Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "analysis subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000009", + "meta" : { + "definition" : { + "val" : "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:59:19Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ribbon subset" + } ] + }, + "type" : "CLASS", + "lbl" : "single layer subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:03Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology file" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000028", + "meta" : { + "definition" : { + "val" : "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "based on Oxford English Dictionary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: James A. Overton" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "symbol" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "20091104, MC: this needs work and will most probably change" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Jonathan Rees" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a written proper name such as \"OBI\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a serial number such as \"12324X\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a stop sign" + } ] + }, + "type" : "CLASS", + "lbl" : "symbol" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand expression to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + } ] + }, + "type" : "PROPERTY", + "lbl" : "expand expression to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000001", + "meta" : { + "definition" : { + "val" : "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "base ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000425", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand assertion to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + } ] + }, + "type" : "PROPERTY", + "lbl" : "expand assertion to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000002", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "source ontology module" + } ] + }, + "type" : "CLASS", + "lbl" : "editors ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000003", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:13Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" + } ] + }, + "type" : "CLASS", + "lbl" : "main release ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "meta" : { + "definition" : { + "val" : "Terms with this status should eventually replaced with a term from another ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "to be replaced with external ontology term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000027", + "meta" : { + "definition" : { + "val" : "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Jonathan Rees" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data item" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Chris Stoeckert" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Data items include counts of things, analyte concentrations, and statistical summaries." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "data" + } ] + }, + "type" : "CLASS", + "lbl" : "data item" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000004", + "meta" : { + "definition" : { + "val" : "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:23Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "bridge ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "meta" : { + "definition" : { + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "defined class" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000005", + "meta" : { + "definition" : { + "val" : "A subset ontology module that is intended to be imported from another ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add axioms that indicate this is the output of a module extraction process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "import file" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/extract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "import ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "meta" : { + "definition" : { + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "named class expression" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000006", + "meta" : { + "definition" : { + "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology slim" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:11Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "subset ontology" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/filter" + } ] + }, + "type" : "CLASS", + "lbl" : "subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000007", + "meta" : { + "definition" : { + "val" : "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:38Z" + } ] + }, + "type" : "CLASS", + "lbl" : "curation subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of your nose" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mass of this piece of gold." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the color of a tomato" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "quality" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the length of the circumference of your waist" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the ambient temperature of this portion of air" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Quality" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of your nostril" + } ] + }, + "type" : "CLASS", + "lbl" : "quality" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "meta" : { + "definition" : { + "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the life of an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the flight of a bird" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "process" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of cell-division, \\ a beating of the heart" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of meiosis" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of sleeping" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "your process of aging." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the course of a disease" + } ] + }, + "type" : "CLASS", + "lbl" : "process" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "requires discussion" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "disposition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "children are innately disposed to categorize objects in certain ways." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Disposition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "certain people have a predisposition to colon cancer" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an atom of element X has the disposition to decay to an atom of element Y" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" + } ] + }, + "type" : "CLASS", + "lbl" : "disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "meta" : { + "definition" : { + "val" : "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of your blood to coagulate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of this piece of metal to conduct electricity." + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "realizable" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "RealizableEntity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of being a doctor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of your reproductive organs" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of this boundary to delineate where Utah and Colorado meet" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "realizable entity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "first order logic expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "first order logic expression" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000427", + "meta" : { + "definition" : { + "val" : "use boolean value xsd:true to indicate that the property is an antisymmetric property", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part_of antisymmetric property xsd:true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "antisymmetric property" + } ] + }, + "type" : "PROPERTY", + "lbl" : "antisymmetric property" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000030", + "meta" : { + "definition" : { + "val" : "A generically dependent continuant that is about some thing.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000142" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "information content entity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples of information content entites include journal articles, data, graphical layouts, and graphs." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Chris Stoeckert" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." + } ] + }, + "type" : "CLASS", + "lbl" : "information content entity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006011", + "meta" : { + "definition" : { + "val" : "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "#40" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "VFB" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-21T16:43:39Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "may be identical to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006012", + "meta" : { + "definition" : { + "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/15532" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "GO ontology" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall, Jie Zheng" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/32" + } ] + }, + "type" : "PROPERTY", + "lbl" : "scheduled for obsoletion on or after" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", + "meta" : { + "definition" : { + "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a spatial region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the bottom right portion of a human torso" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "ic" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a leg" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "IndependentContinuant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an orchestra." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an atom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the interior of your mouth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a chair" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a molecule" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a heart" + } ] + }, + "type" : "CLASS", + "lbl" : "independent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0010000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has axiom id" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has axiom label" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "meta" : { + "definition" : { + "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." + } ] + }, + "type" : "PROPERTY", + "lbl" : "concretizes" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "meta" : { + "definition" : { + "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is concretized as" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has participant" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000600", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "elucidation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Barry Smith" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + } ] + }, + "type" : "PROPERTY", + "lbl" : "elucidation" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Julius Caesar" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Verdi’s Requiem" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "entity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Entity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "your body mass index" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the Second World War" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" + } ] + }, + "type" : "CLASS", + "lbl" : "entity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000601", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom associated with a term expressed using natural language" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(nl)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has associated axiom(nl)" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000002", + "meta" : { + "definition" : { + "val" : "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "continuant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Continuant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" + } ] + }, + "type" : "CLASS", + "lbl" : "continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "meta" : { + "definition" : { + "val" : "An entity that has temporal parts and that happens, unfolds or develops through time.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "occurrent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Occurrent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." + } ] + }, + "type" : "CLASS", + "lbl" : "occurrent" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000602", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom expressed in first order logic using CLIF syntax" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(fol)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has associated axiom(fol)" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000603", + "meta" : { + "definition" : { + "val" : "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\"", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is allocated id range" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is allocated id range" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color inheres in this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility inheres in this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A dependent inheres in its bearer at all times for which the dependent exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + } ] + }, + "type" : "PROPERTY", + "lbl" : "inheres in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + } ] + }, + "type" : "PROPERTY", + "lbl" : "participates in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "meta" : { + "definition" : { + "val" : "is member of is a mereological relation between a item and a collection.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "member part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An organism that is a member of a population of organisms" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is member of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "member of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "bearer of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "meta" : { + "definition" : { + "val" : "has member is a mereological relation between a collection and an item.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has member" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000578", + "meta" : { + "definition" : { + "val" : "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bill Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000120" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "CRID" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records')." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. \n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Original proposal from Bjoern, discussions at IAO calls" + } ] + }, + "type" : "CLASS", + "lbl" : "centrally registered identifier" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000579", + "meta" : { + "definition" : { + "val" : "A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "CRID registry" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Original proposal from Bjoern, discussions at IAO calls" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bill Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000120" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + } ] + }, + "type" : "CLASS", + "lbl" : "centrally registered identifier registry" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "function" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of a hammer to drive in nails" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of amylase in saliva to break down starch into sugar" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Function" + } ] + }, + "type" : "CLASS", + "lbl" : "function" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000577", + "meta" : { + "definition" : { + "val" : "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Original proposal from Bjoern, discussions at IAO calls" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bill Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000120" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "CRID symbol" + } ] + }, + "type" : "CLASS", + "lbl" : "centrally registered identifier symbol" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000178", + "meta" : { + "definition" : { + "val" : "A material entity in which a concretization of an information content entity inheres.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a hard drive" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a brain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP: IAO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "material information bearer" + } ] + }, + "type" : "CLASS", + "lbl" : "material information bearer" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000031", + "meta" : { + "definition" : { + "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "gdc" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "GenericallyDependentContinuant" + } ] + }, + "type" : "CLASS", + "lbl" : "generically dependent continuant" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#Subset", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000219", + "meta" : { + "definition" : { + "val" : "denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.\ng denotes r =def \nr is a portion of reality\nthere is some c that is a concretization of g \nevery c that is a concretization of g specifically denotes r" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named." + } ] + }, + "type" : "PROPERTY", + "lbl" : "denotes" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000011", + "meta" : { + "definition" : { + "val" : "A processual entity that realizes a plan which is the concretization of a plan specification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "planned process" + } ] + }, + "type" : "CLASS", + "lbl" : "planned process" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "type" : "INDIVIDUAL", + "lbl" : "placeholder removed" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which is unique across the OBO Foundry.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBO Foundry " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "OBO foundry unique label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + }, + "type" : "PROPERTY", + "lbl" : "OBO foundry unique label" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000023", + "meta" : { + "definition" : { + "val" : "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a stone in marking a property boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the student role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a building in serving as a military target" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of subject in a clinical trial" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the priest role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a boundary to demarcate two neighboring administrative territories" + } ] + }, + "type" : "CLASS", + "lbl" : "role" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "terms merged" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "meta" : { + "definition" : { + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "failed exploratory term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000224", + "meta" : { + "definition" : { + "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "core" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "meta" : { + "definition" : { + "val" : "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obsolescence reason specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolescence reason specification" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000102", + "meta" : { + "definition" : { + "val" : "data about an ontology part is a data item about a part of an ontology, for example a term", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "CLASS", + "lbl" : "data about an ontology part" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000020", + "meta" : { + "definition" : { + "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "of one-sided specifically dependent continuants: the mass of this tomato" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of this fish to decay" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the pink color of a medium rare piece of grilled filet mignon at its center" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the smell of this portion of mozzarella" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of this heart: to pump blood" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of this hole." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mutual dependence of proton donors and acceptors in chemical reactions [79" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "SpecificallyDependentContinuant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of being a doctor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "sdc" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "specifically dependent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000100", + "meta" : { + "definition" : { + "val" : "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data set" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000042" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Chris Stoeckert" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Allyson Lister" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + } ] + }, + "type" : "CLASS", + "lbl" : "data set" + } ], + "edges" : [ { + "sub" : "http://purl.obolibrary.org/obo/IAO_8000017", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_8000006" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0000219", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000235" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_8000002", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_8000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0000578", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0000421", + "pred" : "type", + "obj" : 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Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (denotes)\n\nAnnotationAssertion(rdfs:comment \"\"@en)\n\n# Object Property: (has_specified_input)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (has_specified_output)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (is_specified_output_of)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (curation status specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (material information bearer)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))\n\n# Class: (obsolescence reason specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (denotator type)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (centrally registered identifier)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: ()\n\nEquivalentClasses( ObjectOneOf())\n\n\n############################\n# Named Individuals\n############################\n\n# Individual: (metadata complete)\n\n\n# Individual: (organizational term)\n\n\n# Individual: (ready for release)\n\n\n# Individual: (metadata incomplete)\n\n\n# Individual: (uncurated)\n\n\n# Individual: (pending final vetting)\n\n\n# Individual: (placeholder removed)\n\n\n# Individual: (terms merged)\n\n\n# Individual: (term imported)\n\n\n# Individual: (term split)\n\n\n# Individual: (to be replaced with external ontology term)\n\n\n# Individual: (requires discussion)\n\n\n\nDifferentIndividuals( )\nDifferentIndividuals( )\n) + +[Term] +id: BFO:0000001 +name: entity +property_value: BFO:0000179 "entity" xsd:string +property_value: BFO:0000180 "Entity" xsd:string +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +property_value: BFO:0000179 "continuant" xsd:string +property_value: BFO:0000180 "Continuant" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +is_a: BFO:0000001 ! entity +property_value: BFO:0000179 "occurrent" xsd:string +property_value: BFO:0000180 "Occurrent" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} +property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "ic" xsd:string +property_value: BFO:0000180 "IndependentContinuant" xsd:string +property_value: IAO:0000112 "a chair" xsd:string +property_value: IAO:0000112 "a heart" xsd:string +property_value: IAO:0000112 "a leg" xsd:string +property_value: IAO:0000112 "a molecule" xsd:string +property_value: IAO:0000112 "a spatial region" xsd:string +property_value: IAO:0000112 "an atom" xsd:string +property_value: IAO:0000112 "an orchestra." xsd:string +property_value: IAO:0000112 "an organism" xsd:string +property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string +property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +is_a: BFO:0000003 ! occurrent +property_value: BFO:0000179 "process" xsd:string +property_value: BFO:0000180 "Process" xsd:string +property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string +property_value: IAO:0000112 "a process of meiosis" xsd:string +property_value: IAO:0000112 "a process of sleeping" xsd:string +property_value: IAO:0000112 "the course of a disease" xsd:string +property_value: IAO:0000112 "the flight of a bird" xsd:string +property_value: IAO:0000112 "the life of an organism" xsd:string +property_value: IAO:0000112 "your process of aging." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string +property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role +property_value: BFO:0000179 "disposition" xsd:string +property_value: BFO:0000180 "Disposition" xsd:string +property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string +property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string +property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string +property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string +property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000017 +name: realizable entity +def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality +property_value: BFO:0000179 "realizable" xsd:string +property_value: BFO:0000180 "RealizableEntity" xsd:string +property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string +property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string +property_value: IAO:0000112 "the function of your reproductive organs" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: BFO:0000179 "quality" xsd:string +property_value: BFO:0000180 "Quality" xsd:string +property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string +property_value: IAO:0000112 "the color of a tomato" xsd:string +property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string +property_value: IAO:0000112 "the mass of this piece of gold." xsd:string +property_value: IAO:0000112 "the shape of your nose" xsd:string +property_value: IAO:0000112 "the shape of your nostril" xsd:string +property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "sdc" xsd:string +property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string +property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000023 +name: role +def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] +is_a: BFO:0000017 ! realizable entity +property_value: BFO:0000179 "role" xsd:string +property_value: BFO:0000180 "Role" xsd:string +property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string +property_value: IAO:0000112 "the priest role" xsd:string +property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string +property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string +property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string +property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string +property_value: IAO:0000112 "the student role" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string +property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +is_a: BFO:0000002 ! continuant +property_value: BFO:0000179 "gdc" xsd:string +property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string +property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition +property_value: BFO:0000179 "function" xsd:string +property_value: BFO:0000180 "Function" xsd:string +property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string +property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string +property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string +property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant +property_value: BFO:0000179 "material" xsd:string +property_value: BFO:0000180 "MaterialEntity" xsd:string +property_value: IAO:0000112 "a flame" xsd:string +property_value: IAO:0000112 "a forest fire" xsd:string +property_value: IAO:0000112 "a human being" xsd:string +property_value: IAO:0000112 "a hurricane" xsd:string +property_value: IAO:0000112 "a photon" xsd:string +property_value: IAO:0000112 "a puff of smoke" xsd:string +property_value: IAO:0000112 "a sea wave" xsd:string +property_value: IAO:0000112 "a tornado" xsd:string +property_value: IAO:0000112 "an aggregate of human beings." xsd:string +property_value: IAO:0000112 "an energy wave" xsd:string +property_value: IAO:0000112 "an epidemic" xsd:string +property_value: IAO:0000112 "the undetached arm of a human being" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: DbXref +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Definition +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: IAO:0000015 +name: information carrier +def: "A quality of an information bearer that imparts the information content" [] +is_a: BFO:0000019 ! quality +intersection_of: BFO:0000019 ! quality +intersection_of: RO:0000059 IAO:0000030 ! concretizes information content entity +property_value: IAO:0000111 "information carrier" xsd:string +property_value: IAO:0000112 "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'." xsd:string +property_value: IAO:0000116 "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string + +[Term] +id: IAO:0000027 +name: data item +def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] +is_a: IAO:0000030 ! information content entity +property_value: IAO:0000111 "data item" xsd:string +property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string +property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string +property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string +property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string +property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000118 "data" xsd:string + +[Term] +id: IAO:0000028 +name: symbol +def: "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." [] +is_a: IAO:0000030 ! information content entity +property_value: IAO:0000111 "symbol" xsd:string +property_value: IAO:0000112 "a serial number such as \"12324X\"" xsd:string +property_value: IAO:0000112 "a stop sign" xsd:string +property_value: IAO:0000112 "a written proper name such as \"OBI\"" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "20091104, MC: this needs work and will most probably change" xsd:string +property_value: IAO:0000116 "2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154)." xsd:string +property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000119 "based on Oxford English Dictionary" xsd:string + +[Term] +id: IAO:0000030 +name: information content entity +def: "A generically dependent continuant that is about some thing." [] +is_a: BFO:0000031 ! generically dependent continuant +relationship: IAO:0000136 BFO:0000001 ! is about entity +property_value: IAO:0000111 "information content entity" xsd:string +property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." xsd:string +property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000119 "OBI_0000142" xsd:string + +[Term] +id: IAO:0000078 +name: curation status specification +def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000100 +name: data set +def: "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets." [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000111 "data set" xsd:string +property_value: IAO:0000112 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" xsd:string +property_value: IAO:0000116 "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction." xsd:string +property_value: IAO:0000117 "person:Allyson Lister" xsd:string +property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string +property_value: IAO:0000119 group:OBI xsd:string +property_value: IAO:0000119 "OBI_0000042" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string + +[Term] +id: IAO:0000178 +name: material information bearer +def: "A material entity in which a concretization of an information content entity inheres." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000111 "material information bearer" xsd:string +property_value: IAO:0000112 "a brain" xsd:string +property_value: IAO:0000112 "a hard drive" xsd:string +property_value: IAO:0000112 "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "GROUP: IAO" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: IAO:0000577 +name: centrally registered identifier symbol +def: "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry." [] +is_a: IAO:0000028 ! symbol +relationship: BFO:0000050 IAO:0000578 ! part of centrally registered identifier +property_value: IAO:0000112 "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000118 "CRID symbol" xsd:string +property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string + +[Term] +id: IAO:0000578 +name: centrally registered identifier +def: "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs." [] +is_a: IAO:0000030 ! information content entity +relationship: BFO:0000051 IAO:0000577 ! has part centrally registered identifier symbol +property_value: IAO:0000112 "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records')." xsd:string +property_value: IAO:0000116 "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. \n" xsd:string +property_value: IAO:0000116 "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000118 "CRID" xsd:string +property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string + +[Term] +id: IAO:0000579 +name: centrally registered identifier registry +def: "A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process." [] +is_a: IAO:0000100 ! data set +property_value: IAO:0000112 "PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. " xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000118 "CRID registry" xsd:string +property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string + +[Term] +id: IAO:8000000 +name: ontology module +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000116 "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000118 "ontology file" xsd:string +property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:03Z + +[Term] +id: IAO:8000001 +name: base ontology module +def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 +created_by: cjm +creation_date: 2018-05-20T20:55:30Z + +[Term] +id: IAO:8000002 +name: editors ontology module +def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "source ontology module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:47Z + +[Term] +id: IAO:8000003 +name: main release ontology module +def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:56:13Z + +[Term] +id: IAO:8000004 +name: bridge ontology module +def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies +created_by: cjm +creation_date: 2018-05-20T20:56:23Z + +[Term] +id: IAO:8000005 +name: import ontology module +def: "A subset ontology module that is intended to be imported from another ontology." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000118 "import file" xsd:string +property_value: seeAlso http://robot.obolibrary.org/extract +created_by: cjm +creation_date: 2018-05-20T20:56:47Z + +[Term] +id: IAO:8000006 +name: subset ontology module +def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "ontology slim" xsd:string +property_value: IAO:0000118 "subset ontology" xsd:string +property_value: seeAlso http://robot.obolibrary.org/filter +property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide +created_by: cjm +creation_date: 2018-05-20T20:58:11Z + +[Term] +id: IAO:8000007 +name: curation subset ontology module +def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:38Z + +[Term] +id: IAO:8000008 +name: analysis subset ontology module +def: "An ontology module that is intended for usage in analysis or discovery applications." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:49Z + +[Term] +id: IAO:8000009 +name: single layer subset ontology module +def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "ribbon subset" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:19Z + +[Term] +id: IAO:8000010 +name: exclusion subset ontology module +def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "antislim" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:57Z + +[Term] +id: IAO:8000011 +name: external import ontology module +def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] +is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000118 "external import" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:00:14Z + +[Term] +id: IAO:8000012 +name: species subset ontology module +def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "taxon subset" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +created_by: cjm +creation_date: 2018-05-20T21:14:16Z + +[Term] +id: IAO:8000013 +name: reasoned ontology module +def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso http://robot.obolibrary.org/reason +created_by: cjm +creation_date: 2018-05-20T21:20:33Z + +[Term] +id: IAO:8000014 +name: generated ontology module +def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:21:12Z + +[Term] +id: IAO:8000015 +name: template generated ontology module +def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] +is_a: IAO:8000014 ! generated ontology module +property_value: seeAlso http://robot.obolibrary.org/template +property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 +property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ +created_by: cjm +creation_date: 2018-05-20T21:21:21Z + +[Term] +id: IAO:8000016 +name: taxonomic bridge ontology module +is_a: IAO:8000004 ! bridge ontology module +created_by: cjm +creation_date: 2018-05-20T21:28:15Z + +[Term] +id: IAO:8000017 +name: ontology module subsetted by expressivity +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-22T04:15:54Z + +[Term] +id: IAO:8000018 +name: obo basic subset ontology module +def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: seeAlso "6.2" +created_by: cjm +creation_date: 2018-05-22T04:16:10Z + +[Term] +id: IAO:8000019 +name: ontology module subsetted by OWL profile +is_a: IAO:8000017 ! ontology module subsetted by expressivity +created_by: cjm +creation_date: 2018-05-22T04:16:28Z + +[Term] +id: IAO:8000020 +name: EL++ ontology module +is_a: IAO:8000019 ! ontology module subsetted by OWL profile +created_by: cjm +creation_date: 2018-05-22T04:16:48Z + +[Term] +id: OBI:0000011 +name: planned process +def: "A processual entity that realizes a plan which is the concretization of a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + +[Term] +id: ObsoleteClass +name: Obsolete Class + +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Synonym +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: SynonymType +is_a: IAO:0000102 ! data about an ontology part + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true + +[Typedef] +id: IAO:0000136 +name: is about +def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." [] +property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string +domain: IAO:0000030 ! information content entity + +[Typedef] +id: IAO:0000219 +name: denotes +def: "denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" [] +property_value: IAO:0000112 "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named." xsd:string +property_value: IAO:0000116 "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.\ng denotes r =def \nr is a portion of reality\nthere is some c that is a concretization of g \nevery c that is a concretization of g specifically denotes r" xsd:string +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan" xsd:string +domain: IAO:0000030 ! information content entity +range: BFO:0000001 ! entity +is_a: IAO:0000136 ! is about +inverse_of: IAO:0000235 ! denoted by + +[Typedef] +id: IAO:0000235 +name: denoted by +def: "inverse of the relation 'denotes'" [] +property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Mike Conlon" xsd:string +property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/206 +domain: BFO:0000001 ! entity +range: IAO:0000030 ! information content entity + +[Typedef] +id: OBI:0000293 +name: has_specified_input +def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "has_specified_input" xsd:string +property_value: IAO:0000111 "has_specified_input" xsd:string +property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl +domain: OBI:0000011 ! planned process +is_a: RO:0000057 ! has participant +inverse_of: OBI:0000295 ! is_specified_input_of + +[Typedef] +id: OBI:0000295 +name: is_specified_input_of + +[Typedef] +id: OBI:0000299 +name: has_specified_output +def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "has_specified_output" xsd:string +property_value: IAO:0000111 "has_specified_output" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl +domain: OBI:0000011 ! planned process +is_a: RO:0000057 ! has participant +inverse_of: OBI:0000312 ! is_specified_output_of + +[Typedef] +id: OBI:0000312 +name: is_specified_output_of +def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "is_specified_output_of" xsd:string +property_value: IAO:0000111 "is_specified_output_of" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl +range: OBI:0000011 ! planned process +is_a: RO:0000056 ! participates in + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: RO:0000053 ! bearer of +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +is_a: RO:0000052 ! inheres in + +[Typedef] +id: RO:0001000 +name: derives from +def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string +property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string +property_value: IAO:0000118 "derives_from" xsd:string +inverse_of: RO:0001001 ! derives into + +[Typedef] +id: RO:0001001 +name: derives into +def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string +property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string +property_value: IAO:0000118 "derives_into" xsd:string + +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000050 ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000051 ! has part + diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index 38752b0..56b32ee 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -1,14 +1,2638 @@ - - + xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + + + + + + + example + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + + + + + + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + + + + + + + + definition + definition + textual definition + + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + textual definition + + + + + + + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + + editor note + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + alternative term + + + + + + + + definition source + + formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + + + + + + + + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + + + + + + is denotator type + relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + imported from + + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + + + + + + + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + + + + + + + first order logic expression + PERSON:Alan Ruttenberg + first order logic expression + + + + + + + + antisymmetric property + part_of antisymmetric property xsd:true + use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + + + + + + OBO foundry unique label + + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + + + + + + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + + has associated axiom(fol) + + + + + + + + is allocated id range + Add as annotation triples in the granting ontology + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + is allocated id range + + + + + + + + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + 2018-09-21T16:43:39Z + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + + + + + + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + https://github.com/geneontology/go-ontology/issues/15532 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + + has axiom label + + + + + + + + term replaced by + + Add as annotation triples in the granting ontology + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + term replaced by + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + has part + + + + + + + + + This document is about information artifacts and their representations + + is_about is a (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + + + + + + A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. + denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically + 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. +g denotes r =def +r is a portion of reality +there is some c that is a concretization of g +every c that is a concretization of g specifically denotes r + person:Alan Ruttenberg + Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan + + denotes + + + + + + + + + + inverse of the relation 'denotes' + Person: Jie Zheng, Chris Stoeckert, Mike Conlon + + denoted by + + + + + + + + + + + + + + + + has_specified_input + has_specified_input + see is_input_of example_of_usage + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot + + has_specified_input + + + + + + + + is_specified_input_of + + + + + + + + + + + + + + + + has_specified_output + has_specified_output + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot + + has_specified_output + + + + + + + + + + + + + + + is_specified_output_of + is_specified_output_of + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters + + is_specified_output_of + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + role of + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + disposition of + + + + + + + + + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + derives from + + + - + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + derives into + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + + + + + + + continuant + Continuant + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + + + + + + + + + + + occurrent + Occurrent + An entity that has temporal parts and that happens, unfolds or develops through time. + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + + + + + + + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process + + + + + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + + + + + + + + + + disposition + Disposition + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocytosis and exocytosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + disposition + + + + + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + + + + + + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + + + + + + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + + + + + + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + + + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + + + + + + + + + quality + Quality + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + quality + + + + + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + + + + + + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + + + + + + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + + + + + + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + + + + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + + + + + + + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant + + + + + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + + + + + + + + + function + Function + the function of a hammer to drive in nails + the function of a heart pacemaker to regulate the beating of a heart through electricity + the function of amylase in saliva to break down starch into sugar + BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + function + + + + + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + + + + + + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + + + + + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + + + + + + + + + + + + + + + + + + + + information carrier + In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. + + A quality of an information bearer that imparts the information content + 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. + 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. + PERSON: Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + information carrier + + + + + + + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item + + + + + + + + + symbol + a serial number such as "12324X" + a stop sign + a written proper name such as "OBI" + + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + 20091104, MC: this needs work and will most probably change + 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). + PERSON: James A. Overton + PERSON: Jonathan Rees + based on Oxford English Dictionary + symbol + + + + + + + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + A generically dependent continuant that is about some thing. + 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data set + Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). + + A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. + 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type + 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000042 + group:OBI + data set + + + + + + + + + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part + + + + + + + + + + + + + + + + + + + + + + + + + material information bearer + A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. + a brain + a hard drive + + A material entity in which a concretization of an information content entity inheres. + GROUP: IAO + material information bearer + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification + + + + + + + + + + + + + + + + + + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + + + + + + + + + + + + + The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. + + A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID symbol + Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier symbol + + + + + + + + + + + + + + + + + + + + + + + + + + The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. + + An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. + 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). + Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. + + Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID + Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier + + + + + + + + + PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. + + A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID registry + Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier registry + + + + + + + + + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + cjm + 2018-05-20T20:55:03Z + ontology module + + + + + + + + + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + cjm + 2018-05-20T20:55:30Z + base ontology module + + + + + + + + + + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + cjm + 2018-05-20T20:55:47Z + editors ontology module + + + + + + + + + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + cjm + 2018-05-20T20:56:13Z + main release ontology module + + + + + + + + + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + cjm + 2018-05-20T20:56:23Z + bridge ontology module + + + + + + + + + + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + cjm + 2018-05-20T20:56:47Z + import ontology module + + + + + + + + + + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + cjm + 2018-05-20T20:58:11Z + subset ontology module + + + + + + + + + + + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + cjm + 2018-05-20T20:58:38Z + curation subset ontology module + + + + + + + + + An ontology module that is intended for usage in analysis or discovery applications. + cjm + 2018-05-20T20:58:49Z + analysis subset ontology module + + + + + + + + + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + cjm + 2018-05-20T20:59:19Z + single layer subset ontology module + + + + + + + + + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + cjm + 2018-05-20T20:59:57Z + exclusion subset ontology module + + + + + + + + + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + cjm + 2018-05-20T21:00:14Z + external import ontology module + + + + + + + + + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + cjm + 2018-05-20T21:14:16Z + species subset ontology module + + + + + + + + + + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + cjm + 2018-05-20T21:20:33Z + reasoned ontology module + + + + + + + + + + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + cjm + 2018-05-20T21:21:12Z + generated ontology module + + + + + + + + + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + cjm + 2018-05-20T21:21:21Z + template generated ontology module + + + + + + + + + + + + cjm + 2018-05-20T21:28:15Z + taxonomic bridge ontology module + + + + + + + + + cjm + 2018-05-22T04:15:54Z + ontology module subsetted by expressivity + + + + + + + + + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + cjm + 2018-05-22T04:16:10Z + obo basic subset ontology module + + + + + + + + + + cjm + 2018-05-22T04:16:28Z + ontology module subsetted by OWL profile + + + + + + + + + cjm + 2018-05-22T04:16:48Z + EL++ ontology module + + + + + + + + + planned process + A processual entity that realizes a plan which is the concretization of a plan specification. + + planned process + + + + + + + + + + + + + + + + + + + + + + + + Obsolete Class + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + core + + + + + + + + + placeholder removed + + + + + + + + + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + + This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. + We expect to be able to mine these new reasons and add instances as required. + other + true + + + + + + + + + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/ro_import.json b/src/ontology/imports/ro_import.json new file mode 100644 index 0000000..19e4750 --- /dev/null +++ b/src/ontology/imports/ro_import.json @@ -0,0 +1,4812 @@ +{ + "graphs" : [ { + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/GO_0003674", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "molecular process" + } ] + }, + "type" : "CLASS", + "lbl" : "molecular_function" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + }, + "type" : "PROPERTY", + "lbl" : "results in formation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. 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Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has positive regulatory component activity" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This relation groups together various other developmental relations. 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", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "RO_0000053 some (RO_0000054 only ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + } ] + }, + "type" : "PROPERTY", + "lbl" : "capable of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003304", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "contributes to condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity" + } ] + }, + "type" : "PROPERTY", + "lbl" : "capable of part of" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001010", + "type" : "CLASS", + "lbl" : "organism or virus or viroid" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this cell derives from this parent cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this nucleus derives from this parent nucleus (nuclear division)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "derives from" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "involved in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "meta" : { + "definition" : { + "val" : "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Hill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Tanya Berardini" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent cell derives into this cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent nucleus derives into this nucleus (nuclear division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + } ] + }, + "type" : "PROPERTY", + "lbl" : "derives into" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "meta" : { + "definition" : { + "val" : "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Brush" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is model of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "meta" : { + "definition" : { + "val" : "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "negatively regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "meta" : { + "definition" : { + "val" : "inverse of enables", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "enabled by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002450", + "meta" : { + "definition" : { + "val" : "Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly increases activity of", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "activates" + } ] + }, + "type" : "PROPERTY", + "lbl" : "activity directly positively regulates activity of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "meta" : { + "definition" : { + "val" : "Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "activity directly regulates activity of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "enables" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "meta" : { + "definition" : { + "val" : "Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly decreases activity of", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inhibits" + } ] + }, + "type" : "PROPERTY", + "lbl" : "activity directly negatively regulates activity of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + } ] + }, + "type" : "PROPERTY", + "lbl" : "functionally related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "part of structure that is capable of" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + } ] + }, + "type" : "PROPERTY", + "lbl" : "part of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "mereotopologically related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is the transitive form of the develops from relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Terry Meehan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Melissa Haendel" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "develops from" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + } ] + }, + "type" : "PROPERTY", + "lbl" : "developmentally related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "meta" : { + "definition" : { + "val" : "inverse of develops from", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Terry Meehan" + } ] + }, + "type" : "PROPERTY", + "lbl" : "develops into" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "meta" : { + "definition" : { + "val" : "Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influences (material entity to material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally influences" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002447", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + } ] + }, + "type" : "PROPERTY", + "lbl" : "phosphorylates" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "editor note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term editor" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "type" : "PROPERTY", + "lbl" : "has curation status" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has part" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "example of usage" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "curator note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "type" : "PROPERTY", + "lbl" : "editor preferred term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "alternative term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition source" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some environmental process", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + } ] + }, + "type" : "PROPERTY", + "lbl" : "evolutionarily related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://xmlns.com/foaf/0.1/page", + "val" : "https://github.com/oborel/obo-relations/wiki/InteractionRelations" + } ] + }, + "type" : "PROPERTY", + "lbl" : "interaction relation helper property" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "molecular interaction relation helper property" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "phenotype of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002559", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influenced by (material entity to material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally influenced by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://xmlns.com/foaf/0.1/page", + "val" : "https://github.com/oborel/obo-relations/wiki/InteractionRelations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + } ] + }, + "type" : "PROPERTY", + "lbl" : "interacts with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "meta" : { + "definition" : { + "val" : "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "inheres in part of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/MI_0915" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "molecularly binds with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "binds" + } ] + }, + "type" : "PROPERTY", + "lbl" : "molecularly interacts with" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "pending final vetting" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "meta" : { + "definition" : { + "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "material entity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "ready for release" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + }, + "type" : "PROPERTY", + "lbl" : "involved in negative regulation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + } ] + }, + "type" : "PROPERTY", + "lbl" : "involved in or involved in regulation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is active in" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass", + "type" : "CLASS", + "lbl" : "Obsolete Class" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of, negative effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally downstream of or within" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0008150", + "type" : "CLASS", + "lbl" : "biological_process" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "involved in regulation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + }, + "type" : "PROPERTY", + "lbl" : "involved in positive regulation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of, positive effect" + }, { + "id" : "http://purl.obolibrary.org/obo/UPHENO_0001001", + "type" : "CLASS", + "lbl" : "phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of or within, positive effect" + }, { + "id" : "http://purl.obolibrary.org/obo/OGMS_0000031", + "meta" : { + "definition" : { + "val" : "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "disease" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of or within, negative effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "meta" : { + "definition" : { + "val" : "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of or within" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002532", + "meta" : { + "definition" : { + "val" : "Any entity that is ordered in discrete units along a linear axis.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "CLASS", + "lbl" : "sequentially ordered entity" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002533", + "meta" : { + "definition" : { + "val" : "Any individual unit of a collection of like units arranged in a linear order", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence atomic unit" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "immediately causally upstream of" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "meta" : { + "definition" : { + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occurs_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "occurs in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" + } ] + }, + "type" : "PROPERTY", + "lbl" : "occurs in" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "site of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "contains process" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + } ] + }, + "type" : "PROPERTY", + "lbl" : "preceded by" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + } ] + }, + "type" : "PROPERTY", + "lbl" : "precedes" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0003824", + "type" : "CLASS", + "lbl" : "catalytic activity" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + }, + "type" : "PROPERTY", + "lbl" : "starts during" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "type" : "CLASS", + "lbl" : "quality" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " + } ] + }, + "type" : "PROPERTY", + "lbl" : "ends during" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "meta" : { + "definition" : { + "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "process" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "requires discussion" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "type" : "CLASS", + "lbl" : "disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "first order logic expression" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "meta" : { + "definition" : { + "val" : "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "realizable entity" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + } ] + }, + "type" : "PROPERTY", + "lbl" : "immediately precedes" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + } ] + }, + "type" : "PROPERTY", + "lbl" : "acts upstream of, negative effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "meta" : { + "definition" : { + "val" : "This relation groups causal relations between material entities and causal relations between processes", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:30Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "acts upstream of or within, positive effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004031", + "meta" : { + "definition" : { + "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-25T23:20:13Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "enables subfunction" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:14Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "acts upstream of, positive effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:51Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "acts upstream of or within, negative effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "meta" : { + "definition" : { + "val" : "inverse of upstream of", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally downstream of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "meta" : { + "definition" : { + "val" : "inverse of has subsequence", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is subsequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + } ] + }, + "type" : "PROPERTY", + "lbl" : "immediately causally downstream of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "meta" : { + "definition" : { + "val" : "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "overlaps sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002527", + "meta" : { + "definition" : { + "val" : "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "disconnected from" + } ] + }, + "type" : "PROPERTY", + "lbl" : "does not overlap sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "meta" : { + "definition" : { + "val" : "inverse of downstream of sequence of", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is upstream of sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0016301", + "type" : "CLASS", + "lbl" : "kinase activity" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "meta" : { + "definition" : { + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "bounds sequence of" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", + "type" : "PROPERTY", + "lbl" : "in_subset" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002523", + "meta" : { + "definition" : { + "val" : "inverse of bounds sequence of", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is bound by sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "meta" : { + "definition" : { + "val" : "x has subsequence y iff all of the sequence parts of x are sequence parts of y", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contains" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has subsequence" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "meta" : { + "definition" : { + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris 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No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + }, + "type" : "PROPERTY", + "lbl" : "during which starts" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + }, + "type" : "PROPERTY", + "lbl" : "during which ends" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "ends after" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts_at_end_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + }, + "type" : "PROPERTY", + "lbl" : "immediately preceded by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002514", + "meta" : { + "definition" : { + "val" : "A relation that holds between two entities that have the property of being sequences or having sequences. ", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + }, + "type" : "PROPERTY", + "lbl" : "sequentially related to" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", + "type" : "PROPERTY", + "lbl" : "has_broad_synonym" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000002", + "meta" : { + "definition" : { + "val" : "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "meta" : { + "definition" : { + "val" : "An entity that has temporal parts and that happens, unfolds or develops through time.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "occurrent" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", + "type" : "PROPERTY", + "lbl" : "has_exact_synonym" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", + "type" : "PROPERTY", + "lbl" : "database_cross_reference" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002630", + "meta" : { + "definition" : { + "val" : "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + }, + "type" : "PROPERTY", + "lbl" : "directly negatively regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002506", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causal relation between material entities" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causal agent in process" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + }, + "type" : "PROPERTY", + "lbl" : "causal relation between processes" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/BFO_0000169" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "depends on" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "type" : "CLASS", + "lbl" : "function" + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", + "type" : "CLASS", + "lbl" : "environmental system" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002629", + "meta" : { + "definition" : { + "val" : "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + }, + "type" : "PROPERTY", + "lbl" : "directly positively regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000031", + "meta" : { + "definition" : { + "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "generically dependent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. 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"chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002093", "http://purl.obolibrary.org/obo/BFO_0000062" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002597", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002212" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0002202" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002449", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002333" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000062", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002091", "http://purl.obolibrary.org/obo/BFO_0000062" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002162" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002333" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000062", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/BFO_0000062" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002428", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002211" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002162" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/BFO_0000066" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000059", "http://purl.obolibrary.org/obo/RO_0000053" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002598", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002213" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002429", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002213" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0002162" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/RO_0000058" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002314", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000063", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/BFO_0000063" ] + } ] + } ] +} \ No newline at end of file diff --git a/src/ontology/imports/ro_import.obo b/src/ontology/imports/ro_import.obo new file mode 100644 index 0000000..d864e3b --- /dev/null +++ b/src/ontology/imports/ro_import.obo @@ -0,0 +1,1804 @@ +format-version: 1.2 +data-version: geno/releases/2019-09-09/imports/ro_import.owl +subsetdef: ro-eco "" +subsetdef: RO:0002259 "" +ontology: geno/imports/ro_import +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (is model of)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +disjoint_from: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000002 ! part of continuant + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +relationship: BFO:0000050 BFO:0000003 ! part of occurrent + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000004 ! part of independent continuant + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +is_a: BFO:0000003 ! occurrent + +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role + +[Term] +id: BFO:0000017 +name: realizable entity +def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality +relationship: BFO:0000050 BFO:0000017 ! part of realizable entity + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +relationship: BFO:0000050 BFO:0000019 ! part of quality + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant + +[Term] +id: BFO:0000023 +name: role +def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] +is_a: BFO:0000017 ! realizable entity + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] +is_a: BFO:0000002 ! continuant +relationship: BFO:0000050 BFO:0000031 ! part of generically dependent continuant + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant + +[Term] +id: CARO:0000000 +name: anatomical entity +is_a: CARO:0030000 ! biological entity +property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl + +[Term] +id: CARO:0000003 +name: connected anatomical structure +is_a: CARO:0000006 ! material anatomical entity +property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl + +[Term] +id: CARO:0000006 +name: material anatomical entity +is_a: BFO:0000040 ! material entity +is_a: CARO:0000000 ! anatomical entity +property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl + +[Term] +id: CARO:0001010 +name: organism or virus or viroid +is_a: BFO:0000040 ! material entity + +[Term] +id: CARO:0030000 +name: biological entity +is_a: BFO:0000004 ! independent continuant + +[Term] +id: CL:0000000 +name: cell +is_a: CARO:0000003 ! connected anatomical structure +property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl + +[Term] +id: ENVO:01000254 +name: environmental system +is_a: RO:0002577 ! system + +[Term] +id: GO:0003674 +name: molecular_function +is_a: BFO:0000015 ! process +property_value: IAO:0000589 "molecular process" xsd:string + +[Term] +id: GO:0003824 +name: catalytic activity +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0008150 +name: biological_process +is_a: BFO:0000015 ! process + +[Term] +id: GO:0016301 +name: kinase activity +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups + +[Term] +id: GO:0016740 +name: transferase activity +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +is_a: GO:0016740 ! transferase activity + +[Term] +id: OGMS:0000031 +name: disease +def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [] +is_a: BFO:0000016 ! disposition + +[Term] +id: ObsoleteClass +name: Obsolete Class + +[Term] +id: PATO:0000001 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000589 "quality (PATO)" xsd:string + +[Term] +id: RO:0002532 +name: sequentially ordered entity +def: "Any entity that is ordered in discrete units along a linear axis." [] +relationship: RO:0002524 RO:0002533 ! has subsequence sequence atomic unit +property_value: IAO:0000117 "Chris Mungall" xsd:string + +[Term] +id: RO:0002533 +name: sequence atomic unit +def: "Any individual unit of a collection of like units arranged in a linear order" [] +is_a: RO:0002532 ! sequentially ordered entity +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." xsd:string + +[Term] +id: RO:0002577 +name: system +def: "A material entity consisting of multiple components that are causally integrated." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string + +[Term] +id: UPHENO:0001001 +name: phenotype +is_a: PATO:0000001 ! quality + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: BFO:0000062 +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: BFO:0000050 BFO:0000062 +holds_over_chain: RO:0002091 BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + +[Typedef] +id: BFO:0000063 +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: BFO:0000050 BFO:0000063 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: BFO:0000066 +name: occurs in +def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "occurs in" xsd:string +property_value: IAO:0000118 "occurs_in" xsd:string +property_value: IAO:0000118 "unfolds in" xsd:string +property_value: IAO:0000118 "unfolds_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000050 BFO:0000066 +inverse_of: BFO:0000067 ! contains process +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: RO:0002314 ! inheres in part of +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: BFO:0000051 RO:0000057 + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: RO:0000053 ! bearer of +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +def: "inverse of has disposition" [] +subset: RO:0002259 +is_a: RO:0000052 ! inheres in + +[Typedef] +id: RO:0001000 +name: derives from +def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +subset: ro-eco +property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string +property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string +property_value: IAO:0000118 "derives_from" xsd:string +property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +inverse_of: RO:0001001 ! derives into + +[Typedef] +id: RO:0001001 +name: derives into +def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +subset: ro-eco +property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string +property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string +property_value: IAO:0000118 "derives_into" xsd:string + +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + +[Typedef] +id: RO:0002019 +name: has ligand +def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] +domain: GO:0004872 +is_a: RO:0002233 ! has input +created_by: dos +creation_date: 2017-07-19T17:30:36Z + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +is_a: RO:0002334 ! regulated by +inverse_of: RO:0002578 ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002630 ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002629 ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002025 +name: has effector activity +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. +is_functional: true +is_a: RO:0002017 ! has component activity +is_a: RO:0002211 ! regulates +created_by: dos +creation_date: 2017-09-22T14:14:36Z + +[Typedef] +id: RO:0002084 +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: RO:0002222 ! temporally related to +inverse_of: RO:0002093 ! ends during + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +holds_over_chain: RO:0002093 BFO:0000062 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002087 +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes + +[Typedef] +id: RO:0002088 +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: RO:0002222 ! temporally related to +inverse_of: RO:0002091 ! starts during + +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: RO:0002575 BFO:0000063 +is_a: BFO:0000063 ! precedes + +[Typedef] +id: RO:0002091 +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002093 +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: RO:0001900 RO:0001901 +holds_over_chain: BFO:0000050 BFO:0000050 +holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 RO:0002131 +is_a: RO:0002323 ! mereotopologically related to +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Jennifer Deegan" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +range: CARO:0001010 ! organism or virus or viroid +holds_over_chain: BFO:0000050 RO:0002162 +holds_over_chain: BFO:0000051 RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002215 RO:0002162 +holds_over_chain: RO:0002217 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002180 +name: has component +def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002200 +name: has phenotype +def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +range: UPHENO:0001001 ! phenotype +inverse_of: RO:0002201 ! phenotype of + +[Typedef] +id: RO:0002201 +name: phenotype of +def: "inverse of has phenotype" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_functional: true + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 "Terry Meehan" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 "Terry Meehan" xsd:string +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + +[Typedef] +id: RO:0002211 +name: regulates +def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Hill" xsd:string +property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000119 "GO" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string +property_value: IAO:0000589 "regulates (processual)" xsd:string +property_value: IAO:0000600 "false" xsd:boolean +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: RO:0002578 RO:0002578 +is_transitive: true +is_a: RO:0002411 ! causally upstream of +inverse_of: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002212 +name: negatively regulates +def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +property_value: RO:0004050 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect +inverse_of: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002213 +name: positively regulates +def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +property_value: RO:0004049 RO:0002211 +holds_over_chain: RO:0002212 RO:0002212 +is_transitive: true +is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect +inverse_of: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002215 +name: capable of +def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] +subset: ro-eco +property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string +property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function realized in" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 +property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of +expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" +holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process +expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] + +[Typedef] +id: RO:0002217 +name: actively participates in +def: "x actively participates in y if and only if x participates in y and x realizes some active role" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "agent in" xsd:string +is_a: RO:0000056 ! participates in +inverse_of: RO:0002218 ! obsolete has active participant + +[Typedef] +id: RO:0002218 +name: obsolete has active participant +def: "x has participant y if and only if x realizes some active role that inheres in y" [] +subset: ro-eco +property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has agent" xsd:string +is_a: RO:0000057 ! has participant +is_obsolete: true + +[Typedef] +id: RO:0002222 +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002233 +name: has input +def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "consumes" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity +is_a: RO:0000057 ! has participant +inverse_of: RO:0002352 ! input of + +[Typedef] +id: RO:0002234 +name: has output +def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "produces" xsd:string +is_a: RO:0000057 ! has participant +inverse_of: RO:0002353 ! output of + +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 ! anatomical entity +range: CARO:0000000 ! anatomical entity +holds_over_chain: BFO:0000051 RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + +[Typedef] +id: RO:0002255 +name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +holds_over_chain: RO:0002203 BFO:0000050 +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002258 +name: developmentally preceded by +def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] +comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "false" xsd:boolean +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002324 ! developmentally related to +inverse_of: RO:0002286 ! developmentally succeeded by + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 RO:0002411 +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 RO:0002418 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002286 +name: developmentally succeeded by +def: "Inverse of developmentally preceded by" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +property_value: RO:0004049 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +property_value: RO:0004050 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: RO:0002314 +name: inheres in part of +def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." [] +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso "defining-property-chains-involving-reflexivity" +holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002502 ! depends on +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002320 +name: evolutionarily related to +def: "A relationship that holds via some environmental process" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string + +[Typedef] +id: RO:0002323 +name: mereotopologically related to +def: "A mereological relationship or a topological relationship" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0002324 +name: developmentally related to +def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string + +[Typedef] +id: RO:0002327 +name: enables +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "catalyzes" xsd:string +property_value: IAO:0000118 "executes" xsd:string +property_value: IAO:0000118 "has" xsd:string +property_value: IAO:0000118 "is catalyzing" xsd:string +property_value: IAO:0000118 "is executing" xsd:string +property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string +is_a: RO:0002215 ! capable of +inverse_of: RO:0002333 ! enabled by +transitive_over: BFO:0000051 ! has part +transitive_over: RO:0002017 ! has component activity + +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "false" xsd:boolean +holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: seeAlso Involved:in +holds_over_chain: RO:0002327 BFO:0000050 +is_a: RO:0002217 ! actively participates in +is_a: RO:0002431 ! involved in or involved in regulation of +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000057 ! has participant +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002334 +name: regulated by +def: "inverse of regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "regulated by (processual)" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002335 +name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002336 +name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000050 ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002353 +name: output of +def: "inverse of has output" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002354 +name: formed as result of +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002353 ! output of + +[Typedef] +id: RO:0002384 +name: has developmental potential involving +def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 ! anatomical entity +range: CARO:0000000 ! anatomical entity +is_a: RO:0002324 ! developmentally related to + +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002388 +name: has potential to directly develop into +def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002387 ! has potential to develop into + +[Typedef] +id: RO:0002404 +name: causally downstream of +def: "inverse of upstream of" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: BFO:0000062 ! preceded by +is_a: RO:0002427 ! causally downstream of or within +inverse_of: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002405 +name: immediately causally downstream of +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002087 ! immediately preceded by +is_a: RO:0002404 ! causally downstream of +inverse_of: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002410 +name: causally related to +def: "This relation groups causal relations between material entities and causal relations between processes" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string + +[Typedef] +id: RO:0002411 +name: causally upstream of +def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_transitive: true +is_a: BFO:0000063 ! precedes +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002412 +name: immediately causally upstream of +def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: RO:0002575 RO:0002411 +is_a: RO:0002090 ! immediately precedes +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002418 +name: causally upstream of or within +def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +synonym: "affects" RELATED [] +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "influences (processual)" xsd:string +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002427 +name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +holds_over_chain: RO:0002327 RO:0002211 +holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 RO:0002213 +holds_over_chain: RO:0002331 RO:0002213 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 RO:0002212 +holds_over_chain: RO:0002331 RO:0002212 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +name: involved in or involved in regulation of +def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002432 +name: is active in +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +synonym: "enables activity in" EXACT [] +property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "executes activity in" xsd:string +holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002131 ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002434 +name: interacts with +def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] +subset: ro-eco +synonym: "in pairwise interaction with" EXACT [] +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: seeAlso ECO:0000353 +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002447 +name: phosphorylates +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002448 +name: activity directly regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002449 +name: activity directly negatively regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "inhibits" xsd:string +is_a: RO:0002448 ! activity directly regulates activity of + +[Typedef] +id: RO:0002450 +name: activity directly positively regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "activates" xsd:string +is_a: RO:0002448 ! activity directly regulates activity of + +[Typedef] +id: RO:0002464 +name: helper property (not for use in curation) +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002479 +name: has part that occurs in +def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] +subset: ro-eco +property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} + +[Typedef] +id: RO:0002481 +name: is kinase activity +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002564 ! molecular interaction relation helper property + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: RO:0002608 ! process has causal agent + +[Typedef] +id: RO:0002501 +name: causal relation between processes +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002502 +name: depends on +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: seeAlso BFO:0000169 + +[Typedef] +id: RO:0002506 +name: causal relation between material entities +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002514 +name: sequentially related to +def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string +domain: RO:0002532 ! sequentially ordered entity +range: RO:0002532 ! sequentially ordered entity + +[Typedef] +id: RO:0002522 +name: bounds sequence of +def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_transitive: true +is_a: RO:0002514 ! sequentially related to +inverse_of: RO:0002523 ! is bound by sequence of + +[Typedef] +id: RO:0002523 +name: is bound by sequence of +def: "inverse of bounds sequence of" [] +subset: RO:0002259 +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_transitive: true +is_a: RO:0002514 ! sequentially related to + +[Typedef] +id: RO:0002524 +name: has subsequence +def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "contains" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +is_transitive: true +is_a: BFO:0000051 ! has part +is_a: RO:0002522 ! bounds sequence of +is_a: RO:0002526 ! overlaps sequence of +inverse_of: RO:0002525 ! is subsequence of + +[Typedef] +id: RO:0002525 +name: is subsequence of +def: "inverse of has subsequence" [] +subset: RO:0002259 +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "contained by" xsd:string +is_transitive: true +is_a: BFO:0000050 ! part of +is_a: RO:0002523 ! is bound by sequence of +is_a: RO:0002526 ! overlaps sequence of + +[Typedef] +id: RO:0002526 +name: overlaps sequence of +def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +holds_over_chain: RO:0002524 RO:0002525 +is_symmetric: true +is_a: RO:0002131 ! overlaps +is_a: RO:0002514 ! sequentially related to + +[Typedef] +id: RO:0002527 +name: does not overlap sequence of +def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "disconnected from" xsd:string +is_symmetric: true +is_a: RO:0002514 ! sequentially related to + +[Typedef] +id: RO:0002528 +name: is upstream of sequence of +def: "inverse of downstream of sequence of" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_transitive: true +is_a: RO:0002527 ! does not overlap sequence of + +[Typedef] +id: RO:0002529 +name: is downstream of sequence of +def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_transitive: true +is_a: RO:0002527 ! does not overlap sequence of +inverse_of: RO:0002529 ! is downstream of sequence of + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (material entity to material entity)" xsd:string +is_a: RO:0002506 ! causal relation between material entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002563 +name: interaction relation helper property +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 +is_a: RO:0002464 ! helper property (not for use in curation) + +[Typedef] +id: RO:0002564 +name: molecular interaction relation helper property +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002563 ! interaction relation helper property + +[Typedef] +id: RO:0002566 +name: causally influences +def: "Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (material entity to material entity)" xsd:string +is_a: RO:0002506 ! causal relation between material entities + +[Typedef] +id: RO:0002578 +name: directly regulates +def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: RO:0002575 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002584 +name: has part structure that is capable of +def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +holds_over_chain: BFO:0000051 RO:0002215 +is_a: RO:0002328 ! functionally related to +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +name: causal relation between material entity and a process +def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002596 +name: capable of regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002211 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +name: capable of negatively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002212 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +name: capable of positively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002213 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002608 +name: process has causal agent +def: "Inverse of 'causal agent in process'" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002610 +name: correlated with +def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] +property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string + +[Typedef] +id: RO:0002615 +name: has model +def: "Inverse of is-model-of" [] +inverse_of: RO:0003301 ! is model of + +[Typedef] +id: RO:0002629 +name: directly positively regulates +def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string +property_value: RO:0004049 RO:0002578 +is_a: RO:0002213 ! positively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0002630 +name: directly negatively regulates +def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string +property_value: RO:0004050 RO:0002578 +is_a: RO:0002212 ! negatively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0003000 +name: produces +def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] +comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Melissa Haendel" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +inverse_of: RO:0003001 ! produced by + +[Typedef] +id: RO:0003001 +name: produced by +def: "a produced_by b iff some process that occurs_in b has_output a." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Melissa Haendel" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity + +[Typedef] +id: RO:0003301 +name: is model of +def: "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] +comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. +property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" xsd:string +property_value: IAO:0000117 "Matthew Brush" xsd:string +is_asymmetric: true + +[Typedef] +id: RO:0003302 +name: causes or contributes to condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. +property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." xsd:string +property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0003303 +name: causes condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003304 +name: contributes to condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003305 +name: contributes to severity of condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." [] +property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003306 +name: contributes to frequency of condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." [] +property_value: IAO:0000118 "contributes to penetrance of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003307 +name: ameliorates condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. +property_value: IAO:0000118 "is preventative for condition" xsd:string +is_a: RO:0003305 ! contributes to severity of condition + +[Typedef] +id: RO:0003308 +name: correlated with condition +def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] +is_a: RO:0002610 ! correlated with + +[Typedef] +id: RO:0004031 +name: enables subfunction +def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] +holds_over_chain: RO:0002327 BFO:0000051 +is_a: RO:0002328 ! functionally related to +created_by: cjm +creation_date: 2018-01-25T23:20:13Z + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 RO:0002304 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: cjm +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 RO:0002305 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: cjm +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: RO:0004050 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: RO:0004049 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:19Z + +[Typedef] +id: RO:0010001 +name: generically depends on +def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] +synonym: "g-depends on" EXACT [] +property_value: IAO:0000112 "Genetic information generically depend on molecules of DNA." xsd:string +property_value: IAO:0000112 "The novel *War and Peace* generically depends on this copy of the novel." xsd:string +property_value: IAO:0000112 "The pattern shared by chess boards generically depends on any chess board." xsd:string +property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string +property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0000052 RO:0000058 +inverse_of: RO:0010002 ! is carrier of + +[Typedef] +id: RO:0010002 +name: is carrier of +def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] +property_value: IAO:0000112 "Molecules of DNA are carriers of genetic information." xsd:string +property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string +property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000031 ! generically dependent continuant +holds_over_chain: RO:0000059 RO:0000053 + +[Typedef] +id: results_in_developmental_progression_of +name: results in developmental progression of +def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: seeAlso Ontology:extensions +domain: GO:0008150 ! biological_process +range: CARO:0000003 ! connected anatomical structure +is_a: RO:0002324 ! developmentally related to + +[Typedef] +id: results_in_formation_of +name: results in formation of +property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string +property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0002234 ! has output +inverse_of: RO:0002354 ! formed as result of + diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 263fa34..831058a 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -1,14 +1,4539 @@ - - + xmlns:swrl="http://www.w3.org/2003/11/swrl#" + xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" + xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" + xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + + + + + + + + + + + + + + editor preferred term + + + + + + + + + example of usage + + + + + + + + has curation status + + + + + + + + + definition + definition + + + + + + + + + editor note + + + + + + + + + term editor + + + + + + + + + alternative term + + + + + + + + + definition source + + + + + + + + + + + + + + + curator note + + + + + + + + + imported from + + + + + + + + expand expression to + + + + + + + + expand assertion to + + + + + + + + An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + first order logic expression + + + + + + + + + OBO foundry unique label + + + + + + + + elucidation + + + + + + + + + + + + + + + + + + + + + + + + + + + + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + is a defining property chain axiom + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subset_property + + + + + + + + + + + + + + + + + + + + has_broad_synonym + + + + + + + + database_cross_reference + + + + + + + + has_exact_synonym + + + + + + + + has_related_synonym + + + + + + + + in_subset + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + + + + + + + + part of + + + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + has part + + + + + + + + + + + + + + + + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + + preceded by + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes + + + + + + + + + + + + + + + + + + + occurs in + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + occurs_in + unfolds in + unfolds_in + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs in + + + + + + + + site of + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + role of + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + disposition of + + + + + + + + + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + + derives from + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + + derives into + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. + dos + 2017-07-19T17:30:36Z + has ligand + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + directly negatively regulated by + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + directly positively regulated by + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + David Osumi-Sutherland + o + overlaps + + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + overlaps + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + Chris Mungall + Jennifer Deegan + + + + Connects a biological entity to its taxon of origin. + in taxon + + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + has component + + + + + + + + + + + + + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + Chris Mungall + + has phenotype + + + + + + + + + + + inverse of has phenotype + Chris Mungall + + + phenotype of + + + + + + + + + + + + + + x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + Chris Mungall + David Osumi-Sutherland + Melissa Haendel + Terry Meehan + This is the transitive form of the develops from relation + develops from + + + + + + + + + + + + + inverse of develops from + Chris Mungall + David Osumi-Sutherland + Terry Meehan + + develops into + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall + David Hill + Tanya Berardini + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + regulates + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + negatively regulates (process to process) + + negatively regulates + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + positively regulates (process to process) + + positively regulates + + + + + + + + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + Chris Mungall + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + + capable of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + Chris Mungall + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + capable of part of + + + + + + + + + + true + + + + + + + + + + x actively participates in y if and only if x participates in y and x realizes some active role + Chris Mungall + agent in + actively participates in + + + + + + + + + 'heart development' has active participant some Shh protein + + x has participant y if and only if x realizes some active role that inheres in y + This may be obsoleted and replaced by the original 'has agent' relation + Chris Mungall + has agent + + obsolete has active participant + true + + + + + + + + + + + Chris Mungall + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + Chris Mungall + consumes + + has input + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + Chris Mungall + produces + + has output + + + + + + + + + + + + + + + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] + + x has developmental contribution from y iff x has some part z such that z develops from y + Chris Mungall + has developmental contribution from + + + + + + + + + + + + + + + inverse of has developmental contribution from + Chris Mungall + + developmentally contributes to + + + + + + + + + + + + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + false + Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one + This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from + developmentally preceded by + + + + + + + + + + + + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of + + + + + + + + + + + + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + acts upstream of or within + + + + + + + + + + + Inverse of developmentally preceded by + Chris Mungall + developmentally succeeded by + + + + + + + + + + + + p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). + This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. + Chris Mungall + results_in_developmental_progression_of + results in developmental progression of + + + + + + + + + + + + an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. + every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + + Chris Mungall + GOC:mtg_berkeley_2013 + results_in_formation_of + results in formation of + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + + + + + + + + + + + + + + q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of inheres in part of + Chris Mungall + + + inheres in part of + + + + + + + + + + true + + + + + + + + A relationship that holds via some environmental process + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + evolutionarily related to + + + + + + + + A mereological relationship or a topological relationship + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + mereotopologically related to + + + + + + + + A relationship that holds between entities participating in some developmental process (GO:0032502) + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development + developmentally related to + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + Chris Mungall + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + Chris Mungall + false + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + Chris Mungall + actively involved in + enables part of + involved in + + + + + + + + + + + inverse of enables + Chris Mungall + enabled by + + + + + + + + + + + + inverse of regulates + Chris Mungall + regulated by (processual) + + regulated by + + + + + + + + + inverse of negatively regulates + Chris Mungall + + negatively regulated by + + + + + + + + + inverse of positively regulates + Chris Mungall + + positively regulated by + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + inverse of has input + Chris Mungall + + + input of + + + + + + + + + + inverse of has output + Chris Mungall + + + output of + + + + + + + + + Chris Mungall + formed as result of + + + + + + + + + + + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). + Chris Mungall + has developmental potential involving + + + + + + + + + + x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + Chris Mungall + has potential to developmentally contribute to + + + + + + + + + + x has the potential to develop into y iff x develops into y or if x is capable of developing into y + Chris Mungall + has potential to develop into + + + + + + + + + + x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + Chris Mungall + has potential to directly develop into + + + + + + + + + + + + inverse of upstream of + Chris Mungall + causally downstream of + + + + + + + + + + + + Chris Mungall + immediately causally downstream of + + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types. + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causally related to + + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + Chris Mungall + causally upstream of + + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + Chris Mungall + + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) + affects + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + Chris Mungall + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + Chris Mungall + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + Chris Mungall + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + Chris Mungall + + involved in negative regulation of + + + + + + + + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union + Chris Mungall + involved in or reguates + involved in or involved in regulation of + + + + + + + + + + + + + + A protein that enables activity in a cytosol. + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + Chris Mungall + executes activity in + enables activity in + + is active in + + + + + + + + + true + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + GOC:cjm + GOC:dos + + + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + Considering relabeling as 'pairwise interacts with' + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + Chris Mungall + binds + molecularly binds with + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + Axiomatization to GO to be added later + Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + phosphorylates + + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + Chris Mungall + molecularly controls + activity directly regulates activity of + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + Chris Mungall + inhibits + molecularly decreases activity of + activity directly negatively regulates activity of + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + Chris Mungall + activates + molecularly increases activity of + activity directly positively regulates activity of + + + + + + + + Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + helper property (not for use in curation) + + + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + Chris Mungall + + has part that occurs in + + + + + + + + + true + + + + + + + + + Chris Mungall + is kinase activity + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + causal agent in process + + + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + + + + + + + + Chris Mungall + depends on + + + + + + + + + + + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between material entities + + + + + + + + + + A relation that holds between two entities that have the property of being sequences or having sequences. + Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. + The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. + + sequentially related to + + + + + + + + + + + The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) + x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + Chris Mungall + + bounds sequence of + + + + + + + + + + inverse of bounds sequence of + Chris Mungall + + + is bound by sequence of + + + + + + + + + + + + + x has subsequence y iff all of the sequence parts of x are sequence parts of y + Chris Mungall + contains + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has subsequence + + + + + + + + + + + + inverse of has subsequence + Chris Mungall + contained by + + + is subsequence of + + + + + + + + + + + + + + + x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. + Chris Mungall + + overlaps sequence of + + + + + + + + + + x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + Chris Mungall + disconnected from + + does not overlap sequence of + + + + + + + + + + inverse of downstream of sequence of + Chris Mungall + + is upstream of sequence of + + + + + + + + + + + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + Chris Mungall + + is downstream of sequence of + + + + + + + + + + Chris Mungall + + causally influenced by (material entity to material entity) + causally influenced by + + + + + + + + + Chris Mungall + interaction relation helper property + + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + Chris Mungall + molecular interaction relation helper property + + + + + + + + + + + + + + + + + + + Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b + Chris Mungall + + causally influences (material entity to material entity) + causally influences + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + Chris Mungall + + directly regulates (processual) + + directly regulates + + + + + + + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + Chris Mungall + has part structure that is capable of + + + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + Chris Mungall + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + capable of negatively regulating + + + + + + + + + + + + + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + + process has causal agent + + + + + + + + A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + Groups both positive and negative correlation + correlated with + + + + + + + + + Inverse of is-model-of + has model + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + + directly positively regulates (process to process) + + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + directly negatively regulates (process to process) + + directly negatively regulates + + + + + + + + + + + + + + + + + + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + Melissa Haendel + + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + produces + + + + + + + + + + + a produced_by b iff some process that occurs_in b has_output a. + Melissa Haendel + + produced by + + + + + + + + + + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + Matthew Brush + The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + is model of + + + + + + + + + The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. + +An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + causes or contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. + causes condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. + contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. + contributes to expressivity of condition + contributes to severity of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. + contributes to penetrance of condition + contributes to frequency of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. + is preventative for condition + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + ameliorates condition + + + + + + + + + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + correlated with condition + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + enables subfunction + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:30Z + acts upstream of or within, positive effect + + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:51Z + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + cjm + 2018-01-26T23:53:14Z + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + cjm + 2018-01-26T23:53:22Z + acts upstream of, negative effect + + + + + + + + + + + cjm + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + + + + + + + + + + cjm + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + + + + + + + + + + + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + + + + + + + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + + disposition + + + + + + + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + + + + + + + + + + + + + + + quality + + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + + + + + + + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + generically dependent continuant + + + + + + + + + function + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + + anatomical entity + + + + + + + + + + connected anatomical structure + + + + + + + + + + + material anatomical entity + + + + + + + + + organism or virus or viroid + + + + + + + + + biological entity + + + + + + + + + + cell + + + + + + + + + environmental system + + + + + + + + + molecular process + molecular_function + + + + + + + + + catalytic activity + + + + + + + + + + + + + + + biological_process + + + + + + + + + + + + true + + + kinase activity + + + + + + + + + transferase activity + + + + + + + + + transferase activity, transferring phosphorus-containing groups + + + + + + + + + + + + + + + A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. + disease + + + + + + + + + quality (PATO) + quality + + + + + + + + + + + + + + Any entity that is ordered in discrete units along a linear axis. + Chris Mungall + sequentially ordered entity + + + + + + + + + Any individual unit of a collection of like units arranged in a linear order + Chris Mungall + An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. + sequence atomic unit + + + + + + + + + A material entity consisting of multiple components that are causally integrated. + May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 + Chris Mungall + http://www.jbiomedsem.com/content/4/1/43 + system + + + + + + + + + phenotype + + + + + + + + Obsolete Class + + + + + + + + + + + + + + ready for release + + + + + + + + + pending final vetting + + + + + + + + + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From ligand activity to has_ligand + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From has_ligand to ligand activity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - diff --git a/src/ontology/imports/so_import.json b/src/ontology/imports/so_import.json new file mode 100644 index 0000000..dc50d99 --- /dev/null +++ b/src/ontology/imports/so_import.json @@ -0,0 +1,3780 @@ +{ + "graphs" : [ { + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/SO_0000165", + "meta" : { + "definition" : { + "val" : "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.", + "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], + "xrefs" : [ { + "val" : "http://en.wikipedia.org/wiki/Enhancer_(genetics)" + } ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "INSDC_feature:regulatory", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "INSDC_qualifier:enhancer", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "sequence" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO." + } ] + }, + "type" : "CLASS", + "lbl" : "enhancer" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000016", + "meta" : { + "definition" : { + "val" : "A transition of a guanine to an adenine.", + "xrefs" : [ "SO:ke" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "G to A transition", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "G_to_A_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000285", + "meta" : { + "definition" : { + "val" : "A gene that is foreign.", + "xrefs" : [ "SO:xp" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "foreign gene", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "foreign_gene" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000015", + "meta" : { + "definition" : { + "val" : "A transition of an adenine to a guanine.", + "xrefs" : [ "SO:ke" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "A to G transition", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "A_to_G_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000442", + "meta" : { + "definition" : { + "val" : "A double stranded oligonucleotide.", + "xrefs" : [ "SO:ke" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "ds oligo", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "double stranded oligonucleotide", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "ds-oligonucleotide", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "ds_oligo" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000167", + "meta" : { + "definition" : { + "val" : "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.", + "xrefs" : [ "SO:regcreative" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], + "xrefs" : [ { + "val" : "http://en.wikipedia.org/wiki/Promoter" + } ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "INSDC_qualifier:promoter", + "xrefs" : [ ] + }, { + "pred" : "hasBroadSynonym", + "val" : "INSDC_feature:regulatory", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "promoter sequence", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "promoter" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001410", + "meta" : { + "definition" : { + "val" : "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.", + "xrefs" : [ "SO:cb" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "experimental_output_artefact", + "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "experimental output artefact", + "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "analysis feature", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "experimental_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000014", + "meta" : { + "definition" : { + "val" : "A substitution of a purine, A or G, for another purine.", + "xrefs" : [ "SO:ke" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "purine transition", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : 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"engineered_foreign_gene" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000018", + "meta" : { + "definition" : { + "val" : "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.", + "xrefs" : [ "SO:ke" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "pyrimidine to purine transversion", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "pyrimidine_to_purine_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000017", + "meta" : { + "definition" : { + "val" : "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.", + "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ] + }, + "xrefs" : [ { + "val" : "http://en.wikipedia.org/wiki/Transversion" + } ], + "basicPropertyValues" : [ { + "pred" : 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A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke] +subset: SOFA +synonym: "sequence" EXACT [] +is_a: SO:0000110 ! sequence_feature + +[Term] +id: SO:0000002 +name: sequence_secondary_structure +namespace: sequence +def: "A folded sequence." [SO:ke] +synonym: "INSDC_feature:misc_structure" EXACT [] +synonym: "sequence secondary structure" EXACT [] +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000005 +name: satellite_DNA +namespace: sequence +def: "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +subset: SOFA +synonym: "INSDC_feature:repeat_region" BROAD [] +synonym: "INSDC_qualifier:satellite" EXACT [] +synonym: "satellite DNA" EXACT [] +xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki" +is_a: SO:0000705 ! tandem_repeat + +[Term] +id: SO:0000034 +name: morpholino_oligo +namespace: sequence +def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/] +synonym: "morphant" BROAD [] +synonym: "morpholino" EXACT [] +synonym: "morpholino oligo" EXACT [] +is_a: SO:0001247 ! synthetic_oligo +intersection_of: SO:0001247 ! synthetic_oligo +intersection_of: has_quality SO:0001183 ! morpholino_backbone +relationship: has_quality SO:0001183 ! morpholino_backbone + +[Term] +id: SO:0000105 +name: chromosome_arm +namespace: sequence +def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152] +synonym: "chromosome arm" EXACT [] +is_a: SO:0000830 ! chromosome_part + +[Term] +id: SO:0000110 +name: sequence_feature +namespace: sequence +def: "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke] +subset: SOFA +synonym: "INSDC_feature:misc_feature" EXACT [] +synonym: "INSDC_note:other" EXACT [] +synonym: "INSDC_note:sequence_feature" EXACT [] +synonym: "located sequence feature" RELATED [] +synonym: "located_sequence_feature" EXACT [] +synonym: "sequence feature" EXACT [] +disjoint_from: SO:0000400 ! sequence_attribute + +[Term] +id: SO:0000143 +name: assembly_component +namespace: sequence +def: "A region of known length which may be used to manufacture a longer region." [SO:ke] +subset: SOFA +synonym: "assembly component" EXACT [] +is_a: SO:0001410 ! experimental_feature + +[Term] +id: SO:0000148 +name: supercontig +namespace: sequence +def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls] +subset: SOFA +synonym: "scaffold" RELATED [] +is_a: SO:0001876 ! partial_genomic_sequence_assembly +relationship: part_of SO:0000719 ! ultracontig + +[Term] +id: SO:0000149 +name: contig +namespace: sequence +def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Contig "wiki" +is_a: SO:0000143 ! assembly_component +is_a: SO:0000353 ! sequence_assembly +relationship: part_of SO:0000148 ! supercontig + +[Term] +id: SO:0000155 +name: plasmid +namespace: sequence +def: "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +synonym: "plasmid sequence" EXACT [] +is_a: SO:0001235 ! replicon + +[Term] +id: SO:0000159 +name: deletion +namespace: sequence +alt_id: SO:1000033 +def: "The point at which one or more contiguous nucleotides were excised." [SO:ke] +subset: SOFA +synonym: "deleted_sequence" EXACT [] +synonym: "nucleotide deletion" EXACT [] +synonym: "nucleotide_deletion" EXACT [] +xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki" +xref: loinc:LA6692-3 "Deletion" +is_a: SO:0001059 ! sequence_alteration +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000165 +name: enhancer +namespace: sequence +def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] +comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO. +subset: SOFA +synonym: "INSDC_feature:regulatory" BROAD [] +synonym: "INSDC_qualifier:enhancer" EXACT [] +xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki" +is_a: SO:0000727 ! CRM + +[Term] +id: SO:0000167 +name: promoter +namespace: sequence +def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. +subset: SOFA +synonym: "INSDC_feature:regulatory" BROAD [] +synonym: "INSDC_qualifier:promoter" EXACT [] +synonym: "promoter sequence" EXACT [] +xref: http://en.wikipedia.org/wiki/Promoter "wiki" +is_a: SO:0001055 ! transcriptional_cis_regulatory_region + +[Term] +id: SO:0000199 +name: translocation +namespace: sequence +def: "A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions." [NCBI:th, SO:ke] +subset: DBVAR +synonym: "transchr" RELATED [http://www.ncbi.nlm.nih.gov/dbvar/] +synonym: "translocated sequence" EXACT [] +is_a: SO:0001785 ! structural_alteration + +[Term] +id: SO:0000207 +name: simple_sequence_length_variation +namespace: sequence +def: "SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ." [SO:ke] +synonym: "simple sequence length polymorphism" RELATED [] +synonym: "simple sequence length variation" EXACT [] +synonym: "SSLP" RELATED [] +xref: http://en.wikipedia.org/wiki/Simple_sequence_length_polymorphism "WIKI" +is_a: SO:0000248 ! sequence_length_alteration + +[Term] +id: SO:0000235 +name: TF_binding_site +namespace: sequence +def: "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke] +subset: SOFA +synonym: "TF binding site" EXACT [] +synonym: "transcription factor binding site" EXACT [] +is_a: SO:0001654 ! nucleotide_to_protein_binding_site +is_a: SO:0001679 ! transcription_regulatory_region + +[Term] +id: SO:0000240 +name: chromosome_variation +namespace: sequence +synonym: "chromosome variation" EXACT [] +is_a: SO:0001507 ! variant_collection +relationship: part_of SO:0001524 ! chromosomally_aberrant_genome + +[Term] +id: SO:0000248 +name: sequence_length_alteration +namespace: sequence +def: "A kind of kind of sequence alteration where the copies of a region present varies across a population." [SO:ke] +synonym: "sequence length alteration" EXACT [] +is_a: SO:0001059 ! sequence_alteration + +[Term] +id: SO:0000280 +name: engineered_gene +namespace: sequence +def: "A gene that is engineered." [SO:xp] +synonym: "engineered gene" EXACT [] +is_a: SO:0000704 ! gene +is_a: SO:0000804 ! engineered_region +intersection_of: SO:0000704 ! gene +intersection_of: has_quality SO:0000783 ! engineered +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000281 +name: engineered_foreign_gene +namespace: sequence +def: "A gene that is engineered and foreign." [SO:xp] +synonym: "engineered foreign gene" EXACT [] +is_a: SO:0000280 ! engineered_gene +is_a: SO:0000285 ! foreign_gene +is_a: SO:0000805 ! engineered_foreign_region +intersection_of: SO:0000280 ! engineered_gene +intersection_of: has_quality SO:0000783 ! engineered +intersection_of: has_quality SO:0000784 ! foreign +relationship: has_quality SO:0000783 ! engineered +relationship: has_quality SO:0000784 ! foreign + +[Term] +id: SO:0000285 +name: foreign_gene +namespace: sequence +def: "A gene that is foreign." [SO:xp] +synonym: "foreign gene" EXACT [] +is_a: SO:0000704 ! gene +intersection_of: SO:0000704 ! gene +intersection_of: has_quality SO:0000784 ! foreign +relationship: has_quality SO:0000784 ! foreign + +[Term] +id: SO:0000289 +name: microsatellite +namespace: sequence +def: "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th] +subset: SOFA +synonym: "INSDC_feature:repeat_region" BROAD [] +synonym: "INSDC_qualifier:microsatellite" EXACT [] +synonym: "microsatellite locus" EXACT [] +synonym: "microsatellite marker" EXACT [] +synonym: "short tandem repeat" EXACT [] +synonym: "STR" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/] +xref: http://en.wikipedia.org/wiki/Microsatellite "wiki" +is_a: SO:0000005 ! satellite_DNA + +[Term] +id: SO:0000293 +name: engineered_foreign_repetitive_element +namespace: sequence +def: "A repetitive element that is engineered and foreign." [SO:xp] +synonym: "engineered foreign repetitive element" EXACT [] +is_a: SO:0000657 ! repeat_region +is_a: SO:0000805 ! engineered_foreign_region +intersection_of: SO:0000657 ! repeat_region +intersection_of: has_quality SO:0000783 ! engineered +intersection_of: has_quality SO:0000784 ! foreign +relationship: has_quality SO:0000783 ! engineered +relationship: has_quality SO:0000784 ! foreign + +[Term] +id: SO:0000337 +name: RNAi_reagent +namespace: sequence +def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd] +subset: SOFA +synonym: "RNAi reagent" EXACT [] +is_a: SO:0000442 ! ds_oligo + +[Term] +id: SO:0000340 +name: chromosome +namespace: sequence +def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +xref: http://en.wikipedia.org/wiki/Chromosome "wiki" +is_a: SO:0001235 ! replicon + +[Term] +id: SO:0000341 +name: chromosome_band +namespace: sequence +def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma] +subset: SOFA +synonym: "chromosome band" EXACT [] +synonym: "cytoband" EXACT [] +synonym: "cytological band" EXACT [] +xref: http://en.wikipedia.org/wiki/Cytological_band "wiki" +is_a: SO:0000830 ! chromosome_part + +[Term] +id: SO:0000348 +name: nucleic_acid +namespace: sequence +def: "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb] +synonym: "nucleic acid" EXACT [] +xref: http://en.wikipedia.org/wiki/Nucleic_acid "wiki" +is_a: SO:0000443 ! polymer_attribute + +[Term] +id: SO:0000353 +name: sequence_assembly +namespace: sequence +def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma] +subset: SOFA +synonym: "sequence assembly" EXACT [] +xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki" +is_a: SO:0001248 ! assembly + +[Term] +id: SO:0000400 +name: sequence_attribute +namespace: sequence +def: "An attribute describes a quality of sequence." [SO:ke] +synonym: "sequence attribute" EXACT [] + +[Term] +id: SO:0000409 +name: binding_site +namespace: sequence +alt_id: BS:00033 +def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke] +comment: See GO:0005488 : binding. +subset: biosapiens +subset: SOFA +synonym: "binding site" EXACT [] +synonym: "binding_or_interaction_site" EXACT [] +synonym: "INSDC_feature:misc_binding" EXACT [] +synonym: "site" RELATED [] +xref: http://en.wikipedia.org/wiki/Binding_site "wiki" +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000410 +name: protein_binding_site +namespace: sequence +def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke] +comment: See GO:0042277 : peptide binding. +subset: SOFA +synonym: "INSDC_feature:protein_bind" EXACT [] +synonym: "protein binding site" EXACT [] +is_a: SO:0000409 ! binding_site + +[Term] +id: SO:0000442 +name: ds_oligo +namespace: sequence +def: "A double stranded oligonucleotide." [SO:ke] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. +subset: SOFA +synonym: "double stranded oligonucleotide" EXACT [] +synonym: "ds oligo" EXACT [] +synonym: "ds-oligonucleotide" EXACT [] +is_a: SO:0000696 ! oligo + +[Term] +id: SO:0000443 +name: polymer_attribute +namespace: sequence +def: "An attribute to describe the kind of biological sequence." [SO:ke] +synonym: "polymer attribute" EXACT [] +is_a: SO:0000400 ! sequence_attribute + +[Term] +id: SO:0000577 +name: centromere +namespace: sequence +def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke] +subset: SOFA +synonym: "INSDC_feature:centromere" EXACT [] +xref: http://en.wikipedia.org/wiki/Centromere "wiki" +is_a: SO:0000628 ! chromosomal_structural_element + +[Term] +id: SO:0000628 +name: chromosomal_structural_element +namespace: sequence +subset: SOFA +synonym: "chromosomal structural element" EXACT [] +is_a: SO:0000830 ! chromosome_part + +[Term] +id: SO:0000637 +name: engineered_plasmid +namespace: sequence +def: "A plasmid that is engineered." [SO:xp] +synonym: "engineered plasmid" EXACT [] +synonym: "engineered plasmid gene" RELATED [] +is_a: SO:0000155 ! plasmid +is_a: SO:0000804 ! engineered_region +intersection_of: SO:0000155 ! plasmid +intersection_of: has_quality SO:0000783 ! engineered +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000657 +name: repeat_region +namespace: sequence +def: "A region of sequence containing one or more repeat units." [SO:ke] +subset: SOFA +synonym: "INSDC_feature:repeat_region" BROAD [] +synonym: "INSDC_qualifier:other" EXACT [] +synonym: "repeat region" EXACT [] +is_a: SO:0001411 ! biological_region +relationship: has_part SO:0000726 ! repeat_unit + +[Term] +id: SO:0000667 +name: insertion +namespace: sequence +alt_id: SO:1000034 +def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke] +subset: DBVAR +subset: SOFA +synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] +synonym: "nucleotide insertion" EXACT [] +synonym: "nucleotide_insertion" EXACT [] +xref: loinc:LA6687-3 "Insertion" +is_a: SO:0001059 ! sequence_alteration +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000694 +name: SNP +namespace: sequence +def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb] +subset: SOFA +synonym: "single nucleotide polymorphism" EXACT [] +is_a: SO:0001483 ! SNV + +[Term] +id: SO:0000695 +name: reagent +namespace: sequence +def: "A sequence used in experiment." [SO:ke] +comment: Requested by Lynn Crosby, jan 2006. +subset: SOFA +is_a: SO:0001409 ! biomaterial_region + +[Term] +id: SO:0000696 +name: oligo +namespace: sequence +def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma] +subset: SOFA +synonym: "oligonucleotide" EXACT [] +xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki" +is_a: SO:0000695 ! reagent + +[Term] +id: SO:0000699 +name: junction +namespace: sequence +def: "A sequence_feature with an extent of zero." [SO:ke] +comment: A junction is a boundary between regions. A boundary has an extent of zero. +subset: SOFA +synonym: "boundary" EXACT [] +synonym: "breakpoint" EXACT [] +is_a: SO:0000110 ! sequence_feature + +[Term] +id: SO:0000704 +name: gene +namespace: sequence +def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop] +comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. +subset: SOFA +synonym: "INSDC_feature:gene" EXACT [] +xref: http://en.wikipedia.org/wiki/Gene "wiki" +is_a: SO:0001411 ! biological_region +relationship: member_of SO:0005855 ! gene_group + +[Term] +id: SO:0000705 +name: tandem_repeat +namespace: sequence +def: "Two or more adjacent copies of a region (of length greater than 1)." [SO:ke] +subset: SOFA +synonym: "INSDC_feature:repeat_region" BROAD [] +synonym: "INSDC_qualifier:tandem" EXACT [] +synonym: "tandem repeat" EXACT [] +xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki" +xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html +is_a: SO:0000657 ! repeat_region + +[Term] +id: SO:0000719 +name: ultracontig +namespace: sequence +def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG] +subset: SOFA +synonym: "pseudochromosome" EXACT [] +synonym: "superscaffold" RELATED [] +is_a: SO:0001876 ! partial_genomic_sequence_assembly + +[Term] +id: SO:0000726 +name: repeat_unit +namespace: sequence +def: "The simplest repeated component of a repeat region. A single repeat." [SO:ke] +comment: Added to comply with the feature table. A single repeat. +synonym: "repeat unit" EXACT [] +xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000727 +name: CRM +namespace: sequence +def: "A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG] +comment: Requested by Stephen Grossmann Dec 2004. +subset: SOFA +synonym: "cis regulatory module" EXACT [] +synonym: "TF module" EXACT [] +synonym: "transcription factor module" EXACT [] +is_a: SO:0001055 ! transcriptional_cis_regulatory_region +intersection_of: SO:0001055 ! transcriptional_cis_regulatory_region +intersection_of: has_part SO:0000235 ! TF_binding_site +relationship: has_part SO:0000235 ! TF_binding_site + +[Term] +id: SO:0000733 +name: feature_attribute +namespace: sequence +def: "An attribute describing a located_sequence_feature." [SO:ke] +synonym: "feature attribute" EXACT [] +is_a: SO:0000400 ! sequence_attribute + +[Term] +id: SO:0000771 +name: QTL +namespace: sequence +def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/] +comment: Added in respose to request by Simon Twigger November 14th 2005. +synonym: "quantitative trait locus" EXACT [] +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0000781 +name: transgenic +namespace: sequence +def: "Attribute describing sequence that has been integrated with foreign sequence." [SO:ke] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000783 +name: engineered +namespace: sequence +def: "An attribute to describe a region that was modified in vitro." [SO:ke] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000784 +name: foreign +namespace: sequence +def: "An attribute to describe a region from another species." [SO:ke] +is_a: SO:0000733 ! feature_attribute + +[Term] +id: SO:0000804 +name: engineered_region +namespace: sequence +def: "A region that is engineered." [SO:xp] +synonym: "construct" EXACT [] +synonym: "engineered region" EXACT [] +synonym: "engineered sequence" EXACT [] +is_a: SO:0001409 ! biomaterial_region +intersection_of: SO:0000001 ! region +intersection_of: has_quality SO:0000783 ! engineered +relationship: has_quality SO:0000783 ! engineered + +[Term] +id: SO:0000805 +name: engineered_foreign_region +namespace: sequence +def: "A region that is engineered and foreign." [SO:xp] +synonym: "engineered foreign region" EXACT [] +is_a: SO:0000804 ! engineered_region +intersection_of: SO:0000001 ! region +intersection_of: has_quality SO:0000783 ! engineered +intersection_of: has_quality SO:0000784 ! foreign +relationship: has_quality SO:0000783 ! engineered +relationship: has_quality SO:0000784 ! foreign + +[Term] +id: SO:0000830 +name: chromosome_part +namespace: sequence +def: "A region of a chromosome." [SO:ke] +comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. +subset: SOFA +synonym: "chromosome part" EXACT [] +is_a: SO:0001411 ! biological_region +relationship: part_of SO:0000340 ! chromosome + +[Term] +id: SO:0000831 +name: gene_member_region +namespace: sequence +def: "A region of a gene." [SO:ke] +comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root. +subset: SOFA +synonym: "gene member region" EXACT [] +is_a: SO:0001411 ! biological_region +relationship: member_of SO:0000704 ! gene + +[Term] +id: SO:0000902 +name: transgene +namespace: sequence +def: "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp] +xref: http://en.wikipedia.org/wiki/Transgene "wiki" +is_a: SO:0000704 ! gene +intersection_of: SO:0000704 ! gene +intersection_of: has_quality SO:0000781 ! transgenic +relationship: has_quality SO:0000781 ! transgenic + +[Term] +id: SO:0001013 +name: MNP +namespace: sequence +def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431] +synonym: "multiple nucleotide polymorphism" RELATED [] +is_a: SO:0002007 ! MNV + +[Term] +id: SO:0001019 +name: copy_number_variation +namespace: sequence +def: "A variation that increases or decreases the copy number of a given region." [SO:ke] +subset: SOFA +synonym: "CNP" EXACT [] +synonym: "CNV" EXACT [] +synonym: "copy number polymorphism" EXACT [] +synonym: "copy number variation" EXACT [] +xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki" +is_a: SO:0000248 ! sequence_length_alteration + +[Term] +id: SO:0001026 +name: genome +namespace: sequence +def: "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop] +xref: http://en.wikipedia.org/wiki/Genome "wiki" +is_a: SO:0001260 ! sequence_collection +intersection_of: SO:0001260 ! sequence_collection +intersection_of: has_part SO:0001235 ! replicon +relationship: has_part SO:0001235 ! replicon + +[Term] +id: SO:0001055 +name: transcriptional_cis_regulatory_region +namespace: sequence +def: "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative] +subset: SOFA +synonym: "INSDC_feature:regulatory" BROAD [] +synonym: "INSDC_qualifier:transcriptional_cis_regulatory_region" EXACT [] +synonym: "transcription-control region" EXACT [] +synonym: "transcriptional cis regulatory region" EXACT [] +is_a: SO:0001679 ! transcription_regulatory_region + +[Term] +id: SO:0001059 +name: sequence_alteration +namespace: sequence +alt_id: SO:1000004 +alt_id: SO:1000007 +def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke] +comment: Merged with partially characterized change in nucleotide sequence. +subset: SOFA +synonym: "INSDC_feature:misc_feature" BROAD [] +synonym: "INSDC_feature:variation" EXACT [] +synonym: "INSDC_note:sequence_alteration" EXACT [] +synonym: "partially characterised change in DNA sequence" NARROW [] +synonym: "partially_characterised_change_in_DNA_sequence" NARROW [] +synonym: "sequence alteration" EXACT [] +synonym: "sequence variation" RELATED [] +synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW [] +is_a: SO:0002072 ! sequence_comparison + +[Term] +id: SO:0001183 +name: morpholino_backbone +namespace: sequence +def: "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb] +comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead. +synonym: "morpholino backbone" EXACT [] +xref: http://en.wikipedia.org/wiki/Morpholino "wiki" +is_a: SO:0000348 ! nucleic_acid + +[Term] +id: SO:0001218 +name: transgenic_insertion +namespace: sequence +def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm] +synonym: "transgenic insertion" EXACT [] +is_a: SO:0000667 ! insertion +intersection_of: SO:0000667 ! insertion +intersection_of: has_quality SO:0000781 ! transgenic +relationship: has_quality SO:0000781 ! transgenic + +[Term] +id: SO:0001235 +name: replicon +namespace: sequence +def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki" +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:0001247 +name: synthetic_oligo +namespace: sequence +def: "An oligo composed of synthetic nucleotides." [SO:ke] +synonym: "synthetic oligo" EXACT [] +is_a: SO:0000696 ! oligo + +[Term] +id: SO:0001248 +name: assembly +namespace: sequence +def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke] +subset: SOFA +xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki" +is_a: SO:0001410 ! experimental_feature + +[Term] +id: SO:0001260 +name: sequence_collection +namespace: sequence +def: "A collection of discontinuous sequences." [SO:ke] +synonym: "sequence collection" EXACT [] + +[Term] +id: SO:0001409 +name: biomaterial_region +namespace: sequence +def: "A region which is intended for use in an experiment." [SO:cb] +subset: SOFA +synonym: "biomaterial region" EXACT [] +is_a: SO:0000001 ! region + +[Term] +id: SO:0001410 +name: experimental_feature +namespace: sequence +def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb] +subset: SOFA +synonym: "analysis feature" RELATED [] +synonym: "experimental output artefact" EXACT [] +synonym: "experimental_output_artefact" EXACT [] +is_a: SO:0000001 ! region + +[Term] +id: SO:0001411 +name: biological_region +namespace: sequence +def: "A region defined by its disposition to be involved in a biological process." [SO:cb] +subset: SOFA +synonym: "biological region" EXACT [] +synonym: "INSDC_misc_feature" BROAD [] +synonym: "INSDC_note:biological_region" EXACT [] +is_a: SO:0000001 ! region + +[Term] +id: SO:0001477 +name: gene_trap_construct +namespace: sequence +def: "A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh] +synonym: "gene trap construct" EXACT [] +is_a: SO:0000637 ! engineered_plasmid +created_by: kareneilbeck +creation_date: 2009-09-01T03:49:09Z + +[Term] +id: SO:0001478 +name: promoter_trap_construct +namespace: sequence +def: "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh] +synonym: "promoter trap construct" EXACT [] +is_a: SO:0000637 ! engineered_plasmid +created_by: kareneilbeck +creation_date: 2009-09-01T03:52:01Z + +[Term] +id: SO:0001479 +name: enhancer_trap_construct +namespace: sequence +def: "An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh] +synonym: "enhancer trap construct" EXACT [] +is_a: SO:0000637 ! engineered_plasmid +created_by: kareneilbeck +creation_date: 2009-09-01T03:53:26Z + +[Term] +id: SO:0001483 +name: SNV +namespace: sequence +def: "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm] +subset: SOFA +synonym: "single nucleotide variant" EXACT [] +is_a: SO:1000002 ! substitution +created_by: kareneilbeck +creation_date: 2009-10-08T11:37:49Z + +[Term] +id: SO:0001500 +name: heritable_phenotypic_marker +namespace: sequence +def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene] +synonym: "heritable phenotypic marker" EXACT [] +synonym: "phenotypic marker" EXACT [] +is_a: SO:0001645 ! genetic_marker +created_by: kareneilbeck +creation_date: 2009-12-07T01:50:55Z + +[Term] +id: SO:0001505 +name: reference_genome +namespace: sequence +def: "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke] +synonym: "reference genome" RELATED [] +is_a: SO:0001026 ! genome +created_by: kareneilbeck +creation_date: 2010-03-03T02:10:03Z + +[Term] +id: SO:0001506 +name: variant_genome +namespace: sequence +def: "A collection of sequences (often chromosomes) of an individual." [SO:ke] +synonym: "variant genome" RELATED [] +is_a: SO:0001026 ! genome +created_by: kareneilbeck +creation_date: 2010-03-03T02:11:25Z + +[Term] +id: SO:0001507 +name: variant_collection +namespace: sequence +def: "A collection of one or more sequences of an individual." [SO:ke] +synonym: "variant collection" RELATED [] +is_a: SO:0001260 ! sequence_collection +intersection_of: SO:0001260 ! sequence_collection +intersection_of: has_part SO:0001059 ! sequence_alteration +relationship: has_part SO:0001059 ! sequence_alteration +created_by: kareneilbeck +creation_date: 2010-03-03T02:13:28Z + +[Term] +id: SO:0001524 +name: chromosomally_aberrant_genome +namespace: sequence +synonym: "chromosomally aberrant genome" RELATED [] +is_a: SO:0001506 ! variant_genome +created_by: kareneilbeck +creation_date: 2010-03-05T02:21:00Z + +[Term] +id: SO:0001645 +name: genetic_marker +namespace: sequence +def: "A measurable sequence feature that varies within a population." [SO:db] +synonym: "genetic marker" RELATED [] +is_a: SO:0001411 ! biological_region +created_by: kareneilbeck +creation_date: 2010-05-28T02:33:07Z + +[Term] +id: SO:0001654 +name: nucleotide_to_protein_binding_site +namespace: sequence +def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] +subset: SOFA +synonym: "nucleotide to protein binding site" RELATED [] +is_a: SO:0000410 ! protein_binding_site +created_by: kareneilbeck +creation_date: 2010-08-03T12:26:05Z + +[Term] +id: SO:0001679 +name: transcription_regulatory_region +namespace: sequence +def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke] +subset: SOFA +synonym: "transcription regulatory region" EXACT [] +is_a: SO:0005836 ! regulatory_region +created_by: kareneilbeck +creation_date: 2010-10-12T03:49:35Z + +[Term] +id: SO:0001742 +name: copy_number_gain +namespace: sequence +def: "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke] +subset: DBVAR +synonym: "copy number gain" EXACT [] +synonym: "gain" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] +is_a: SO:0001019 ! copy_number_variation +created_by: kareneilbeck +creation_date: 2011-02-28T01:54:09Z + +[Term] +id: SO:0001743 +name: copy_number_loss +namespace: sequence +def: "A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke] +subset: DBVAR +synonym: "copy number loss" EXACT [] +synonym: "loss" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] +is_a: SO:0001019 ! copy_number_variation +created_by: kareneilbeck +creation_date: 2011-02-28T01:55:02Z + +[Term] +id: SO:0001744 +name: UPD +namespace: sequence +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM] +subset: DBVAR +synonym: "uniparental disomy" EXACT [] +synonym: "UPD" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] +xref: http:http\://en.wikipedia.org/wiki/Uniparental_disomy "wikipedia" +is_a: SO:0001059 ! sequence_alteration +created_by: kareneilbeck +creation_date: 2011-02-28T02:01:05Z + +[Term] +id: SO:0001745 +name: maternal_uniparental_disomy +namespace: sequence +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [SO:bm] +synonym: "maternal uniparental disomy" EXACT [] +is_a: SO:0001744 ! UPD +created_by: kareneilbeck +creation_date: 2011-02-28T02:03:01Z + +[Term] +id: SO:0001746 +name: paternal_uniparental_disomy +namespace: sequence +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [SO:bm] +synonym: "paternal uniparental disomy" EXACT [] +is_a: SO:0001744 ! UPD +created_by: kareneilbeck +creation_date: 2011-02-28T02:03:30Z + +[Term] +id: SO:0001784 +name: complex_structural_alteration +namespace: sequence +alt_id: SO:1000146 +def: "A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints." [FB:reference_manual, NCBI:th, SO:ke] +subset: DBVAR +synonym: "complex" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] +synonym: "complex chromosomal mutation" EXACT [] +synonym: "complex_chromosomal_mutation" EXACT [] +is_a: SO:0001785 ! structural_alteration +is_a: SO:1000183 ! chromosome_structure_variation +created_by: kareneilbeck +creation_date: 2011-03-23T03:21:19Z + +[Term] +id: SO:0001785 +name: structural_alteration +namespace: sequence +subset: DBVAR +synonym: "structural alteration" EXACT [] +is_a: SO:0001059 ! sequence_alteration +created_by: kareneilbeck +creation_date: 2011-03-25T02:27:41Z + +[Term] +id: SO:0001876 +name: partial_genomic_sequence_assembly +namespace: sequence +def: "A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea] +comment: Requested by Bayer Cropscience January, 2012. +synonym: "partial genomic sequence assembly" EXACT [] +synonym: "pseudomolecule" BROAD [] +synonym: "sequence assembly with N-gaps" EXACT [] +is_a: SO:0000353 ! sequence_assembly +created_by: kareneilbeck +creation_date: 2012-02-14T05:05:32Z + +[Term] +id: SO:0002007 +name: MNV +namespace: sequence +def: "An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th] +synonym: "multiple nucleotide substitution" EXACT [] +synonym: "multiple nucleotide variant" EXACT [] +is_a: SO:1000002 ! substitution +created_by: kareneilbeck +creation_date: 2014-01-13T03:48:40Z + +[Term] +id: SO:0002072 +name: sequence_comparison +namespace: sequence +def: "A position or feature where two sequences have been compared." [] +synonym: "INSDC_feature:misc_feature" BROAD [] +synonym: "INSDC_note:sequence_comparison" EXACT [] +synonym: "sequence comparison" EXACT [] +is_a: SO:0000110 ! sequence_feature +created_by: kareneilbeck +creation_date: 2015-11-23T14:14:32Z + +[Term] +id: SO:0005836 +name: regulatory_region +namespace: sequence +def: "A region of sequence that is involved in the control of a biological process." [SO:ke] +subset: SOFA +synonym: "INSDC_feature:regulatory" BROAD [] +synonym: "INSDC_qualifier:other" EXACT [] +synonym: "regulatory region" EXACT [] +xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki" +is_a: SO:0000831 ! gene_member_region + +[Term] +id: SO:0005855 +name: gene_group +namespace: sequence +def: "A collection of related genes." [SO:ma] +subset: SOFA +synonym: "gene group" EXACT [] +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:1000002 +name: substitution +namespace: sequence +def: "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke] +subset: SOFA +xref: loinc:LA6690-7 "Substitution" +is_a: SO:0001059 ! sequence_alteration +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:1000005 +name: complex_substitution +namespace: sequence +def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +subset: SOFA +synonym: "complex substitution" EXACT [] +is_a: SO:1000002 ! substitution + +[Term] +id: SO:1000008 +name: point_mutation +namespace: sequence +def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop] +subset: SOFA +synonym: "point mutation" EXACT [] +xref: http://en.wikipedia.org/wiki/Point_mutation "wiki" +is_a: SO:0001483 ! SNV + +[Term] +id: SO:1000009 +name: transition +namespace: sequence +def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +is_a: SO:0001483 ! SNV + +[Term] +id: SO:1000010 +name: pyrimidine_transition +namespace: sequence +def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke] +synonym: "pyrimidine transition" EXACT [] +is_a: SO:1000009 ! transition + +[Term] +id: SO:1000011 +name: C_to_T_transition +namespace: sequence +def: "A transition of a cytidine to a thymine." [SO:ke] +synonym: "C to T transition" EXACT [] +is_a: SO:1000010 ! pyrimidine_transition + +[Term] +id: SO:1000012 +name: C_to_T_transition_at_pCpG_site +namespace: sequence +def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +synonym: "C to T transition at pCpG site" EXACT [] +is_a: SO:1000011 ! C_to_T_transition + +[Term] +id: SO:1000013 +name: T_to_C_transition +namespace: sequence +synonym: "T to C transition" EXACT [] +is_a: SO:1000010 ! pyrimidine_transition + +[Term] +id: SO:1000014 +name: purine_transition +namespace: sequence +def: "A substitution of a purine, A or G, for another purine." [SO:ke] +synonym: "purine transition" EXACT [] +is_a: SO:1000009 ! transition + +[Term] +id: SO:1000015 +name: A_to_G_transition +namespace: sequence +def: "A transition of an adenine to a guanine." [SO:ke] +synonym: "A to G transition" EXACT [] +is_a: SO:1000014 ! purine_transition + +[Term] +id: SO:1000016 +name: G_to_A_transition +namespace: sequence +def: "A transition of a guanine to an adenine." [SO:ke] +synonym: "G to A transition" EXACT [] +is_a: SO:1000014 ! purine_transition + +[Term] +id: SO:1000017 +name: transversion +namespace: sequence +def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +xref: http://en.wikipedia.org/wiki/Transversion "wiki" +is_a: SO:0001483 ! SNV + +[Term] +id: SO:1000018 +name: pyrimidine_to_purine_transversion +namespace: sequence +def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke] +synonym: "pyrimidine to purine transversion" EXACT [] +is_a: SO:1000017 ! transversion + +[Term] +id: SO:1000019 +name: C_to_A_transversion +namespace: sequence +def: "A transversion from cytidine to adenine." [SO:ke] +synonym: "C to A transversion" EXACT [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion + +[Term] +id: SO:1000020 +name: C_to_G_transversion +namespace: sequence +synonym: "C to G transversion" EXACT [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion + +[Term] +id: SO:1000021 +name: T_to_A_transversion +namespace: sequence +def: "A transversion from T to A." [SO:ke] +synonym: "T to A transversion" EXACT [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion + +[Term] +id: SO:1000022 +name: T_to_G_transversion +namespace: sequence +def: "A transversion from T to G." [SO:ke] +synonym: "T to G transversion" EXACT [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion + +[Term] +id: SO:1000023 +name: purine_to_pyrimidine_transversion +namespace: sequence +def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke] +synonym: "purine to pyrimidine transversion" EXACT [] +is_a: SO:1000017 ! transversion + +[Term] +id: SO:1000024 +name: A_to_C_transversion +namespace: sequence +def: "A transversion from adenine to cytidine." [SO:ke] +synonym: "A to C transversion" EXACT [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion + +[Term] +id: SO:1000025 +name: A_to_T_transversion +namespace: sequence +def: "A transversion from adenine to thymine." [SO:ke] +synonym: "A to T transversion" EXACT [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion + +[Term] +id: SO:1000026 +name: G_to_C_transversion +namespace: sequence +def: "A transversion from guanine to cytidine." [SO:ke] +synonym: "G to C transversion" EXACT [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion + +[Term] +id: SO:1000027 +name: G_to_T_transversion +namespace: sequence +def: "A transversion from guanine to thymine." [SO:ke] +synonym: "G to T transversion" EXACT [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion + +[Term] +id: SO:1000032 +name: delins +namespace: sequence +def: "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [http://varnomen.hgvs.org/recommendations/DNA/variant/delins/] +comment: Indels can have a different number of bases than the corresponding reference sequence. The term name was changed from indel to delins on 2/24/2019 to align with the HGVS nomenclature term for a deletion-insertion. Indel was causing confusion in the annotation community (github issue 445). The HGVS nomenclature definition of deletion-insertion (delins) is a sequence change where, compared to a reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution, inversion or conversion. +synonym: "deletion-insertion" EXACT [] +synonym: "indel" EXACT [] +xref: http://en.wikipedia.org/wiki/Indel "wiki" +xref: loinc:LA9659-9 "Insertion and Deletion" +is_a: SO:0001059 ! sequence_alteration + +[Term] +id: SO:1000035 +name: duplication +namespace: sequence +def: "An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th] +synonym: "nucleotide duplication" EXACT [] +synonym: "nucleotide_duplication" RELATED [] +xref: loinc:LA6686-5 "Duplication" +is_a: SO:0000667 ! insertion + +[Term] +id: SO:1000036 +name: inversion +namespace: sequence +def: "A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] +subset: DBVAR +subset: SOFA +synonym: "inversion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] +xref: loinc:LA6689-9 "Inversion" +is_a: SO:0001059 ! sequence_alteration +is_a: SO:0001411 ! biological_region + +[Term] +id: SO:1000039 +name: direct_tandem_duplication +namespace: sequence +def: "A tandem duplication where the individual regions are in the same orientation." [SO:ke] +synonym: "direct tandem duplication" EXACT [] +is_a: SO:1000173 ! tandem_duplication + +[Term] +id: SO:1000040 +name: inverted_tandem_duplication +namespace: sequence +def: "A tandem duplication where the individual regions are not in the same orientation." [SO:ke] +synonym: "inverted tandem duplication" EXACT [] +synonym: "mirror duplication" RELATED [] +is_a: SO:1000173 ! tandem_duplication + +[Term] +id: SO:1000173 +name: tandem_duplication +namespace: sequence +def: "A duplication consisting of 2 identical adjacent regions." [SO:ke] +subset: DBVAR +synonym: "erverted" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] +synonym: "tandem duplication" EXACT [] +is_a: SO:1000035 ! duplication + +[Term] +id: SO:1000183 +name: chromosome_structure_variation +namespace: sequence +synonym: "chromosome structure variation" EXACT [] +synonym: "snpEff:CHROMOSOME_LARGE_DELETION" EXACT VAR [] +xref: http://snpeff.sourceforge.net/SnpEff_manual.html +is_a: SO:0000240 ! chromosome_variation + +[Typedef] +id: has_part +name: has_part +namespace: sequence +def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: operon has_part gene. + +[Typedef] +id: has_quality +name: has_quality +namespace: sequence +comment: The relationship between a feature and an attribute. + +[Typedef] +id: member_of +name: member_of +namespace: sequence +comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. +subset: SOFA +is_transitive: true +is_a: part_of ! part_of + +[Typedef] +id: part_of +name: part_of +namespace: sequence +def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1] +comment: Example: amino_acid part_of polypeptide. +subset: SOFA +is_transitive: true + diff --git a/src/ontology/imports/so_import.owl b/src/ontology/imports/so_import.owl index e27f414..6842dac 100644 --- a/src/ontology/imports/so_import.owl +++ b/src/ontology/imports/so_import.owl @@ -1,14 +1,3356 @@ - - + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + database_cross_reference + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Inverse of part_of. + sequence + has_part + Example: operon has_part gene. + has_part + + + + + Inverse of part_of. + http://precedings.nature.com/documents/3495/version/1 + + + + + + + + sequence + has_quality + The relationship between a feature and an attribute. + has_quality + + + + + + + + + + sequence + member_of + + A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. + member_of + + + + + + + + + X part_of Y if X is a subregion of Y. + sequence + part_of + + Example: amino_acid part_of polypeptide. + part_of + + + + + X part_of Y if X is a subregion of Y. + http://precedings.nature.com/documents/3495/version/1 + + + + + + + + + + + + + sequence + SO:0000000 + + Sequence_Ontology + true + + + + + + + + + A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. + sequence + sequence + SO:0000001 + + region + + + + + A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. + SO:ke + + + + + + + + + A folded sequence. + INSDC_feature:misc_structure + sequence secondary structure + sequence + SO:0000002 + sequence_secondary_structure + + + + + A folded sequence. + SO:ke + + + + + + + + + The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA. + INSDC_feature:repeat_region + http://en.wikipedia.org/wiki/Satellite_DNA + INSDC_qualifier:satellite + satellite DNA + sequence + SO:0000005 + + satellite_DNA + + + + + The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA. + http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html + + + + + http://en.wikipedia.org/wiki/Satellite_DNA + wiki + + + + + + + + + + + + + + + + + + + + + + + + + + Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. + morphant + morpholino + morpholino oligo + sequence + SO:0000034 + morpholino_oligo + + + + + Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. + http://www.gene-tools.com/ + + + + + + + + + A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. + chromosome arm + sequence + SO:0000105 + chromosome_arm + + + + + A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. + http://www.medterms.com/script/main/art.asp?articlekey=5152 + + + + + + + + + Any extent of continuous biological sequence. + INSDC_feature:misc_feature + INSDC_note:other + INSDC_note:sequence_feature + located_sequence_feature + sequence feature + sequence + located sequence feature + SO:0000110 + + sequence_feature + + + + + Any extent of continuous biological sequence. + LAMHDI:mb + SO:ke + + + + + + + + + A region of known length which may be used to manufacture a longer region. + assembly component + sequence + SO:0000143 + + assembly_component + + + + + A region of known length which may be used to manufacture a longer region. + SO:ke + + + + + + + + + + + + + + + One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. + sequence + scaffold + SO:0000148 + + supercontig + + + + + One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. + SO:ls + + + + + + + + + + + + + + + + A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. + http://en.wikipedia.org/wiki/Contig + sequence + SO:0000149 + + contig + + + + + A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. + SO:ls + + + + + http://en.wikipedia.org/wiki/Contig + wiki + + + + + + + + + A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism. + plasmid sequence + sequence + SO:0000155 + This term is mapped to MGED. Do not obsolete without consulting MGED ontology. + plasmid + + + + + A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism. + SO:ma + + + + + + + + + + The point at which one or more contiguous nucleotides were excised. + SO:1000033 + http://en.wikipedia.org/wiki/Nucleotide_deletion + loinc:LA6692-3 + deleted_sequence + nucleotide deletion + nucleotide_deletion + sequence + SO:0000159 + + deletion + + + + + The point at which one or more contiguous nucleotides were excised. + SO:ke + + + + + http://en.wikipedia.org/wiki/Nucleotide_deletion + wiki + + + + + loinc:LA6692-3 + Deletion + + + + + + + + + A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. + INSDC_feature:regulatory + http://en.wikipedia.org/wiki/Enhancer_(genetics) + INSDC_qualifier:enhancer + sequence + SO:0000165 + + An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO. + enhancer + + + + + A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. + http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html + + + + + http://en.wikipedia.org/wiki/Enhancer_(genetics) + wiki + + + + + + + + + A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. + INSDC_feature:regulatory + http://en.wikipedia.org/wiki/Promoter + INSDC_qualifier:promoter + promoter sequence + sequence + SO:0000167 + + This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. + promoter + + + + + A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. + SO:regcreative + + + + + http://en.wikipedia.org/wiki/Promoter + wiki + + + + + + + + + A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions. + translocated sequence + sequence + transchr + SO:0000199 + + translocation + + + + + A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions. + NCBI:th + SO:ke + + + + + transchr + http://www.ncbi.nlm.nih.gov/dbvar/ + + + + + + + + + SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ. + http://en.wikipedia.org/wiki/Simple_sequence_length_polymorphism + simple sequence length variation + sequence + SSLP + simple sequence length polymorphism + SO:0000207 + simple_sequence_length_variation + + + + + SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ. + SO:ke + + + + + http://en.wikipedia.org/wiki/Simple_sequence_length_polymorphism + WIKI + + + + + + + + + + A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]. + TF binding site + transcription factor binding site + sequence + SO:0000235 + + TF_binding_site + + + + + A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]. + SO:ke + + + + + + + + + + + + + + + chromosome variation + sequence + SO:0000240 + chromosome_variation + + + + + + + + + A kind of kind of sequence alteration where the copies of a region present varies across a population. + sequence length alteration + sequence + SO:0000248 + sequence_length_alteration + + + + + A kind of kind of sequence alteration where the copies of a region present varies across a population. + SO:ke + + + + + + + + + + + + + + + + + + + + + + + + + + + A gene that is engineered. + engineered gene + sequence + SO:0000280 + engineered_gene + + + + + A gene that is engineered. + SO:xp + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A gene that is engineered and foreign. + engineered foreign gene + sequence + SO:0000281 + engineered_foreign_gene + + + + + A gene that is engineered and foreign. + SO:xp + + + + + + + + + + + + + + + + + + + + + + + + + + A gene that is foreign. + foreign gene + sequence + SO:0000285 + foreign_gene + + + + + A gene that is foreign. + SO:xp + + + + + + + + + A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. + INSDC_feature:repeat_region + http://en.wikipedia.org/wiki/Microsatellite + INSDC_qualifier:microsatellite + STR + microsatellite locus + microsatellite marker + short tandem repeat + sequence + SO:0000289 + + microsatellite + + + + + A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. + NCBI:th + http://www.informatics.jax.org/silver/glossary.shtml + + + + + http://en.wikipedia.org/wiki/Microsatellite + wiki + + + + + STR + http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A repetitive element that is engineered and foreign. + engineered foreign repetitive element + sequence + SO:0000293 + engineered_foreign_repetitive_element + + + + + A repetitive element that is engineered and foreign. + SO:xp + + + + + + + + + A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. + RNAi reagent + sequence + SO:0000337 + + RNAi_reagent + + + + + A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. + SO:rd + + + + + + + + + Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. + http://en.wikipedia.org/wiki/Chromosome + sequence + SO:0000340 + + This term is mapped to MGED. Do not obsolete without consulting MGED ontology. + chromosome + + + + + Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. + SO:ma + + + + + http://en.wikipedia.org/wiki/Chromosome + wiki + + + + + + + + + A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. + http://en.wikipedia.org/wiki/Cytological_band + chromosome band + cytoband + cytological band + sequence + SO:0000341 + + chromosome_band + + + + + A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. + SO:ma + + + + + http://en.wikipedia.org/wiki/Cytological_band + wiki + + + + + + + + + An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. + http://en.wikipedia.org/wiki/Nucleic_acid + nucleic acid + sequence + SO:0000348 + nucleic_acid + + + + + An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. + CHEBI:33696 + RSC:cb + + + + + http://en.wikipedia.org/wiki/Nucleic_acid + wiki + + + + + + + + + A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. + http://en.wikipedia.org/wiki/Sequence_assembly + sequence assembly + sequence + SO:0000353 + + sequence_assembly + + + + + A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. + SO:ma + + + + + http://en.wikipedia.org/wiki/Sequence_assembly + wiki + + + + + + + + An attribute describes a quality of sequence. + sequence attribute + sequence + SO:0000400 + sequence_attribute + + + + + An attribute describes a quality of sequence. + SO:ke + + + + + + + + + A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. + BS:00033 + http://en.wikipedia.org/wiki/Binding_site + INSDC_feature:misc_binding + binding site + binding_or_interaction_site + sequence + site + SO:0000409 + + + See GO:0005488 : binding. + binding_site + + + + + A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. + EBIBS:GAR + SO:ke + + + + + http://en.wikipedia.org/wiki/Binding_site + wiki + + + + + + + + + A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. + INSDC_feature:protein_bind + protein binding site + sequence + SO:0000410 + + See GO:0042277 : peptide binding. + protein_binding_site + + + + + A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. + SO:ke + + + + + + + + + A double stranded oligonucleotide. + double stranded oligonucleotide + ds oligo + ds-oligonucleotide + sequence + SO:0000442 + + This term is mapped to MGED. Do not obsolete without consulting MGED ontology. + ds_oligo + + + + + A double stranded oligonucleotide. + SO:ke + + + + + + + + + An attribute to describe the kind of biological sequence. + polymer attribute + sequence + SO:0000443 + polymer_attribute + + + + + An attribute to describe the kind of biological sequence. + SO:ke + + + + + + + + + A region of chromosome where the spindle fibers attach during mitosis and meiosis. + http://en.wikipedia.org/wiki/Centromere + INSDC_feature:centromere + sequence + SO:0000577 + + centromere + + + + + A region of chromosome where the spindle fibers attach during mitosis and meiosis. + SO:ke + + + + + http://en.wikipedia.org/wiki/Centromere + wiki + + + + + + + + + chromosomal structural element + sequence + SO:0000628 + + chromosomal_structural_element + + + + + + + + + + + + + + + + + + + + + + + + + + + A plasmid that is engineered. + engineered plasmid + sequence + engineered plasmid gene + SO:0000637 + engineered_plasmid + + + + + A plasmid that is engineered. + SO:xp + + + + + + + + + + + + + + + A region of sequence containing one or more repeat units. + INSDC_feature:repeat_region + INSDC_qualifier:other + repeat region + sequence + SO:0000657 + + repeat_region + + + + + A region of sequence containing one or more repeat units. + SO:ke + + + + + + + + + + The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. + SO:1000034 + loinc:LA6687-3 + insertion + nucleotide insertion + nucleotide_insertion + sequence + SO:0000667 + + + insertion + + + + + The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. + SO:ke + + + + + loinc:LA6687-3 + Insertion + + + + + insertion + http://www.ncbi.nlm.nih.gov/dbvar/ + + + + + + + + + + SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. + single nucleotide polymorphism + sequence + SO:0000694 + + SNP + + + + + SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. + SO:cb + + + + + + + + + A sequence used in experiment. + sequence + SO:0000695 + + Requested by Lynn Crosby, jan 2006. + reagent + + + + + A sequence used in experiment. + SO:ke + + + + + + + + + A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. + http://en.wikipedia.org/wiki/Oligonucleotide + oligonucleotide + sequence + SO:0000696 + + oligo + + + + + http://en.wikipedia.org/wiki/Oligonucleotide + wiki + + + + + A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. + SO:ma + + + + + + + + + A sequence_feature with an extent of zero. + boundary + breakpoint + sequence + SO:0000699 + + A junction is a boundary between regions. A boundary has an extent of zero. + junction + + + + + A sequence_feature with an extent of zero. + SO:ke + + + + + + + + + + + + + + + A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. + http://en.wikipedia.org/wiki/Gene + INSDC_feature:gene + sequence + SO:0000704 + + This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. + gene + + + + + A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. + SO:immuno_workshop + + + + + http://en.wikipedia.org/wiki/Gene + wiki + + + + + + + + + Two or more adjacent copies of a region (of length greater than 1). + INSDC_feature:repeat_region + http://en.wikipedia.org/wiki/Tandem_repeat + http://www.sci.sdsu.edu/~smaloy/Glossary/T.html + INSDC_qualifier:tandem + tandem repeat + sequence + SO:0000705 + + tandem_repeat + + + + + Two or more adjacent copies of a region (of length greater than 1). + SO:ke + + + + + http://en.wikipedia.org/wiki/Tandem_repeat + wiki + + + + + + + + + An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers. + pseudochromosome + sequence + superscaffold + SO:0000719 + + ultracontig + + + + + An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers. + FB:WG + + + + + + + + + The simplest repeated component of a repeat region. A single repeat. + http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html + repeat unit + sequence + SO:0000726 + Added to comply with the feature table. A single repeat. + repeat_unit + + + + + The simplest repeated component of a repeat region. A single repeat. + SO:ke + + + + + + + + + + + + + + + + + + + + + + + + + + A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. + TF module + cis regulatory module + transcription factor module + sequence + SO:0000727 + + Requested by Stephen Grossmann Dec 2004. + CRM + + + + + A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. + PMID:19660565 + SO:SG + + + + + + + + + An attribute describing a located_sequence_feature. + feature attribute + sequence + SO:0000733 + feature_attribute + + + + + An attribute describing a located_sequence_feature. + SO:ke + + + + + + + + + A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. + quantitative trait locus + sequence + SO:0000771 + Added in respose to request by Simon Twigger November 14th 2005. + QTL + + + + + A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. + http://rgd.mcw.edu/tu/qtls/ + + + - + + + + + Attribute describing sequence that has been integrated with foreign sequence. + sequence + SO:0000781 + transgenic + + + + + Attribute describing sequence that has been integrated with foreign sequence. + SO:ke + + + + + + + + + An attribute to describe a region that was modified in vitro. + sequence + SO:0000783 + engineered + + + + + An attribute to describe a region that was modified in vitro. + SO:ke + + + + + + + + + An attribute to describe a region from another species. + sequence + SO:0000784 + foreign + + + + + An attribute to describe a region from another species. + SO:ke + + + + + + + + + + + + + + + + + + + + + + + + + + A region that is engineered. + construct + engineered region + engineered sequence + sequence + SO:0000804 + engineered_region + + + + + A region that is engineered. + SO:xp + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A region that is engineered and foreign. + engineered foreign region + sequence + SO:0000805 + engineered_foreign_region + + + + + A region that is engineered and foreign. + SO:xp + + + + + + + + + + + + + + + A region of a chromosome. + chromosome part + sequence + SO:0000830 + + This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. + chromosome_part + + + + + A region of a chromosome. + SO:ke + + + + + + + + + + + + + + + A region of a gene. + gene member region + sequence + SO:0000831 + + A manufactured term used to allow the parts of a gene to have an is_a path to the root. + gene_member_region + + + + + A region of a gene. + SO:ke + + + + + + + + + + + + + + + + + + + + + + + + + + A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. + http://en.wikipedia.org/wiki/Transgene + sequence + SO:0000902 + transgene + + + + + A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. + SO:xp + + + + + http://en.wikipedia.org/wiki/Transgene + wiki + + + + + + + + + A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. + sequence + multiple nucleotide polymorphism + SO:0001013 + MNP + + + + + A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. + http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431 + + + + + + + + + A variation that increases or decreases the copy number of a given region. + http://en.wikipedia.org/wiki/Copy_number_variation + CNP + CNV + copy number polymorphism + copy number variation + sequence + SO:0001019 + + copy_number_variation + + + + + A variation that increases or decreases the copy number of a given region. + SO:ke + + + + + http://en.wikipedia.org/wiki/Copy_number_variation + wiki + + + + + + + + + + + + + + + + + + + + + + + + + + A genome is the sum of genetic material within a cell or virion. + http://en.wikipedia.org/wiki/Genome + sequence + SO:0001026 + genome + + + + + A genome is the sum of genetic material within a cell or virion. + SO:immuno_workshop + + + + + http://en.wikipedia.org/wiki/Genome + wiki + + + + + + + + + A regulatory_region that modulates the transcription of a gene or genes. + INSDC_feature:regulatory + INSDC_qualifier:transcriptional_cis_regulatory_region + transcription-control region + transcriptional cis regulatory region + sequence + SO:0001055 + + transcriptional_cis_regulatory_region + + + + + A regulatory_region that modulates the transcription of a gene or genes. + PMID:9679020 + SO:regcreative + + + + + + + + + A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. + SO:1000004 + SO:1000007 + INSDC_feature:misc_feature + INSDC_feature:variation + INSDC_note:sequence_alteration + sequence alteration + partially characterised change in DNA sequence + partially_characterised_change_in_DNA_sequence + uncharacterised_change_in_nucleotide_sequence + sequence + sequence variation + SO:0001059 + + Merged with partially characterized change in nucleotide sequence. + sequence_alteration + + + + + A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. + SO:ke + + + + + + + + + An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages. + http://en.wikipedia.org/wiki/Morpholino + morpholino backbone + sequence + SO:0001183 + Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead. + morpholino_backbone + + + + + An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages. + RSC:cb + + + + + http://en.wikipedia.org/wiki/Morpholino + wiki + + + + + + + + + + + + + + + + + + + + + + + + + + An insertion that derives from another organism, via the use of recombinant DNA technology. + transgenic insertion + sequence + SO:0001218 + transgenic_insertion + + + + + An insertion that derives from another organism, via the use of recombinant DNA technology. + SO:bm + + + + + + + + + A region containing at least one unique origin of replication and a unique termination site. + http://en.wikipedia.org/wiki/Replicon_(genetics) + sequence + SO:0001235 + + replicon + + + + + A region containing at least one unique origin of replication and a unique termination site. + ISBN:0716719207 + + + + + http://en.wikipedia.org/wiki/Replicon_(genetics) + wiki + + + + + + + + + An oligo composed of synthetic nucleotides. + synthetic oligo + sequence + SO:0001247 + synthetic_oligo + + + + + An oligo composed of synthetic nucleotides. + SO:ke + + + + + + + + + A region of the genome of known length that is composed by ordering and aligning two or more different regions. + http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly + sequence + SO:0001248 + + assembly + + + + + A region of the genome of known length that is composed by ordering and aligning two or more different regions. + SO:ke + + + + + http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly + wiki + + + + + + + + A collection of discontinuous sequences. + sequence collection + sequence + SO:0001260 + sequence_collection + + + + + A collection of discontinuous sequences. + SO:ke + + + + + + + + + A region which is intended for use in an experiment. + biomaterial region + sequence + SO:0001409 + + biomaterial_region + + + + + A region which is intended for use in an experiment. + SO:cb + + + + + + + + + A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. + experimental output artefact + experimental_output_artefact + sequence + analysis feature + SO:0001410 + + experimental_feature + + + + + A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. + SO:cb + + + + + + + + + A region defined by its disposition to be involved in a biological process. + INSDC_misc_feature + INSDC_note:biological_region + biological region + sequence + SO:0001411 + + biological_region + + + + + A region defined by its disposition to be involved in a biological process. + SO:cb + + + + + + + + + A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. + kareneilbeck + 2009-09-01T03:49:09Z + gene trap construct + sequence + SO:0001477 + gene_trap_construct + + + + + A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. + ZFIN:dh + + + + + + + + + A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. + kareneilbeck + 2009-09-01T03:52:01Z + promoter trap construct + sequence + SO:0001478 + promoter_trap_construct + + + + + A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. + ZFIN:dh + + + + + + + + + An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. + kareneilbeck + 2009-09-01T03:53:26Z + enhancer trap construct + sequence + SO:0001479 + enhancer_trap_construct + + + + + An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. + ZFIN:dh + + + + + + + + + SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. + kareneilbeck + 2009-10-08T11:37:49Z + single nucleotide variant + sequence + SO:0001483 + + SNV + + + + + SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. + SO:bm + + + + + + + + + A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. + kareneilbeck + 2009-12-07T01:50:55Z + heritable phenotypic marker + phenotypic marker + sequence + SO:0001500 + heritable_phenotypic_marker + + + + + A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. + JAX:hdene + + + + + + + + + A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly. + kareneilbeck + 2010-03-03T02:10:03Z + sequence + reference genome + SO:0001505 + reference_genome + + + + + A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly. + SO:ke + + + + + + + + + A collection of sequences (often chromosomes) of an individual. + kareneilbeck + 2010-03-03T02:11:25Z + sequence + variant genome + SO:0001506 + variant_genome + + + + + A collection of sequences (often chromosomes) of an individual. + SO:ke + + + + + + + + + + + + + + + + + + + + + + + + + + A collection of one or more sequences of an individual. + kareneilbeck + 2010-03-03T02:13:28Z + sequence + variant collection + SO:0001507 + variant_collection + + + + + A collection of one or more sequences of an individual. + SO:ke + + + + + + + + + kareneilbeck + 2010-03-05T02:21:00Z + sequence + chromosomally aberrant genome + SO:0001524 + chromosomally_aberrant_genome + + + + + + + + + A measurable sequence feature that varies within a population. + kareneilbeck + 2010-05-28T02:33:07Z + sequence + genetic marker + SO:0001645 + genetic_marker + + + + + A measurable sequence feature that varies within a population. + SO:db + + + + + + + + + A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. + kareneilbeck + 2010-08-03T12:26:05Z + sequence + nucleotide to protein binding site + SO:0001654 + + nucleotide_to_protein_binding_site + + + + + A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. + SO:ke + + + + + + + + + A regulatory region that is involved in the control of the process of transcription. + kareneilbeck + 2010-10-12T03:49:35Z + transcription regulatory region + sequence + SO:0001679 + + transcription_regulatory_region + + + + + A regulatory region that is involved in the control of the process of transcription. + SO:ke + + + + + + + + + A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. + kareneilbeck + 2011-02-28T01:54:09Z + copy number gain + sequence + gain + SO:0001742 + + copy_number_gain + + + + + A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. + SO:ke + + + + + gain + http://www.ncbi.nlm.nih.gov/dbvar/ + + + + + + + + + + A sequence alteration whereby the copy number of a given region is less than the reference sequence. + kareneilbeck + 2011-02-28T01:55:02Z + copy number loss + sequence + loss + SO:0001743 + + copy_number_loss + + + + + A sequence alteration whereby the copy number of a given region is less than the reference sequence. + SO:ke + + + + + loss + http://www.ncbi.nlm.nih.gov/dbvar/ + + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. + kareneilbeck + 2011-02-28T02:01:05Z + http:http://en.wikipedia.org/wiki/Uniparental_disomy + UPD + uniparental disomy + sequence + SO:0001744 + + UPD + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. + SO:BM + + + + + http:http://en.wikipedia.org/wiki/Uniparental_disomy + wikipedia + + + + + UPD + http://www.ncbi.nlm.nih.gov/dbvar/ + + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. + kareneilbeck + 2011-02-28T02:03:01Z + maternal uniparental disomy + sequence + SO:0001745 + maternal_uniparental_disomy + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. + SO:bm + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. + kareneilbeck + 2011-02-28T02:03:30Z + paternal uniparental disomy + sequence + SO:0001746 + paternal_uniparental_disomy + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. + SO:bm + + + + + + + + + + A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints. + kareneilbeck + 2011-03-23T03:21:19Z + SO:1000146 + complex chromosomal mutation + complex_chromosomal_mutation + sequence + complex + SO:0001784 + + complex_structural_alteration + + + + + A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints. + FB:reference_manual + NCBI:th + SO:ke + + + + + complex + http://www.ncbi.nlm.nih.gov/dbvar/ + + + + + + + + + + kareneilbeck + 2011-03-25T02:27:41Z + structural alteration + sequence + SO:0001785 + + structural_alteration + + + + + + + + + A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's. + kareneilbeck + 2012-02-14T05:05:32Z + pseudomolecule + partial genomic sequence assembly + sequence assembly with N-gaps + sequence + SO:0001876 + Requested by Bayer Cropscience January, 2012. + partial_genomic_sequence_assembly + + + + + A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's. + GMOD:ea + + + + + + + + + An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence. + kareneilbeck + 2014-01-13T03:48:40Z + multiple nucleotide substitution + multiple nucleotide variant + sequence + SO:0002007 + MNV + + + + + An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence. + NCBI:th + + + + + + + + + A position or feature where two sequences have been compared. + kareneilbeck + 2015-11-23T14:14:32Z + INSDC_feature:misc_feature + INSDC_note:sequence_comparison + sequence comparison + sequence + SO:0002072 + sequence_comparison + + + + + + + + + A region of sequence that is involved in the control of a biological process. + INSDC_feature:regulatory + http://en.wikipedia.org/wiki/Regulatory_region + INSDC_qualifier:other + regulatory region + sequence + SO:0005836 + + regulatory_region + + + + + A region of sequence that is involved in the control of a biological process. + SO:ke + + + + + http://en.wikipedia.org/wiki/Regulatory_region + wiki + + + + + + + + + A collection of related genes. + gene group + sequence + SO:0005855 + + gene_group + + + + + A collection of related genes. + SO:ma + + + + + + + + + + A sequence alteration where the length of the change in the variant is the same as that of the reference. + loinc:LA6690-7 + sequence + SO:1000002 + + substitution + + + + + A sequence alteration where the length of the change in the variant is the same as that of the reference. + SO:ke + + + + + loinc:LA6690-7 + Substitution + + + + + + + + + When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change. + complex substitution + sequence + SO:1000005 + + complex_substitution + + + + + When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change. + EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html + + + + + + + + + A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. + http://en.wikipedia.org/wiki/Point_mutation + point mutation + sequence + SO:1000008 + + point_mutation + + + + + A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. + SO:immuno_workshop + + + + + http://en.wikipedia.org/wiki/Point_mutation + wiki + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. + sequence + SO:1000009 + transition + + + + + Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. + EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html + + + + + + + + + A substitution of a pyrimidine, C or T, for another pyrimidine. + pyrimidine transition + sequence + SO:1000010 + pyrimidine_transition + + + + + A substitution of a pyrimidine, C or T, for another pyrimidine. + SO:ke + + + + + + + + + A transition of a cytidine to a thymine. + C to T transition + sequence + SO:1000011 + C_to_T_transition + + + + + A transition of a cytidine to a thymine. + SO:ke + + + + + + + + + The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine. + C to T transition at pCpG site + sequence + SO:1000012 + C_to_T_transition_at_pCpG_site + + + + + The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine. + EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html + + + + + + + + + T to C transition + sequence + SO:1000013 + T_to_C_transition + + + + + + + + + A substitution of a purine, A or G, for another purine. + purine transition + sequence + SO:1000014 + purine_transition + + + + + A substitution of a purine, A or G, for another purine. + SO:ke + + + + + + + + + A transition of an adenine to a guanine. + A to G transition + sequence + SO:1000015 + A_to_G_transition + + + + + A transition of an adenine to a guanine. + SO:ke + + + + + + + + + A transition of a guanine to an adenine. + G to A transition + sequence + SO:1000016 + G_to_A_transition + + + + + A transition of a guanine to an adenine. + SO:ke + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. + http://en.wikipedia.org/wiki/Transversion + sequence + SO:1000017 + transversion + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. + EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html + + + + + http://en.wikipedia.org/wiki/Transversion + wiki + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. + pyrimidine to purine transversion + sequence + SO:1000018 + pyrimidine_to_purine_transversion + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. + SO:ke + + + + + + + + + A transversion from cytidine to adenine. + C to A transversion + sequence + SO:1000019 + C_to_A_transversion + + + + + A transversion from cytidine to adenine. + SO:ke + + + + + + + + + C to G transversion + sequence + SO:1000020 + C_to_G_transversion + + + + + + + + + A transversion from T to A. + T to A transversion + sequence + SO:1000021 + T_to_A_transversion + + + + + A transversion from T to A. + SO:ke + + + + + + + + + A transversion from T to G. + T to G transversion + sequence + SO:1000022 + T_to_G_transversion + + + + + A transversion from T to G. + SO:ke + + + + + + + + + Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. + purine to pyrimidine transversion + sequence + SO:1000023 + purine_to_pyrimidine_transversion + + + + + Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. + SO:ke + + + + + + + + + A transversion from adenine to cytidine. + A to C transversion + sequence + SO:1000024 + A_to_C_transversion + + + + + A transversion from adenine to cytidine. + SO:ke + + + + + + + + + A transversion from adenine to thymine. + A to T transversion + sequence + SO:1000025 + A_to_T_transversion + + + + + A transversion from adenine to thymine. + SO:ke + + + + + + + + + A transversion from guanine to cytidine. + G to C transversion + sequence + SO:1000026 + G_to_C_transversion + + + + + A transversion from guanine to cytidine. + SO:ke + + + + + + + + + A transversion from guanine to thymine. + G to T transversion + sequence + SO:1000027 + G_to_T_transversion + + + + + A transversion from guanine to thymine. + SO:ke + + + + + + + + + A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. + http://en.wikipedia.org/wiki/Indel + loinc:LA9659-9 + deletion-insertion + indel + sequence + SO:1000032 + Indels can have a different number of bases than the corresponding reference sequence. The term name was changed from indel to delins on 2/24/2019 to align with the HGVS nomenclature term for a deletion-insertion. Indel was causing confusion in the annotation community (github issue 445). The HGVS nomenclature definition of deletion-insertion (delins) is a sequence change where, compared to a reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution, inversion or conversion. + delins + + + + + A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. + http://varnomen.hgvs.org/recommendations/DNA/variant/delins/ + + + + + http://en.wikipedia.org/wiki/Indel + wiki + + + + + loinc:LA9659-9 + Insertion and Deletion + + + + + + + + + An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome. + loinc:LA6686-5 + nucleotide duplication + sequence + nucleotide_duplication + SO:1000035 + duplication + + + + + An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome. + EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html + NCBI:th + + + + + loinc:LA6686-5 + Duplication + + + + + + + + + + A continuous nucleotide sequence is inverted in the same position. + loinc:LA6689-9 + inversion + sequence + SO:1000036 + + + inversion + + + + + A continuous nucleotide sequence is inverted in the same position. + EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html + + + + + loinc:LA6689-9 + Inversion + + + + + inversion + http://www.ncbi.nlm.nih.gov/dbvar/ + + + + + + + + + + A tandem duplication where the individual regions are in the same orientation. + direct tandem duplication + sequence + SO:1000039 + direct_tandem_duplication + + + + + A tandem duplication where the individual regions are in the same orientation. + SO:ke + + + + + + + + + A tandem duplication where the individual regions are not in the same orientation. + inverted tandem duplication + sequence + mirror duplication + SO:1000040 + inverted_tandem_duplication + + + + + A tandem duplication where the individual regions are not in the same orientation. + SO:ke + + + + + + + + + A duplication consisting of 2 identical adjacent regions. + tandem duplication + sequence + erverted + SO:1000173 + + tandem_duplication + + + + + A duplication consisting of 2 identical adjacent regions. + SO:ke + + + + + erverted + http://www.ncbi.nlm.nih.gov/dbvar/ + + + + + + + + + + http://snpeff.sourceforge.net/SnpEff_manual.html + chromosome structure variation + snpEff:CHROMOSOME_LARGE_DELETION + sequence + SO:1000183 + chromosome_structure_variation + + + + + snpEff:CHROMOSOME_LARGE_DELETION + + + + + + + diff --git a/src/ontology/pre_odk/catalog-v001.xml b/src/ontology/pre_odk/catalog-v001.xml new file mode 100644 index 0000000..2341e5a --- /dev/null +++ b/src/ontology/pre_odk/catalog-v001.xml @@ -0,0 +1,9 @@ + + + + + + + + + diff --git a/src/ontology/pre_odk/geno_imports.owl b/src/ontology/pre_odk/geno_imports.owl new file mode 100644 index 0000000..256ec64 --- /dev/null +++ b/src/ontology/pre_odk/geno_imports.owl @@ -0,0 +1,25 @@ + + + + + + + + + + + diff --git a/src/ontology/pre_odk/oboInOwl.owl b/src/ontology/pre_odk/oboInOwl.owl new file mode 100644 index 0000000..2b8c2ae --- /dev/null +++ b/src/ontology/pre_odk/oboInOwl.owl @@ -0,0 +1,713 @@ + + + + + This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi + + OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties + + + + + + + + + + + + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + This annotation property groups all subsets declared in the ontology + + + subset_property + + + + + + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + This annotation property groups all synonym types declared in the ontology + + + synonym_type_property + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_consider + oboFormat:consider + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + Gives a term which may be an appropriate substitute for an obsolete term, but needs to be looked at carefully by a human expert before the replacement is done + + + consider + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_alt_id + oboFormat:alt_id + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + An alternative identifier for this class; should follow ID syntax. These can result from class merges + + + has_alternative_id + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_broad_synonym + oboFormat:broad_synonym + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis + + + has_broad_synonym + + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_date + oboFormat:date + + + has_date + + + + + + + + database_cross_reference + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_default-namespace + oboFormat:default-namespace + + + has_default_namespace + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_def + oboFormat:def + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + a relation between a class and an instance of a oboInOwl:Definition + + + we are forced to use the n-ary relation pattern in OWL1.0. For OWL2 we may make this a direct axiom between a class and the string + has_definition + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_exact_synonym + oboFormat:exact_synonym + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle + + + has_exact_synonym + + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_narrow_synonym + oboFormat:narrow_synonym + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + An alias in which the alias is narrower than the primary class name. Example: pyrimidine-dimer repair by photolyase is a narrow synonym of photoreactive repair + + + has_narrow_synonym + + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_namespace + oboFormat:namespace + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + A relation between a class and an OBO namespace string. OBO namespaces are to be distinguished from IDspaces; for example, biological_process is a namespace, GO is an idspace. + + + has_obo_namespace + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_related_synonym + oboFormat:related_synonym + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + An alias in which the alias is related the primary class name, but not necessarily broader or narrower. Example: cytochrome bc1 complex is a related synonym of ubiquinol-cytochrome-c reductase activity; virulence is a related synonym of pathogenesis + + + has_related_synonym + + + + + + + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + relation between an ontology and a oboInOwl:Subset, indicating classes in the ontology belong to the subset + + + has_subset + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_synonym + oboFormat:synonym + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + A relation between a class and an alias term. + + + Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL + has_synonym + + + + + + + + + + + http://www.geneontology.org/GO.usage.shtml#type + URL:http://www.geneontology.org/GO.usage.shtml#type + + + has_synonym_type + + + + + + + + has_URI + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_version + oboFormat:version + + + has_version + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_subset + oboFormat:subset + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + relation between a class and a oboInOwl:Subset, indicating the class belongs (is a member of) the subset + + + in_subset + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_is_cyclic + oboFormat:is_cyclic + + + + + + + + + is_cyclic + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_replaced_by + oboFormat:replaced_by + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + Gives a term which replaces an obsolete term. The value is the id of the replacement term. The value of this tag can safely be used to automatically reassign links to an obsolete term. The replaced_by tag may only be specified for obsolete terms. A single obsolete term may have more than one replaced_by tag. This tag can be used in conjunction with the consider tag. + + + replaced_by + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_saved_by + oboFormat:saved_by + + + saved_by + + + + + + + + + + + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + pseudo-property. in the oboInOwl translation, all obsolete relations are subProperties of this class + + + Note that this is not a metaclass + obsolete_property + + + + + + + + + + + + + database_cross_reference + + + + + + + + + + + http://www.obofoundry.org/wiki/index.php/Definitions + URL:http://www.obofoundry.org/wiki/index.php/Definitions + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + The textual definition of the current term. There must be zero or one instances of this tag per term description + + + we are forced to use the n-ary relation pattern in OWL1.0. For OWL2 we may make this a direct axiom between a class and the string + definition + + + + + + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + pseudo-class. in the oboInOwl translation, all obsolete classes are subclasses of this class. Note that this is not a metaclass + + + obsolete_class + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_subsetdef + oboFormat:subsetdef + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + A grouping of terms from an ontology or ontologies. Note that this is not a metaclass - classes are linked to subsets via oboInOwl:inSubset + + + + + + slim + + + + + + GO-slim + + + + + + view + + + + + + partition + + + subset + + + + + + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + An instance of synonym usage. synonym instances are linked to classes via oboInOwl:has*Synonym properties + + + we are forced to use the n-ary relation pattern in OWL1.0. For OWL2 we may make this a direct axiom between a class and the string + synonym + + + + + + + + synonym_type + + + + http://purl.org/obo/owl/oboFormat#oboFormat_xref + oboFormat:xref + + + + + + + diff --git a/src/ontology/pre_odk/ontology-metadata.owl b/src/ontology/pre_odk/ontology-metadata.owl new file mode 100644 index 0000000..a749335 --- /dev/null +++ b/src/ontology/pre_odk/ontology-metadata.owl @@ -0,0 +1,881 @@ + + + + en + $Revision$ + + + + + + + + + + + + + + + + + + + editor preferred term + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + editor preferred term + + + + + + + + example + + A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage + + + + + + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + + + + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition + + + + + + + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + editor note + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + alternative term + + + + + + + + definition source + + formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + + + + + + + + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + + + + + + is denotator type + relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from + + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + + + + + + + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + + + + + + + first order logic expression + PERSON:Alan Ruttenberg + first order logic expression + + + + + + + + antisymmetric property + part_of antisymmetric property xsd:true + use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + + + + + + OBO foundry unique label + + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + + + + + + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + has associated axiom(fol) + + + + + + + + is allocated id range + Add as annotation triples in the granting ontology + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + is allocated id range + + + + + + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + has axiom label + + + + + + + + term replaced by + + Add as annotation triples in the granting ontology + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + term replaced by + + + + + + + + A related resource from which the described resource is derived. + This relation can be used to link artifacts such as information to other information resources from with it was retrieved or derived in whole or in part. This includes cases where information was extracted and its structure modified, but not cases where significant modifications were made to its meaning or content. + The described resource may be derived from the related resource in whole or in part. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system. + source + + + + + + + + + + + + + + + + + + + + data item + + + + + + + + + information content entity + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification + + + + + + + + + + + + + + + + + + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + core + + + + + + + + + placeholder removed + + + + + + + + + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 701c51c10aa2b0871c7d3bce0b632603daef9299 Mon Sep 17 00:00:00 2001 From: matentzn Date: Mon, 9 Sep 2019 16:37:16 +0100 Subject: [PATCH 03/11] Create geno.owl --- src/ontology/pre_odk/geno.owl | 8198 +++++++++++++++++++++++++++++++++ 1 file changed, 8198 insertions(+) create mode 100644 src/ontology/pre_odk/geno.owl diff --git a/src/ontology/pre_odk/geno.owl b/src/ontology/pre_odk/geno.owl new file mode 100644 index 0000000..bcec2b8 --- /dev/null +++ b/src/ontology/pre_odk/geno.owl @@ -0,0 +1,8198 @@ + + + + + + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. + +Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 + + + + + + + + + + + + + Used to annotation axioms that define identity criteria for instances of a class. + is_identity_criteria + + + + + + + + + proabalistic_quantifier + + + + + + + + Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models. + mixin + + + + + + + + + gene symbol + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + begin + + + + + + + + + end + + + + + + + + + location + + + + + + + + + The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly. + reference + + + + + + + + + + + is part of + + + + + + + + + + has part + + + + + + + + + + + + + + + + + + A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'. + Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants. + http://purl.obolibrary.org/obo/so_has_quality + has_sequence_attribute + + + + + + + + + + + + A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes + materializes + Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence. + bears_concretization_of + + + + + + + + + is_genotype_of + + + + + + + + + + + + + + + + + + + A relationship that holds between a biological entity and some level of genetic variation present in its genome. + This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype. + The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations. + has_genotype + + + + + + + + + + + An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO) + No proper part relation anymore in RO/BFO? + http://semanticscience.org/resource/SIO_000053 + has_proper_part + + + + + + + + + + A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears. + has_sequence_component + has_state + VMC:state + 'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule. + has_sequence + + + + + + + + + + A geno:intrinnsic genotype 'specifies' a SO:genome. +A geno:karyotype 'specifies' a geno:karyotype feature collection. + A relationship between an information content entity representing a specification, and the entity it specifies. + obsolete_specifies + + + + + + + + + Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. + obsolete_approximates_sequence + + + + + + + + + Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. + obsolete_resolves_to_sequence + + + + + + + + + An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole. + http://semanticscience.org/resource/SIO_000093 + is_proper_part_of + + + + + + + + + is_sequence_of + + + + + + + + + is_subject_of + + + + + + + + + obsolete_is_specified_by + + + + + + + + + + shortcut relation used to link a phenotype directly to a genotype of an organism + is_phenotype_of_organism_with_genotype + is_phenotype_with_genotype + phenotype_has_genotype + Might expand to something like: + +phenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype))))))) + obsolete_is_phenotype_of_genotype + + + + + + + + + + A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next. + Exploratory/temporary property, as we formalize our phenotypic inheritance model. + obsolete_participates_in_inheritance_process + + + + + + + + + + + A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression. + has_variant_part + + + + + + + + + + is_variant_part_of + + + + + + + + + + + A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant. + has_reference_sequence_part + has_reference_part + + + + + + + + + is_reference_part_of + + + + + + + + + + + <fgf8a^ti282a> is_allele_of the 'danio rerio fgf8a' gene locus. + A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size. + Domain = allele +Range = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation). + Note that the allele <fgf8a^ti282a> is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the <fgf8a^ti282a> allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product. + is_sequence_variant_of + To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size). + +While conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like "fgf8a<ti282a> is an allele of the Danio rerio fgf8a gene", and we may create data where fgf8a<ti282a> is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene). + +It is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. + +This departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\GAL4 gene. + +At the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'. + is_allele_of + + + + + + + + + + A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level). + is_variant_instance_of + formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus) + Domain = genomic feature instance +Range = punned gene class IRI + obsolete_is_genetic_variant_of + + + + + + + + + A relation linking a gene class to a sequence-varaint or expression-variant of the gene. + has_variant_instance + formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by) + Domain = punned gene class +Range = genomic feature + obsolete_has_genetic_variant + + + + + + + + + A relation linking a gene class to one of its sequence-variant alleles. + Domain = punned gene class +Range = allele + has_sequence_variant + has_allele + + + + + + + + + + A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets. + This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets. + targets_gene + + + + + + + + + + + + + + + + + A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression. + This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset. + has_affected_feature + + + + + + + + + + A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents. + Domain = expression variant feature. +Range = punned gene class + This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class. + is_expression_variant_of + + + + + + + + A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature. + class_to_feature_relation + This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases) + is_feature_affected_by + + + + + + + + + A relation between a gene class and a gene targeting reagent that targets it. + is_target_of + Domain = punned gene class +Range = gene knockdown reagent + is_gene_target_of + + + + + + + + + A relation linking a gene class to one of an expression-variant of that gene.. + Domain = punned gene class +Range = expression variant feature + has_expression_variant_instance + has_expression_variant + + + + + + + + + A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression. + Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property. + This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of. + obsolete_is_variant_with + + + + + + + + + A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways). + obsolete_is_expression_variant_with + + + + + + + + A relation used to describe a context or conditions that define and/or identify an entity. + Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association. + +Used in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features. + has_qualifying_context + has_qualifier + + + + + + + + + + + a relation to link a single locus complement to its zygosity. + has_zygosity + + + + + + + + + + A relationship between a reference locus/allele and the gene class it is an allele of. + is_reference_allele_of + + + + + + + + + Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed. + has_color_value + Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized. + has_staining_intensity + + + + + + + + Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant. + relation between an molecular agent and its molecular target + is_targeted_by + + + + + + + + + + + + + 1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. + +2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds. + +3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC) + Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence. + sequence_derives_from + + + + + + + + + + A relationship between a variant allele and the gene class it is an allele of. + is_variant_allele_of + + + + + + + + + + Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases. + has_sex_agnostic_part + + + + + + + + + + A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of. + is_mutant_allele_of + + + + + + + + + + A relationship between a polymorphic allele and the gene class it is an allele of. + is_polymorphic_allele_of + + + + + + + + + + A relationship between a wild-type allele and the gene class it is an allele of. + is_wild_type_allele_of + + + + + + + + + + An organizational class to hold relations of parthood between sequences/features. + has_sequence_part + + + + + + + + + is_sequence_part_of + + + + + + + + + Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases. + is_sex_agnostic_part_of + + + + + + + + + A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part). + This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of) + varies_with + + + + + + + + organizational property to hold imports from faldo. + faldo properties + + + + + + + + + + + + + + + + + A relation linking a qualified sequence feature to its component sequence feature. + has_sequence_feature_component + In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism. + has_sequence_feature + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_inferred_phenotype + + + + + + + + + Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype. + + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration. + + + + + + + + + + Property chain to propagate inferred phenotype associations from an intrinsic genotype component (e.g. a (sequence-)variant locus instance) to a gene class. + + + + + + + + + Property chain to propagate inferred phenotype associations from a (sequence-)variant locus instance to a gene class (to support cases where the phenotype association is made at the level of the variant gene locus). + + + + + + + + + + Property chain to propagate inferred phenotype associations from an extrinnsic genotype component (e.g. a expression-variant gene instance) to a gene class. + + + + + + + + + Property chain to propagate inferred phenotype associations from an expression-variant gene instance to a gene class (to support cases where the phenotype association is made at the level of the expression-variant gene). + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components) + + + + + + + + + Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes. + obsolete_has_regulatory_part + + + + + + + + + + + + + + A relation linking a sequence_alteration to the gene it alters. + is_within_allele_of + obsolete_is_alteration_within + + + + + + + + + has_asserted_phenotype + + + + + + + + + Proposal for a property linking regulatory elements to larger features of which they are a part. + is_regulatory_part_of + + + + + + + + + A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances. + For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them. + obsolete_has_position_component + + + + + + + + + A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues) + has_sequence_unit + + + + + + + + + + A relation between two seqeunces or features that are considered variant with each other along their entire extents. + completely_varies_with + + + + + + + + related_condition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene) + The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains. + +Below are the different kinds/paths of propagation we desire: +1. Propagation 'down' a genotype (from larger components to smaller ones) +2. Propagation 'up' a genotype (from smaller components to larger ones) +3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype). +4. From an effective genotype to its intrinsic and extrinsic components. +5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele). +6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this. + +Note that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha<tbx392>/shha<tbx392> [AB] to shha<tbx392>/shha<tbx392> [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition') + inferred_to_cause_condition + + + + + + + + + + This is a case of inter-gneotype phenotype propagation, requiring propagation down oen genotype and then up another. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to have this chain. + +This property chain propagates a phenotype asserted on a sex-qualified intrinsic genotype, down to its sex-agnostic genotype part, and then up to a parent effective genotype that has it as a variant part. I think this is OK in all cases, so we can implement this as the one case where we can have inter-genotype pheno propagation. But as noted, there will likely be no data that actually meets criteria to use this chain, so we can probably leave it out. + + + + + + + + + Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype. + + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, to the coompnent variant parts of this sex-agnostic genotype. + + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to move past the sex-agnostic genotype and down to its parts. + +The following shorter chain would also suffice here: +is_variant_part_of o inferred_to_cause_condition + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration. + + + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, through the coompnent variant parts of this sex-agnostic genotype, and to the affected gene. + + + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to propagate to genes. + +The shorter chain below would also suffice for this propagation: +has_allele o inferred_to_cause_condition + + + + + + + + + + Property chain to propagate inferred condition associations from an sequence alteration through the variant locus to a gene class. (separate chains are needed to propagate from the variant locus to the gene class, and another to propagate from a genotype, GVC, or VSLC to the gene class). + + +NOTE that i dont need this property chain if I have a property chain to infer a has_affected_locus link from a sequence alteration to a gene when the link is asserted from the variant locus to the gene: + +is_variant_part_of o has_affected_locus --> has_affected_locus + + + + + + + + + + Obsolete comment: Property chain to propagate inferred condition associations from an intrinsic genotype, GC, or VLSC to a gene class. (a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class). + +The following, shorter chain, would also suffice here: +has_allele o inferred_to_cause_condition -> inferred_to_cause_condition + Property chain to propagate inferred condition associations from an intrinsic genotype, GVC, or VLSC to an affected gene class, or from an extrinsic gneotype or component to an affected gene class. + +The following, shorter chain, would also suffice here: +has_affected_locus o inferred_to_cause_condition -> inferred_to_cause_condition + +Note that a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class in cases where the link to gene is through the variant locus rather than the seq alteration). + + + + + + + + + Property chain to propagate inferred condition associations from a variant locus instance to a gene class (to support cases where the phenotype association is made directly at the level of the variant locus/allele). + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype to a sex-agnostic intrinsic genotype. + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components) + + + + + + + + + inferred_to_contribute_to_condition + + + + + + + + + inferred_to_correlate_with_condition + + + + + + + + + LOINC:LA6668-3 + pathogenic_for_condition + + + + + + + + + LOINC:LA26332-9 + likely_pathogenic_for_condition + + + + + + + + + Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to. + non-causal_for_condition + + + + + + + + + LOINC:LA6675-8 + benign_for_condition + + + + + + + + + LOINC:LA26334-5 + likely_benign_for_condition + + + + + + + + + LOINC:LA26333-7 + has_uncertain_significance_for_condition + + + + + + + + + A relation used to describe a process contextualizing the identity of an entity. + has_qualifying_process + + + + + + + + + A relation used to describe an environment contextualizing the identity of an entity. + has_qualifying_environment + + + + + + + + + is_candidate_variant_for + + + + + + + + + + A relation linking a sequence feature to the location it occupies on some reference sequence. + occupies + has_location + + + + + + + + Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from. + on strand + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location. + +For copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. + has_defining_location + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement. + has_defining_sequence + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference. + +For copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. + has_defining_feature + + + + + + + + + Relates a sequence feature location to an interval that defines its start and end position. + Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects. + has_interval + + + + + + + + Relates a 'sequence feature location' to a sequence that it is anchored to. + has_reference_sequence + + + + + + + + is_about is a (currently) primitive relation that relates an information artifact to an entity. + is about + + + + + + + + + Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically + Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of. + denotes + + + + + + + + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + has_specified_input + + + + + + + + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + has_specified_output + + + + + + + + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + inheres_in + + + + + + + + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + bearer of + + + + + + + + + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates in + + + + + + + + a relation between a process and a continuant, in which the continuant is somehow involved in the process + has participant + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + has quality + + + + + + + + + has_role + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + derives from + + + + + + + + + starts during + + + + + + + + + ends during + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + overlaps + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + in taxon + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + has phenotype + + + + + + + + + phenotype of + + + + + + + + temporally related to + + + + + + + + + p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + has input + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + has output + + + + + + + + + + is member of + + + + + + + + + Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes + +Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component + has member is a mereological relation between a collection and an item. + has member + + + + + + + + + input of + + + + + + + + + output of + + + + + + + + + obsolete_formed as result of + + + + + + + + Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b + molecularly controls + + + + + + + + + x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + Chris Mungall + bounds sequence of + + + + + + + + + + x has subsequence y iff all of the sequence parts of x are sequence parts of y + has subsequence + + + + + + + + + is subsequence of + + + + + + + + + x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. + http://biorxiv.org/content/early/2014/06/27/006650.abstract + overlaps sequence of + + + + + + + + inverse of downstream of sequence of + is upstream of sequence of + + + + + + + + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + is downstream of sequence of + + + + + + + + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + Matthew Brush + The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + is model of + + + + + + + + + The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. + +An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition. + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. + causes or contributes to condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition. + causes condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition. + contributes to condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual. + contributes to expressivity of condition + contributes to severity of condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population. + contributes to penetrance of condition + contributes to frequency of condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. + is preventative for condition + + + + + + + + + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + correlated with condition + + + + + + + + association has object + + + + + + + + association has predicate + + + + + + + + association has subject + + + + + + + + + + + + + The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is. + position + + + + + + + + + Property linking a sequence or sequence feature to an integer representing its length in terms of the number of units in the sequence. + has_extent + + + + + + + + + + Shortcut relation linking a sequence feature directly to a string representing the 'state' of its sequence - i.e. the ordering of units that comprise it (e.g. 'atgcagctagctaccgtcgatcg'). + has_sequence_string + + + + + + + + ObsoleteDataProperty + + + + + + + + The 'rank' quantifier in Bgee gene-anatomy associations, that indicates the imporatnace/specificity of a gene expression in a given anatommy relative to expressionin other anatomies for the same gene. + Property to link an assertion or association with some value quantifying its relevance or ranking. + has_quantifier + + + + + + + + The starting position of a sequence feature or interval. + start_position + + + + + + + + The ending position of a sequence feature or interval. + end_position + + + + + + + + + + Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg'). + has_string + + + + + + + + Describes the number of members in some set. + has_count + In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'. + has_member_count + + + + + + + + + + + + + + Both strands + + + + + + + + + A position that is exactly known. + Exact position + + + + + + + + + Positive strand + + + + + + + + + Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate. + We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region). + FALDO + Position + + + + + + + + + + + + + + 1 + + + + + 1 + + + + + + A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene. + From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence. + Region + + + + + + + + + Negative strand + + + + + + + + + Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'. + Stranded position + + + + + + + + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + + + + + + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + continuant + continuant + + + + + + + + + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + occurrent + occurrent + + + + + + + + + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + independent continuant + independent continuant + + + + + + + + + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + + process + process + + + + + + + + + + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocitosis and exocitosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89 + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + + disposition + disposition + + + + + + + + + + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + realizable entity + realizable entity + + + + + + + + + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + + quality + quality + + + + + + + + + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + specifically dependent continuant + specifically dependent continuant + + + + + + + + + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + role + role + + + + + + + + + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + generically dependent continuant + generically dependent continuant + + + + + + + + + the function of a hammer to drive in nails + the function of a heart pacemaker to regulate the beating of a heart through electricity + the function of amylase in saliva to break down starch into sugar + BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + + function + + + + + + + + + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + material entity + material entity + + + + + + + + + Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology. + molecular entity + + + + + + + + + nucleic acid + + + + + + + + + + + + + + + A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). + cell line + + + + + + + + + Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies. + cell + + + + + + + + + 1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions. + +2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity). + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system + + + + + + + + + A technique is a planned process used to accomplish a specific activity or task. + technique + + + + + + + + + A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo. + embryonic stem cell line + + + + + + + + + A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types. + stem cell line + + + + + + + + + Example zebrafish intrinsic genotype: + +Genotype = fgf8a<ti282a/+>; shha<tb392/tb392> (AB) +reference component (genomic background) = AB +variant component ('genomic variation complement') = fgf8a<ti282a/+>; shha<tb392/tb392> + +. . . and within this variant component, there are two 'variant single locus complements' represented: + +allele complement 1 = fgf8a<ti282a/+> +allele complement 2 = shha<tb392/tb392> + +and within each of these 'variant single locus complements' there is one or more variant gene locus member: + +in complement 1: fgf8a<ti282a> +in complement 2: shha<ttb392> + A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement) + This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). + +Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. + genotype + organismal genotype + sex-agnostic intrinsic genotype + In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances). + genomic genotype (sex-agnostic) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An allele that varies in it sequence from what is considered the reference or canonical sequence at that location. + The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles. + alternate allele + sequence-variant feature + variant feature + Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another. + +A variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence. + variant allele + + + + + + + + + + + + + + + + + + + A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype. + Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases. + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation. + +In model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a<t1282a/+>(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)). + genomic variation complement + + + + + + + + + The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB) + A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). + Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it. + genomic background + OBI:genetic population background information + background genome + + + + + + + + + + + + + + + The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The "mn004Gt" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome. + +http://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722 + +http://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8 + A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene) + Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment). + +This design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not. + http://purl.obolibrary.org/obo/SO_0001023 ! allele + In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion. + +A genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene. + gene allele + + + + + + + + + + + + + + + + + + + A sequence that serves as a standard against which other sequences at the same location are compared. + The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant. + reference sequence + A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence. + reference sequence + + + + + + + + + a collection more than one sequence features (ie a collection of discontinuous sequence features) + perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one) + 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. + obsolete_sequence feature collection + + + + + + + + + A sequence feature collection comprised of discontiguous sequences from a single genome + Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system. + genomic feature collection + Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. + obsolete_genomic feature collection + + + + + + + + + A single locus complement that serves as a standard against which 'variant' sequences are compared + reference allelic complement + reference single locus feature complement + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class axiom: +'single locus complement' + and (has_sequence_attribute some reference) + +SC axioms: +'has member' exactly 0 'variant allele' +'has member' only 'reference genomic feature' +'has member' some 'reference genomic feature' + obsolete_reference single locus complement + + + + + + + + + + + + + + + + + + + A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13). + variant allelic complement + Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members. + +Note that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant. + variant single locus complement + + + + + + + + + + + + + + + + + + + + + + + + + A genome that varies at one or more loci from the sequence of some reference genome. + http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here) + variant genome + + + + + + + + + + + + + + + + + + + An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome. + Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population. + +In model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared. + reference allele + + + + + + + + + + A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus). + Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '. + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class def: 'genomic feature' + and (has_sequence_attribute some unspecified) + An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). + obsolete_unspecified feature + + + + + + + + + A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature. + hemizygous reference junction + Eliminating unecessary defined/organizational classes. Former logical def: + +junction + and (has_sequence_attribute some reference) + +Subclass axiom: +is_variant_with some insertion + In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. + +The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. + obsolete_reference junction + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a danio rerio. + danio rerio gene + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a homo sapiens. + homo sapiens gene + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a mus musculus. + mus musculus gene + + + + + + + + + A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development. +http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690 + +Note that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469 + A version/allele of a gene that serves as a standard against which variant genes are compared. + reference gene + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class axiom: +'gene allele' + and (has_sequence_attribute some reference) + +SC axioms: +is_variant_with some 'gene allele' +is_reference_allele_of some gene + Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. + +In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. + obsolete_reference gene allele + + + + + + + + + obsolete_experimental insertion + + + + + + + + + + + + + + + gene trap insertion + + + + + + + + + + + + + + + A transgene that has been integrated into a chrromosome in the host genome. + An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion. + +An 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome. + integrated transgene + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny. + 1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. + +2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way. + 1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. + +2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms. + genomic material + + + + + + + + + A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion. + physical genome + A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements. + +Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome. + material genome + + + + + + + + + a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role) + Consider http://semanticscience.org/resource/SIO_001062 ! human population ("A human population refers to a collection of human beings"). + homo sapiens population + human population + + + + + + + + + + + + + + + A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical. + organism strain or breed + Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR) + strain or breed + + + + + + + + + A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon) + taxonomic group + + + + + + + + + mus musculus strain + + + + + + + + + + + + + + + + + + + + + danio rerio strain + + + + + + + + + sequence attribute that can inhere only in a collection of more than one sequence features + obsolete_sequence feature collection attribute + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes). + in cis + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes). + in trans + + + + + + + + + + + + + + + An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different). + allelic state + derived from https://en.wikipedia.org/wiki/Zygosity + http://semanticscience.org/resource/SIO_001263 + zygosity + + + + + + + + + hemizygous + + + + + + + + + heterozygous + + + + + + + + + homozygous + + + + + + + + + indeterminite zygosity + no-call zygosity + unknown zygosity + unspecified zygosity + + + + + indeterminite zygosity + MGI uses this term when zygosity is not known. + + + + + no-call zygosity + (this is how the GVF10 format/standard refers to loci without enough data to make an accurate call . . . see http://www.sequenceontology.org/resources/gvf.html#quick_gvf_examples) + + + + + + + + + The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event. + We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells). + +We can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms. + heritabililty + + + + + + + + + heritable + + + + + + + + + non-heritable + + + + + + + + + The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment. + The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family. + mode of inheritance + phenotypic inheritance pattern + http://purl.obolibrary.org/obo/HP_0000005 + http://purl.obolibrary.org/obo/NCIT_C45827 + An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, "genetic context" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. + +These genetic and environmental "interactions" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y. + inheritance pattern + + + + + + + + + disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes + Triage until decide if want to define this as grouping class that would result in multiple-inheritance. + obsolete_dominant inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant autosomal inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + pure dominant inheritance + complete autosomal dominant inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + intermediate dominant autosomal inheritance + semi-dominant autosomal inheritance + incomplete autosomal dominant inheritance + + + + + + + + + An X-linked inheritance pattern wherein the trait manifests in heterozygotes. + http://purl.obolibrary.org/obo/HP_0001423 + X-linked dominant inheritance + + + + + + + + + An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes. + vertical inheritance + http://purl.obolibrary.org/obo/HP_0000006 + autosomal dominant inheritance + + + + + + + + + An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals. + autosomal recessive inheritance + + + + + + + + + An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals. + http://purl.obolibrary.org/obo/HP_0001419 + X-linked recessive inheritance + + + + + + + + + duplicate term, use GENO:0000148 + obsolete_autosomal recessive inheritance + + + + + + + + + An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared. + Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another. + reference + + + + + + + + + unspecified life cycle stage + + + + + + + + + objective is to insert some specified sequence into the genome of a cell or virus + genetic insertion technique + + + + + + + + + mutagen treatment technique + + + + + + + + + + + + + + + a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). + This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. + targeted gene mutation technique + + + + + + + + + Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. + random genetic insertion technique + + + + + + + + + + + + + + + targeted genetic insertion technique + + + + + + + + + + + + + + + enhancer trapping technique + + + + + + + + + + + + + + + gene trapping technique + + + + + + + + + + + + + + + promoter trapping technique + + + + + + + + + + + + + + + targeted knock-in technique + + + + + + + + + random transgene insertion technique + + + + + + + + + A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome + obsolete_chromosome complement + + + + + + + + + + + + + + + + A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation + duplicate chromosome + This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome. + gained aneusomic chromosome + + + + + + + + + + + + 0 + + + + A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation. + This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as "the point at which one or more contiguous nucleotides were excised". + absent aneusomic chromosome + lost aneusomic chromosome + + + + + + + + + + + + + + + + + + + + + + A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation. + Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism. + aneuploid chromosomal segment + aneusomic chromosomal subregion/segment + partial aneusomic chromosomal element + Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome." + aneusomic chromosomal part + + + + + + + + + + A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event. + duplicate partial aneuploid chromosomal element + translocated duplicate chromosomal element + translocated duplicate chromosomal segment + Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location. + gained aneusomic chromosomal segment + + + + + + + + + + + + 0 + + + + A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome. + In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement + dropped partial anneuploid chromosomal element + translocated absent chromosomal segment + truncated chromosome terminus + This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome. + +Loss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus. + lost aneusomic chromosomal segment + + + + + + + + + + + + + + + + + A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation + complete aneusomic chromosome + Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism. + +Similarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication. + aneusomic chromosome + + + + + + + + + Stub class to serve as root of hierarchy for imports of biological processes from GO-BP. + biological process + + + + + + + + + disomic zygosity + + + + + + + + + aneusomic zygosity + + + + + + + + + trisomic homozygous + + + + + + + + + trisomic heterozygous + + + + + + + + + A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a<ti282a>/fgf8a<x15>) + trans-heterozygous + compound heterozygous + + + + + + + + + A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe) + replaced with SO:engineered_region + extra-genomic sequence + obsolete_reagent sequence feature + + + + + + + + + a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a<ti282a/+>) + simple heterozygous + + + + + + + + + + + + + + + + + + + A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc) + transgene part + + + + + + + + + An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level + variant + + + + + + + + + An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant. + polymorphic + + + + + + + + + An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence. + mutant + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism) + This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology. + 1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. + +2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). + +3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome. + genomic feature + + + + + + + + + + A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion). + This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material. + genetic material + + + + + + + + + + An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain. + Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines + Not required for any specific use case at this point so removed for simplicity. +Formely asserted as allele and inferred as varaint allele. +Eq class definition: +allele + and (mutation or ('has subsequence' some mutation)) + 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. + obsolete_mutant allele + + + + + + + + + + + + + + + A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain. + mutation + + + + + + + + + + + + + + + + + + + + + + + + + + + A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon) + Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element + episomal replicon + Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. + extrachromosomal replicon + + + + + + + + + expression construct feature + expression construct + + + + + + + + + An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population. + PMID: 25741868 ACMG Guidelines + Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%). + polymorphic allele + + + + + + + + + A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location. + major allele + major polymorphic allele + + + + + + + + + A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location). + minor allele + minor polymorphic allele + + + + + + + + + A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree. + ancestral allele + ancestral polymorphic allele + + + + + + + + + + + + + + + An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared. + wild-type allele + 'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain. + +The notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis. + wild-type allele + + + + + + + + + + wild-type gene allele + A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation. + wild-type gene + + + + + + + + + + + + + + + + + + + + + A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi. + The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position. + reagent targeted gene + + + + + + + + + A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome). + experimentally-expressed transgene + extrinsic transgene + transiently-expressed transgene + + + + + + + + + An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared. + wild-type + + + + + + + + + + + + + + + + + + + One of a set of sequence features known to exist at a particular genomic location. + A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene. + +To be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene. + +[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17) +[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17) +[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17) +[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17) +[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17) +[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17) +[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483 +[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17) +[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17) +[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17) +[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17) +[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17) + variable feature + An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). + +Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence). + allele + + + + + + + + + + a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation. + aneusomic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An allele of a gene that contains some sequence alteration. + A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset. + variant gene allele + + + + + + + + + The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a<ti282a/+>. + +The collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome. + A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism. + TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label. + allelic complement + homologous allele complement + single locus feature complement + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes. + +The fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. + single locus complement + + + + + + + + + In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as: + + shha<MO1-1ng/ul>; shhb<pFLAG-mmusShhb> + +This notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct. + A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state. + We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. + +Our rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. + +Finally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." + experimental genotype + expression genotype + An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment. + +The 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations. + extrinsic genotype + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs). + Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." + An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment. + effective genotype + + + + + + + + + + + + + + + A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes). + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment. + reagent-targeted gene complement + + + + + + + + + + + + + + + The set of all transgenes trransiently expressed in a biological system in the context of a given experiment. + experimental transgene complement + transiently-expressed transgene complement + + + + + + + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes). + A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism). + See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself. + expression allele + Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism). + +The identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system. + expression-variant gene + + + + + + + + + gene targeting reagent + sequence targeting reagent + gene knockdown reagent + + + + + + + + + A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent. + targeted gene segment + reagent-targeted gene subregion + + + + + + + + + + + + + + + + + + + + + + A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference. + As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh<tbx292>, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above. + Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). +Note however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO. + 1. Scope of 'Genetic State': +'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs. + +2. Genotype Subtypes: +In GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. + +Two more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features. + +3. The Genotype Partonomy: +'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a<ti282a/ti282a>; fgf3<t24149/+>[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements: + + - GVC: fgf8a<ti282a/ti282a>; fgf3<t24149/+> (total intrinsic variation in the genome) + - Genomic Background: AB (the reference against which the GVC is variant) + - VSLC1: fgf8a<ti282a/ti282a> (homozygous complement of gene alleles at one known variant locus) + - VSLC2: fgf3<t24149/+> (heterozygous complement of gene alleles at another known variant locus) + - Allele 1: fgf8a<ti282a> (variant version of the fgf8a gene, present in two copies) + - Allele 2: fgf3<t24149> (variant version of the fgf3 gene, present in one copy) + - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy) + - Sequence Alteration1: <ti282a> (the specific mutation within the fgf8a gene that makes it variant) + - Sequence Alteration2: <t24149> (the specific mutation within the fgf3 gene that makes it variant) + +A graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md + +One reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data. + genotype + + + + + + + + + ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl +This ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes. + zebrafish phenotype + + + + + + + + + an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. + homoplasmic + + + + + + + + + an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. + heteroplasmic + + + + + + + + + hemizygous X-linked + + + + + + + + + hemizygous Y-linked + + + + + + + + + hemizygous insertion-linked + + + + + + + + + + + + + + + + + + + + + + + + + A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). + Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it. + background genotype + genomic background + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. + New term request for SO. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosomal region + + + + + + + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosome sub-band + + + + + + + + + chromosomal band brightness + chromosomal band intensity + + + + + + + + + gpos + + + + + + + + + gneg + + + + + + + + + gvar + + + + + + + + + gpos100 + + + + + + + + + gpos75 + + + + + + + + + gpos50 + + + + + + + + + gpos25 + + + + + + + + + A chromosome arm that is the shorter of the two arms of a given chromosome. + p-arm + stalk + short chromosome arm + + + + + + + + + A chromosome arm that is the longer of the two arms of a given chromosome. + q-arm + long chromosome arm + + + + + + + + + gpos66 + + + + + + + + + gpos33 + + + + + + + + + + + + + + + A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed. + regulatory transgene region + + + + + + + + + + + + + + + A transgene part whose sequence is expressed in a gene product through transcription and/or translation. + coding transgene feature + expressed transgene region + + + + + + + + + reporter region + + + + + + + + + + + + + + + + + + + + + + + + + A transgene whose product is used as a selectable marker. + selectable marker transgene + + + + + + + + + + + + + + + A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell. + Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28) + Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). + +A base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation). + karyotype + + + + + + + + + + + + + + + A genomic genotype where the genomic background specifies a male or female sex chromosome complement. + This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). + +In the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former. + intrinsic genotype (sex-specific) + sex-qualified genotype + sex-qualified intrinsic genotype + We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances. + +Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. + genomic genotype (sex-qualified) + + + + + + + + + A genomic genotype here the genomic background specifies a male sex chromosome complement. + male intrinsic genotype + + + + + + + + + A genomic genotype here the genomic background specifies a female sex chromosome complement. + female intrinsic genotype + + + + + + + + + A background genotype whose sequence or identity is not known or specified. + unspecified background genotype + unspecified genomic background + + + + + + + + + + + + + + + + + + + + + 1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus + +2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele. + +3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y} + A set of sequence features. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature). + +The notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3]. + +[1] https://www.snpedia.com/index.php/APOE-%CE%B54 +[2] https://www.snpedia.com/index.php/APOE-%CE%B52 +[3] https://www.snpedia.com/index.php/Gs270 + sequence feature set + + + + + + + + + + + + + + + + + + + + + A set of genomic features (i.e. sequence features that are of genomic origin). + In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member. + genomic locus complement + A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature. + +The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. + genomic feature set + + + + + + + + + + + + + + + + + + + A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc). + defined gene part + SO:0000831 (gene member region) + gene part + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A transgene that codes for a product used as a reporter of gene expression or activity. + reporter transgene + + + + + + + + + A junction between bases, a deletion variant, a terminus at the end of a chromosome. + A genomic feature that has an extent of zero. + Former logical def: +'genomic feature' + and (has_extent value 0) + obsolete_null feature + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found. + aberrant extrachromosomal replicon + exogenous extrachromosomal replicon + transgenic extrachromosomal replicon + Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. + novel extrachromosomal replicon + + + + + + + + + + + + + + + + A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome. + This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature. + Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles. + novel replicon + + + + + + + + + An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome. + novel + + + + + + + + + A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide). + terminus + + + + + + + + + + + + + + + + + A sequence feature or a set of such features. + sequence feature or collection + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location. + sequence feature or set + + + + + + + + + + + + + + + + + A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides). + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + biomacromolecular sequence + state + VMC:State + 'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome. + biological sequence + + + + + + + + + + + true + + + + + state + In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele. + + + + + + + + + A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification. + qualified sequence feature or collection + + + + + + + + + + + + + + + + + + + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes). + A qualified sequence feature that carries sequence derived from the genome of a cell or organism. + qualified genomic feature + + + + + + + + + + + true + This axiom is an initial attempt to formalize the identity criteria of an extrinnsic context that separates qualified sequence features from sequence features (i.e. the context of its material bearer). As we further develop our efforts here this will get refined and more precise. + + + + + + + + + + + true + Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position). + + + + + + + + + + + + + + + + + + + + + + + + + + + A set of qualified sequence features that carry genomic sequence. + Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member. + A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele. + +A complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome. + qualified genomic feature set + + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. + Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome. + 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. + +2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. + intrinsic genotype + + + + + + + + + + + + + + + + + + + + + + + DNA sequence + + + + + + + + + + + + + + + + + + + + + + + RNA sequence + + + + + + + + + + + + + + + + + + + + + + + amino acid sequence + + + + + + + + + obsolete_biological sequence or collection + + + + + + + + + obsolete_biological sequence collection + + + + + + + + + + A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature. + As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell). + location-qualified sequence feature + + + + + + + + + A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct) + expression-qualified sequence feature + + + + + + + + + A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence. + This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature. + genomic coordinates + remodeling notion of sequence feature position around the idea of a 'genomic locus' + obsolete_genomic position + + + + + + + + + phenotypic inheritance process + + + + + + + + + A sequence attribute inhering in a feature whose identity is not specified. + obsolete_unspecified + + + + + + + + + An attribute describing a type of variation inhering in a sequence feature or collection. + allele attribute + variation attribute + + + + + + + + + + + + + + + + + + + An intrinsic genotype that specifies variation from a defined reference genome. + variant genomic genotype + + + + + + + + + An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities. + eliminating classes that are not necessary or add uneeded complexity. + obsolete_sequence information entity + + + + + + + + + + + + + + 1 + + + + + biological sequence residue + monomeric residue + biological sequence unit + + + + + + + + + deoxyribonucleic acid residue + DNA residue + + + + + + + + + ribonucleic acid residue + RNA residue + + + + + + + + + amino acid residue + + + + + + + + + An attribute, quality, or state of a sequence feature or collection. + http://purl.obolibrary.org/obo/SO_0000400 + Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity. + sequence feature attribute + + + + + + + + + + The location of a sequence feature as defined by its start and end position on some reference coordinate system. + 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). + +2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there. + sequence feature location + + + + + + + + + + A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature) + modification-qualified sequence feature + + + + + + + + + + + + + + + + + + + 1. The zebrafish "fgf8a<ti282a>/fgf8a<+>" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state). + +2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308. + + ##fileformat=VCFv4.2 + ##FORMAT=<ID=GT, Description="Genotype, 0=REF, 1=ALT"> + #CHROM POS REF ALT FILTER FORMAT SAMP001 + 20 2300608 C T PASS GT 0/1 + 20 2301308 T G PASS GT 1/1 + (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html) + +3. Some allelic genotype formats encode the genotype as a single string - e.g. "GRCh38 Chr12:258635(A;T)" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12. + A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes. + single locus genotype + An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location. + +This contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background. + allelic genotype + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each. + genotype-phenotype association + + + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + + + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + true + + + + + + + + + + + + + + + knockdown reagent targeted gene complement + + + + + + + + + + A sequence alteration within the coding sequence of a gene. + Not required at this poitn, so marked exploratory and obsoleted. +Asserted under sequence_alteration. + obsolete_coding sequence alteration + + + + + + + + + A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome. + P-element construct + + + + + + + + + An engineered region that is used to transfer foreign genetic material into a host cell. + engineered_genetic_vector + Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. + +Constructs are typically packaged as part of delivery systems such as plasmids or viral vectors. + engineered genetic construct + + + + + + + + + A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct. + non-integrated transgene + extra-chromosomal transgene + + + + + + + + + A collection of more than one sequence feature. + http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection + obsolete_sequence feature collection + + + + + + + + + + + + + + + A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block. + Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block. + +Instead, we can create an 'allele set' class as the haplotype parent? + Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype. + A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. + +As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': + +1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. + +2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). "Star alleles" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/). + +3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. + +Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. + haplotype + + + + + + + + + A set of genomic sequences (a biological sequence that is of genomic origin). + copy number complement + A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. + genomic sequence set + + + + + + + + + A relation used to describe an environment contextualizing the identity of an entity. + microsatellite alteration + + + + + + + + + A relation used to describe a process contextualizing the identity of an entity. + repeat region alteration + + + + + + + + + A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism + allelic state + + + + + + + + + allelic dosage + an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome. + gene dosage + Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute. + Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. + +Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. + obsolete_genetic dosage + + + + + + + + + A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent. + genetic origin + variant origin + allele origin + + + + + + + + + Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg. + maternally inherited + maternal allele origin + + + + + + + + + Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm. + paternally inherited + paternal allele origin + + + + + + + + + Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis. + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. + +De novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder. + de novo allele origin + + + + + + + + + Describes an allele whose origin is not known. + unknown allele origin + + + + + + + + + Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body. + acquired + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells. + +These acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations. + somatic allele origin + + + + + + + + + a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells). + germ-line + replaced by GENO:0000900 ! 'germline' + obsolete_gametic + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement') + +Alt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome. + "Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes." +From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/ +https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/ + diplotype + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes. + allelic phase + + + + + + + + + + + + + + + + + + + + + oryzias latipes strain + + + + + + + + + Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg). + hereditary + parental origin + parentally inherited + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells. + germline allele origin + + + + + + + + + An inheritance pattern that is not determined or not known. + unknown inheritance + undetermined inheritance + + + + + + + + + The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”. + One of a set of sequence features or haplotypes that exist at a particular genetic locus. <see ClinGen Allele Model> + The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. + http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/ + No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. + ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) + As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. + +In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) + obsolete_canonical allele + + + + + + + + + An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence. + The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. + http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ + No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. + +Former axiom: denotes some 'obsolete_canonical allele' + ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) + The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. + obsolete_contextual allele + + + + + + + + + A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not. + heteroplasmic mitochondrial inheritance + + + + + + + + + A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited. + homoplasmic mitochondrial inheritance + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + An generically dependent continuant that carries biological sequence that is part of or derived from a genome. + An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities. + genomic entity + + + + + + + + + A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations. + Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as +"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations." Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location. + +Current definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele. + Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424. + A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. + haplotype block + + + + + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. + 'Genomic Genotype' vs 'Genome' in GENO: +A genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome. + complete genotype + 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. + +2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. + genomic genotype + + + + + + + + + A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells) + decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin + Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. + obsolete_allele cellular context + + + + + + + + + The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system + In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. + +We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences. + In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. + +For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus). + genomic location + genomic locus + VMC:Location + 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. + +2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. + +3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there. + genomic feature location + + + + + + + + + + + + + + + + + + + + + + + + true + A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc). + useful organizational term to collect entities that have genomes/genotypes. + organismal entity + + + + + + + + + The molecular product resulting from transcription of a single gene (either a protein or RNA molecule) + gene product + + + + + + + + + reporter role + + + + + + + + + selectable marker role + + + + + + + + + selectable marker region + + + + + + + + + + + + + + + A genome whose sequence is identical to that of a genome sequence considered to be the reference. + reference genome + + + + + + + + + A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it. + Former comment: "Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project." + Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype. + Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. + +Former SC axioms: +- is_allele_of some 'haplotype block' +- 'has part' some sequence_alteration + 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene). + +2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. + +GENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. + +3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': + +a. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. +b. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. +c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. + +The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. + obsolete_haplotype + + + + + + + + + A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations. + Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block. + Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. + A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. + +The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. + +----------------------- + +* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. + obsolete_haplotype block + + + + + + + + + An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell. + Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene. + organellar plasmy + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes). + A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification. + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes. + qualified sequence feature + + + + + + + + + + + + + + + + + + + + + A set of qualified seqeunce features. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'. + qualified sequence feature set + + + + + + + + + A biolocical sequence, or set of such sequences. + biological sequence or collection + biological sequence or set + + + + + + + + + A set of biological sequences. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. + +A set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence. + biological sequence set + + + + + + + + + A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome. + Formerly considered modeling this as an informational entity, defined as "An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome." + functional feature complement + genetic dosage + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963. + As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). + The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. + obsolete_functional copy number complement + + + + + + + + + A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form. + obsolete_intrinsic sequence feature attribute + + + + + + + + + A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.) + obsolete_extrinsic sequence feature attribute + + + + + + + + + A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism). + allelic cellular distribution + + + + + + + + + A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin. + constitutional + + + + + + + + + A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin. + clonal + + + + + + + + + An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors. + complex inherritance + multi-factorial inheritance + multi-genic inheritance + multi-locus inheritance + multigenic inheritance + http://purl.obolibrary.org/obo/HP_0001426 + Diseases inherited in this manner are termed 'complex diseases'. + multifactorial inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes. + http://purl.obolibrary.org/obo/HP_0010984 + digenic inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes. + http://purl.obolibrary.org/obo/HP_0010983 + It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform. + oligogenic inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes. + http://purl.obolibrary.org/obo/HP_0010982 + Typically used for traits/conditions governed by more than three gene loci. + polygenic inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors. + single-gene inheritance + monogenic inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome. + autosomal inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome. + gonosomal inheritance + http://purl.obolibrary.org/obo/HP_0010985 + allosomal inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome. + http://purl.obolibrary.org/obo/HP_0001417 + X-linked inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + complete X-linked dominant inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + semi-dominant X-linked inheritance + incomplete X-linked dominant inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant X-linked inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome. + holandric inheritance + http://purl.obolibrary.org/obo/HP_0001450 + Y-linked inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome. + Z-linked inheritance + + + + + + + + + A Z-linked inheritance pattern wherein the trait manifests in heterozygotes. + Z-linked dominant inheritance + + + + + + + + + A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + complete Z-linked dominant inheritance + + + + + + + + + A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + semi-dominant Z-linked inheritance + incomplete Z-linked dominant inheritance + + + + + + + + + An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant Z-linked inheritance + + + + + + + + + A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals. + Z-linked reccessive inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome. + W-linked inheritance + + + + + + + + + An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome. + http://purl.obolibrary.org/obo/HP_0001427 + Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy). + mitochondrial inheritance + + + + + An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome. + Human Phenotype Ontology (HPO) + + + + + Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy). + Human Phenotype Ontology (HPO) + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females). + http://purl.obolibrary.org/obo/HP_0001470 + sex-limited autosomal dominant inheritance + + + + + + + + + An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females). + http://purl.obolibrary.org/obo/HP_0031362 + sex-limited autosomal recessive inheritance + + + + + + + + + A set of discrete alleles within a particular genome. + 'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An "Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'. + allele set + + + + + + + + + A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s). + copy number variation + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. + In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). + +Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. + obsolete_variant copy number complement + + + + + + + + + A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger. + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961. + 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. + +2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. + +3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. + obsolete_copy number complement + + + + + + + + + + + + + + + A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism). + A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. + genomic sequence + + + + + + + + + A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome. + The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome. + +We represent the notion of copy number at the "sequence level" (as opposed to the "sequence feature level") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The "sequence level" representation here supports this use case. By contrast, a "feature level" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity). + The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result. + +A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. + +The fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. + The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence. + copy number complement + + + + + + + + + A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s). + Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a "sequence feature level" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred). + +For example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains. + 'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome. + variant copy number complement + + + + + + + + + A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome. + functional genetic dosage + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence. + +'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. + +As we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele. + functional copy complement + + + + + + + + + A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type. + mosaic + + + + + + + + + A pair of integers representing start and end position of a location on a sequence coordinate system. + sequence interval + + + + + + + + + molecular function + + + + + + + + + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete] + developmental process + + + + + + + + + pulling in HP 'phenotypic abnormality' root here + human phenotypic abnormality + + + + + + + + + Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology. + A spatiotemporal region encompassing some part of the life cycle of an organism. + human life cycle stage + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + information content entity + + + + + + + + + ontology metadata + data about an ontology part + + + + + + + + + where to place this depends on if we take the organismal view or the quality centric view. + mammalian phenotype + + + + + + + + + Mus musculus + + + + + + + + + Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies. + Viruses + + + + + + + + + Danio rerio + + + + + + + + + Oryzias latipes + + + + + + + + + Homo sapiens + + + + + + + + + A processual entity that realizes a plan which is the concretization of a plan specification. + Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO. + planned process + + + + + + + + + reagent role + + + + + + + + + a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area + population + + + + + + + + + An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. + genotyping assay + + + + + + + + + A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. + A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. + targeted gene knock-out technique + + + + + + + + + targeted gene knock-in technique + + + + + + + + + Stub class to serve as root of hierarchy for imports from NCBI Taxonomy. + organism + + + + + + + + + + + + + + + + + + + + + + + + + the introduction. alteration or integration of genetic material into a cell or organism + genetic modification technique + + + + + + + + + 'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html + Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute. + color value + obsolete_color brightness + + + + + + + + + female + + + + + + + + + male + + + + + + + + + phenotypic sex + + + + + + + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role). + collection of organisms + + + + + + + + + A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. + family + + + + + + + + + Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. + morpholino_oligo + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. + Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosome arm + + + + + + + + + + + + + + + + + + + + + Any extent of continuous biological sequence. + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome. + sequence_feature + + + + + + + + + + + true + Formalizes the first identity criteria for a sequence feature of its sequence. + + + + + + + + + + + true + Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property). + + + + + + + + + A region of known length which may be used to manufacture a longer region. + obsolete_assembly_component + + + + + + + + + A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. + obsolete_contig + + + + + + + + + + + + 0 + + + The point at which one or more contiguous nucleotides were excised. + deleted_sequence + nucleotide deletion + nucleotide_deletion + + SO:1000033 + SO:0000159 + SOFA + http://en.wikipedia.org/wiki/Nucleotide_deletion + deletion + + + + + + + + + enhancer + + + + + + + + + A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. + promoter + + + + + + + + + A region of nucleotide sequence that has translocated to a new position. + transchr + translocated sequence + + SO:0000199 + DBVAR + translocation + + + + + + + + + SSLP + simple sequence length polymorphism + simple sequence length variation + + SO:0000207 + simple_sequence_length_variation + + + + + + + + + sequence length variation + + SO:0000248 + sequence_length_variation + + + + + + + + + + + + + + + See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25. + +Includes things like loxP sites, inducible promoters, ires elements, etc. + engineered_foreign_gene + + + + + + + + + A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. + http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29 + A defined feature that includes any type of VNTR or SSLP locus. + microsatellite + + + + + + + + + RNAi_reagent + + + + + + + + + Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. + A complete chromosome sequence. + chromosome + + + + + + + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + + "Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. + chromosome band + + + + + + + + + centromere + + + + + + + + + Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct. + obsolete_engineered_plasmid + + + + + + + + + The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. + insertion + nucleotide insertion + nucleotide_insertion + + SO:1000034 + SO:0000667 + DBVAR + SOFA + insertion + + + + + + + + + SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. + single nucleotide polymorphism + + SO:0000694 + SOFA + SNP + + + + + + + + + A junction is a boundary between regions. A boundary has an extent of zero. + junction + + + + + + + + + A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. + Regarding the distinction between a 'gene' and a 'gene allele': +Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment). + A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion. + gene + + + + + + + + + A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. + quantitative trait locus + QTL + + + + + + + + + An attribute to describe a region that was modified in vitro. + engineered + + + + + + + + + + + + + + + + + + + construct + engineered_region + + + + + + + + + + + + + + + + + + + An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'. + chromosomal feature + gross chromosomal part + chromosome part + + + + + + + + + A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome). + On the relationship between 'transgenic insertions', 'transgenes', and 'alleles' +Transgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete. + +In addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. + +For the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach. + Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism). + +Note that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome. + transgene + + + + + + + + + A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. + multiple nucleotide polymorphism + + SO:0001013 + MNP + + + + + + + + + A variation that increases or decreases the copy number of a given region. + CNP + CNV + copy number polymorphism + copy number variation + + SO:0001019 + SOFA + http://en.wikipedia.org/wiki/Copy_number_variation + copy_number_variation + + + + + + + + + + + + + + + A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny) + Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. + 'genome sequence' + A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'. + genome + + + + + + + + + + + + + + + + + + + A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': + +1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871. + +2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112. + +3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112. + A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. + sequence variation + + SO:1000004 + SO:1000007 + SO:0001059 + SOFA + 1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. + +Alleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part. + +2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. + +For a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference. + +3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism. + sequence_alteration + + + + + + + + + + + + + + + An insertion that derives from another organism, via the use of recombinant DNA technology. + transgenic insertion + + SO:0001218 + transgenic_insertion + + + + + + + + + A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. + not currently needed to support modeling use cases. can re-introduce if becomes necessary. + obsolete_experimental_feature + + + + + + + + + A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. + gene_trap_construct + + + + + + + + + A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. + promoter_trap_construct + + + + + + + + + A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. + enhancer_trap_construct + + + + + + + + + SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist. + single nucleotide variant + + kareneilbeck + Thu Oct 08 11:37:49 PDT 2009 + SO:0001483 + SOFA + SNV + + + + + + + + + A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. + heritable_phenotypic_marker + + + + + + + + + + + + + + + 'GRCh37.p10' (a human reference genome build) + A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced. + reference genome sequence + + + + + + + + + A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. + copy number gain + gain + + kareneilbeck + Mon Feb 28 01:54:09 PST 2011 + SO:0001742 + DBVAR + copy_number_gain + + + + + + + + + A sequence alteration whereby the copy number of a given region is less than the reference sequence. + copy number loss + loss + + kareneilbeck + Mon Feb 28 01:55:02 PST 2011 + SO:0001743 + DBVAR + copy_number_loss + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. + UPD + uniparental disomy + + kareneilbeck + Mon Feb 28 02:01:05 PST 2011 + SO:0001744 + DBVAR + http:http\://en.wikipedia.org/wiki/Uniparental_disomy + UPD + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. + maternal uniparental disomy + + kareneilbeck + Mon Feb 28 02:03:01 PST 2011 + SO:0001745 + maternal_uniparental_disomy + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. + paternal uniparental disomy + + kareneilbeck + Mon Feb 28 02:03:30 PST 2011 + SO:0001746 + paternal_uniparental_disomy + + + + + + + + + A structural sequence alteration where there are multiple equally plausible explanations for the change. + complex + + kareneilbeck + Wed Mar 23 03:21:19 PDT 2011 + SO:0001784 + DBVAR + complex_structural_alteration + + + + + + + + + + kareneilbeck + Fri Mar 25 02:27:41 PDT 2011 + SO:0001785 + DBVAR + structural_alteration + + + + + + + + + Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term. + regulatory element + regulatory gene region + regulatory_region + + + + + + + + + Any change in genomic DNA caused by a single event. + + SO:1000002 + SOFA + substitution + + + + + + + + + When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change. + complex substitution + + SO:1000005 + SOFA + complex_substitution + + + + + + + + + A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. + point mutation + + SO:1000008 + SOFA + http://en.wikipedia.org/wiki/Point_mutation + point_mutation + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. + + SO:1000009 + transition + + + + + + + + + A substitution of a pyrimidine, C or T, for another pyrimidine. + pyrimidine transition + + SO:1000010 + pyrimidine_transition + + + + + + + + + A transition of a cytidine to a thymine. + C to T transition + + SO:1000011 + C_to_T_transition + + + + + + + + + The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine. + C to T transition at pCpG site + + SO:1000012 + C_to_T_transition_at_pCpG_site + + + + + + + + + T to C transition + + SO:1000013 + T_to_C_transition + + + + + + + + + A substitution of a purine, A or G, for another purine. + purine transition + + SO:1000014 + purine_transition + + + + + + + + + A transition of an adenine to a guanine. + A to G transition + + SO:1000015 + A_to_G_transition + + + + + + + + + A transition of a guanine to an adenine. + G to A transition + + SO:1000016 + G_to_A_transition + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. + + SO:1000017 + http://en.wikipedia.org/wiki/Transversion + transversion + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. + pyrimidine to purine transversion + + SO:1000018 + pyrimidine_to_purine_transversion + + + + + + + + + A transversion from cytidine to adenine. + C to A transversion + + SO:1000019 + C_to_A_transversion + + + + + + + + + C to G transversion + + SO:1000020 + C_to_G_transversion + + + + + + + + + A transversion from T to A. + T to A transversion + + SO:1000021 + T_to_A_transversion + + + + + + + + + A transversion from T to G. + T to G transversion + + SO:1000022 + T_to_G_transversion + + + + + + + + + Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. + purine to pyrimidine transversion + + SO:1000023 + purine_to_pyrimidine_transversion + + + + + + + + + A transversion from adenine to cytidine. + A to C transversion + + SO:1000024 + A_to_C_transversion + + + + + + + + + A transversion from adenine to thymine. + A to T transversion + + SO:1000025 + A_to_T_transversion + + + + + + + + + A transversion from guanine to cytidine. + G to C transversion + + SO:1000026 + G_to_C_transversion + + + + + + + + + A transversion from guanine to thymine. + G to T transversion + + SO:1000027 + G_to_T_transversion + + + + + + + + + A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. + + SO:1000032 + http://en.wikipedia.org/wiki/Indel + Indels can have a different number of bases than the corresponding reference sequence. + indel + + + + + + + + + One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point. + nucleotide duplication + nucleotide_duplication + + SO:1000035 + duplication + + + + + + + + + A continuous nucleotide sequence is inverted in the same position. + inversion + + SO:1000036 + DBVAR + SOFA + inversion + + + + + + + + + A tandem duplication where the individual regions are in the same orientation. + direct tandem duplication + + SO:1000039 + direct_tandem_duplication + + + + + + + + + A tandem duplication where the individual regions are not in the same orientation. + inverted tandem duplication + mirror duplication + + SO:1000040 + inverted_tandem_duplication + + + + + + + + + A duplication consisting of 2 identical adjacent regions. + erverted + tandem duplication + + SO:1000173 + DBVAR + tandem_duplication + + + + + + + + + Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms) + life cycle stage + + + + + + + + + + + + + + + Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies. + http://purl.obolibrary.org/obo/CARO_0000000 + anatomical entity + + + + + + + + + Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework. + 1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition) + +2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment + Phenotype + + + + + + + + + Animals exhibit variations compared to a given control. + 'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes. + Variant + c. elegans phenotype + worm phenotype + + + + + + + + + abnormal(ly) malformed endocardium cell + + + + + + + + + abnormal(ly) absent dorso-rostral cluster + + + + + + + + + abnormal(ly) disrupted diencephalon development + + + + + + + + + abnormal(ly) disrupted neutrophil aggregation + + + + + + + + + abnormal(ly) absent adaxial cell + + + + + + + + + association + + + + + + + + + + Equivalent to: http://www.informatics.jax.org/marker/MGI:98297 + mus musculus shh gene + + + + + + + + + + http://zfin.org/ZDB-GENE-980526-166 + danio rerio shha gene + + + + + + + + + + http://zfin.org/ZDB-GENE-040123-1 + danio rerio cdkn1ca gene + + + + + + + + + + Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690 + +Codes for: http://www.uniprot.org/uniprot/Q15465 + homo sapiens SHH gene + + + + + + + + + + + + + + exploratory term + + + + + + + + + exemplar term + + + + + + + + + + + + + + + + + Initially created such that integrated transgene infers as child of sequence_alteration. + + + + + + + From 34d2a515b268fd703b10ef8c3b014d69d641b765 Mon Sep 17 00:00:00 2001 From: matentzn Date: Mon, 9 Sep 2019 16:37:34 +0100 Subject: [PATCH 04/11] changes edit file --- src/ontology/geno-edit.owl | 5058 +++++++++++++++++++++++++++++++++++- 1 file changed, 5045 insertions(+), 13 deletions(-) diff --git a/src/ontology/geno-edit.owl b/src/ontology/geno-edit.owl index 52f0f7b..3239bc6 100644 --- a/src/ontology/geno-edit.owl +++ b/src/ontology/geno-edit.owl @@ -1,39 +1,5071 @@ - Prefix(:=) +Prefix(dce:=) +Prefix(obi:=) +Prefix(obo:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) Prefix(rdfs:=) -Prefix(dce:=) +Prefix(terms:=) Prefix(dcterms:=) +Prefix(protege:=) +Prefix(oboInOwl:=) +Prefix(property:=) +Prefix(urigen-plugin:=) +Prefix(genotype_model:=) Ontology( +Import() +Import() +Annotation(dce:description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. -Import() +Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013") +Annotation(dce:title "GENO ontology") +Annotation(dcterms:license "Unspecified") -Import() +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class(obo:BFO_0000001)) +Declaration(Class(obo:BFO_0000002)) +Declaration(Class(obo:BFO_0000003)) +Declaration(Class(obo:BFO_0000004)) +Declaration(Class(obo:BFO_0000015)) +Declaration(Class(obo:BFO_0000016)) +Declaration(Class(obo:BFO_0000017)) +Declaration(Class(obo:BFO_0000019)) +Declaration(Class(obo:BFO_0000020)) +Declaration(Class(obo:BFO_0000023)) +Declaration(Class(obo:BFO_0000031)) +Declaration(Class(obo:BFO_0000034)) +Declaration(Class(obo:BFO_0000040)) +Declaration(Class(obo:CHEBI_23367)) +Declaration(Class(obo:CHEBI_33696)) +Declaration(Class(obo:CLO_0000031)) +Declaration(Class(obo:CL_0000000)) +Declaration(Class(obo:ENVO_01000254)) +Declaration(Class(obo:ERO_0000007)) +Declaration(Class(obo:ERO_0002002)) +Declaration(Class(obo:ERO_0002003)) +Declaration(Class(obo:GENO_0000000)) +Declaration(Class(obo:GENO_0000002)) +Declaration(Class(obo:GENO_0000009)) +Declaration(Class(obo:GENO_0000010)) +Declaration(Class(obo:GENO_0000014)) +Declaration(Class(obo:GENO_0000017)) +Declaration(Class(obo:GENO_0000019)) +Declaration(Class(obo:GENO_0000022)) +Declaration(Class(obo:GENO_0000029)) +Declaration(Class(obo:GENO_0000030)) +Declaration(Class(obo:GENO_0000033)) +Declaration(Class(obo:GENO_0000036)) +Declaration(Class(obo:GENO_0000037)) +Declaration(Class(obo:GENO_0000042)) +Declaration(Class(obo:GENO_0000047)) +Declaration(Class(obo:GENO_0000054)) +Declaration(Class(obo:GENO_0000057)) +Declaration(Class(obo:GENO_0000060)) +Declaration(Class(obo:GENO_0000091)) +Declaration(Class(obo:GENO_0000092)) +Declaration(Class(obo:GENO_0000093)) +Declaration(Class(obo:GENO_0000106)) +Declaration(Class(obo:GENO_0000108)) +Declaration(Class(obo:GENO_0000111)) +Declaration(Class(obo:GENO_0000112)) +Declaration(Class(obo:GENO_0000113)) +Declaration(Class(obo:GENO_0000118)) +Declaration(Class(obo:GENO_0000119)) +Declaration(Class(obo:GENO_0000125)) +Declaration(Class(obo:GENO_0000131)) +Declaration(Class(obo:GENO_0000132)) +Declaration(Class(obo:GENO_0000133)) +Declaration(Class(obo:GENO_0000134)) +Declaration(Class(obo:GENO_0000135)) +Declaration(Class(obo:GENO_0000136)) +Declaration(Class(obo:GENO_0000137)) +Declaration(Class(obo:GENO_0000138)) +Declaration(Class(obo:GENO_0000139)) +Declaration(Class(obo:GENO_0000140)) +Declaration(Class(obo:GENO_0000141)) +Declaration(Class(obo:GENO_0000142)) +Declaration(Class(obo:GENO_0000143)) +Declaration(Class(obo:GENO_0000144)) +Declaration(Class(obo:GENO_0000145)) +Declaration(Class(obo:GENO_0000146)) +Declaration(Class(obo:GENO_0000147)) +Declaration(Class(obo:GENO_0000148)) +Declaration(Class(obo:GENO_0000149)) +Declaration(Class(obo:GENO_0000150)) +Declaration(Class(obo:GENO_0000152)) +Declaration(Class(obo:GENO_0000160)) +Declaration(Class(obo:GENO_0000164)) +Declaration(Class(obo:GENO_0000165)) +Declaration(Class(obo:GENO_0000166)) +Declaration(Class(obo:GENO_0000169)) +Declaration(Class(obo:GENO_0000170)) +Declaration(Class(obo:GENO_0000171)) +Declaration(Class(obo:GENO_0000172)) +Declaration(Class(obo:GENO_0000173)) +Declaration(Class(obo:GENO_0000174)) +Declaration(Class(obo:GENO_0000175)) +Declaration(Class(obo:GENO_0000324)) +Declaration(Class(obo:GENO_0000338)) +Declaration(Class(obo:GENO_0000339)) +Declaration(Class(obo:GENO_0000343)) +Declaration(Class(obo:GENO_0000344)) +Declaration(Class(obo:GENO_0000345)) +Declaration(Class(obo:GENO_0000346)) +Declaration(Class(obo:GENO_0000351)) +Declaration(Class(obo:GENO_0000391)) +Declaration(Class(obo:GENO_0000392)) +Declaration(Class(obo:GENO_0000393)) +Declaration(Class(obo:GENO_0000394)) +Declaration(Class(obo:GENO_0000402)) +Declaration(Class(obo:GENO_0000415)) +Declaration(Class(obo:GENO_0000458)) +Declaration(Class(obo:GENO_0000460)) +Declaration(Class(obo:GENO_0000476)) +Declaration(Class(obo:GENO_0000477)) +Declaration(Class(obo:GENO_0000480)) +Declaration(Class(obo:GENO_0000481)) +Declaration(Class(obo:GENO_0000482)) +Declaration(Class(obo:GENO_0000491)) +Declaration(Class(obo:GENO_0000492)) +Declaration(Class(obo:GENO_0000494)) +Declaration(Class(obo:GENO_0000495)) +Declaration(Class(obo:GENO_0000497)) +Declaration(Class(obo:GENO_0000498)) +Declaration(Class(obo:GENO_0000499)) +Declaration(Class(obo:GENO_0000500)) +Declaration(Class(obo:GENO_0000501)) +Declaration(Class(obo:GENO_0000502)) +Declaration(Class(obo:GENO_0000504)) +Declaration(Class(obo:GENO_0000506)) +Declaration(Class(obo:GENO_0000511)) +Declaration(Class(obo:GENO_0000512)) +Declaration(Class(obo:GENO_0000513)) +Declaration(Class(obo:GENO_0000515)) +Declaration(Class(obo:GENO_0000516)) +Declaration(Class(obo:GENO_0000524)) +Declaration(Class(obo:GENO_0000525)) +Declaration(Class(obo:GENO_0000527)) +Declaration(Class(obo:GENO_0000528)) +Declaration(Class(obo:GENO_0000529)) +Declaration(Class(obo:GENO_0000533)) +Declaration(Class(obo:GENO_0000534)) +Declaration(Class(obo:GENO_0000536)) +Declaration(Class(obo:GENO_0000575)) +Declaration(Class(obo:GENO_0000602)) +Declaration(Class(obo:GENO_0000603)) +Declaration(Class(obo:GENO_0000604)) +Declaration(Class(obo:GENO_0000605)) +Declaration(Class(obo:GENO_0000606)) +Declaration(Class(obo:GENO_0000611)) +Declaration(Class(obo:GENO_0000614)) +Declaration(Class(obo:GENO_0000616)) +Declaration(Class(obo:GENO_0000618)) +Declaration(Class(obo:GENO_0000619)) +Declaration(Class(obo:GENO_0000620)) +Declaration(Class(obo:GENO_0000621)) +Declaration(Class(obo:GENO_0000622)) +Declaration(Class(obo:GENO_0000623)) +Declaration(Class(obo:GENO_0000624)) +Declaration(Class(obo:GENO_0000625)) +Declaration(Class(obo:GENO_0000628)) +Declaration(Class(obo:GENO_0000629)) +Declaration(Class(obo:GENO_0000632)) +Declaration(Class(obo:GENO_0000633)) +Declaration(Class(obo:GENO_0000637)) +Declaration(Class(obo:GENO_0000638)) +Declaration(Class(obo:GENO_0000640)) +Declaration(Class(obo:GENO_0000642)) +Declaration(Class(obo:GENO_0000644)) +Declaration(Class(obo:GENO_0000645)) +Declaration(Class(obo:GENO_0000646)) +Declaration(Class(obo:GENO_0000647)) +Declaration(Class(obo:GENO_0000649)) +Declaration(Class(obo:GENO_0000659)) +Declaration(Class(obo:GENO_0000660)) +Declaration(Class(obo:GENO_0000666)) +Declaration(Class(obo:GENO_0000667)) +Declaration(Class(obo:GENO_0000680)) +Declaration(Class(obo:GENO_0000681)) +Declaration(Class(obo:GENO_0000684)) +Declaration(Class(obo:GENO_0000685)) +Declaration(Class(obo:GENO_0000688)) +Declaration(Class(obo:GENO_0000701)) +Declaration(Class(obo:GENO_0000702)) +Declaration(Class(obo:GENO_0000713)) +Declaration(Class(obo:GENO_0000714)) +Declaration(Class(obo:GENO_0000715)) +Declaration(Class(obo:GENO_0000719)) +Declaration(Class(obo:GENO_0000720)) +Declaration(Class(obo:GENO_0000721)) +Declaration(Class(obo:GENO_0000722)) +Declaration(Class(obo:GENO_0000724)) +Declaration(Class(obo:GENO_0000725)) +Declaration(Class(obo:GENO_0000736)) +Declaration(Class(obo:GENO_0000737)) +Declaration(Class(obo:GENO_0000768)) +Declaration(Class(obo:GENO_0000770)) +Declaration(Class(obo:GENO_0000772)) +Declaration(Class(obo:GENO_0000773)) +Declaration(Class(obo:GENO_0000777)) +Declaration(Class(obo:GENO_0000778)) +Declaration(Class(obo:GENO_0000779)) +Declaration(Class(obo:GENO_0000780)) +Declaration(Class(obo:GENO_0000781)) +Declaration(Class(obo:GENO_0000782)) +Declaration(Class(obo:GENO_0000788)) +Declaration(Class(obo:GENO_0000815)) +Declaration(Class(obo:GENO_0000818)) +Declaration(Class(obo:GENO_0000823)) +Declaration(Class(obo:GENO_0000833)) +Declaration(Class(obo:GENO_0000839)) +Declaration(Class(obo:GENO_0000848)) +Declaration(Class(obo:GENO_0000850)) +Declaration(Class(obo:GENO_0000856)) +Declaration(Class(obo:GENO_0000861)) +Declaration(Class(obo:GENO_0000870)) +Declaration(Class(obo:GENO_0000871)) +Declaration(Class(obo:GENO_0000872)) +Declaration(Class(obo:GENO_0000873)) +Declaration(Class(obo:GENO_0000874)) +Declaration(Class(obo:GENO_0000875)) +Declaration(Class(obo:GENO_0000876)) +Declaration(Class(obo:GENO_0000877)) +Declaration(Class(obo:GENO_0000878)) +Declaration(Class(obo:GENO_0000879)) +Declaration(Class(obo:GENO_0000880)) +Declaration(Class(obo:GENO_0000881)) +Declaration(Class(obo:GENO_0000882)) +Declaration(Class(obo:GENO_0000883)) +Declaration(Class(obo:GENO_0000885)) +Declaration(Class(obo:GENO_0000886)) +Declaration(Class(obo:GENO_0000887)) +Declaration(Class(obo:GENO_0000888)) +Declaration(Class(obo:GENO_0000889)) +Declaration(Class(obo:GENO_0000890)) +Declaration(Class(obo:GENO_0000891)) +Declaration(Class(obo:GENO_0000892)) +Declaration(Class(obo:GENO_0000893)) +Declaration(Class(obo:GENO_0000897)) +Declaration(Class(obo:GENO_0000898)) +Declaration(Class(obo:GENO_0000899)) +Declaration(Class(obo:GENO_0000901)) +Declaration(Class(obo:GENO_0000902)) +Declaration(Class(obo:GENO_0000904)) +Declaration(Class(obo:GENO_0000907)) +Declaration(Class(obo:GENO_0000910)) +Declaration(Class(obo:GENO_0000911)) +Declaration(Class(obo:GENO_0000912)) +Declaration(Class(obo:GENO_0000914)) +Declaration(Class(obo:GENO_0000915)) +Declaration(Class(obo:GENO_0000916)) +Declaration(Class(obo:GENO_0000918)) +Declaration(Class(obo:GENO_0000919)) +Declaration(Class(obo:GENO_0000920)) +Declaration(Class(obo:GENO_0000921)) +Declaration(Class(obo:GENO_0000922)) +Declaration(Class(obo:GENO_0000923)) +Declaration(Class(obo:GENO_0000924)) +Declaration(Class(obo:GENO_0000925)) +Declaration(Class(obo:GENO_0000926)) +Declaration(Class(obo:GENO_0000927)) +Declaration(Class(obo:GENO_0000928)) +Declaration(Class(obo:GENO_0000929)) +Declaration(Class(obo:GENO_0000930)) +Declaration(Class(obo:GENO_0000931)) +Declaration(Class(obo:GENO_0000932)) +Declaration(Class(obo:GENO_0000933)) +Declaration(Class(obo:GENO_0000934)) +Declaration(Class(obo:GENO_0000935)) +Declaration(Class(obo:GENO_0000936)) +Declaration(Class(obo:GENO_0000937)) +Declaration(Class(obo:GENO_0000938)) +Declaration(Class(obo:GENO_0000939)) +Declaration(Class(obo:GENO_0000941)) +Declaration(Class(obo:GENO_0000942)) +Declaration(Class(obo:GENO_0000943)) +Declaration(Class(obo:GENO_0000944)) +Declaration(Class(obo:GENO_0000945)) +Declaration(Class(obo:GENO_0000946)) +Declaration(Class(obo:GENO_0000947)) +Declaration(Class(obo:GENO_0000948)) +Declaration(Class(obo:GENO_0000949)) +Declaration(Class(obo:GENO_0000952)) +Declaration(Class(obo:GENO_0000953)) +Declaration(Class(obo:GENO_0000954)) +Declaration(Class(obo:GENO_0000955)) +Declaration(Class(obo:GENO_0000956)) +Declaration(Class(obo:GENO_0000960)) +Declaration(Class(obo:GENO_0000961)) +Declaration(Class(obo:GENO_0000962)) +Declaration(Class(obo:GENO_0000963)) +Declaration(Class(obo:GENO_0000964)) +Declaration(Class(obo:GENO_0000965)) +Declaration(Class(obo:GO_0003674)) +Declaration(Class(obo:GO_0032502)) +Declaration(Class(obo:HP_0000118)) +Declaration(Class(obo:HsapDv_0000000)) +Declaration(Class(obo:IAO_0000030)) +Declaration(Class(obo:IAO_0000102)) +Declaration(Class(obo:MP_0000001)) +Declaration(Class(obo:NCBITaxon_10090)) +Declaration(Class(obo:NCBITaxon_10239)) +Declaration(Class(obo:NCBITaxon_7955)) +Declaration(Class(obo:NCBITaxon_8090)) +Declaration(Class(obo:NCBITaxon_9606)) +Declaration(Class(obo:OBI_0000011)) +Declaration(Class(obo:OBI_0000086)) +Declaration(Class(obo:OBI_0000181)) +Declaration(Class(obo:OBI_0000435)) +Declaration(Class(obo:OBI_0001148)) +Declaration(Class(obo:OBI_0001149)) +Declaration(Class(obo:OBI_0100026)) +Declaration(Class(obo:OBI_0600043)) +Declaration(Class(obo:PATO_0000016)) +Declaration(Class(obo:PATO_0000383)) +Declaration(Class(obo:PATO_0000384)) +Declaration(Class(obo:PATO_0001894)) +Declaration(Class(obo:PCO_0000000)) +Declaration(Class(obo:PCO_0000020)) +Declaration(Class(obo:SO_0000034)) +Declaration(Class(obo:SO_0000105)) +Declaration(Class(obo:SO_0000110)) +Declaration(Class(obo:SO_0000143)) +Declaration(Class(obo:SO_0000149)) +Declaration(Class(obo:SO_0000159)) +Declaration(Class(obo:SO_0000165)) +Declaration(Class(obo:SO_0000167)) +Declaration(Class(obo:SO_0000199)) +Declaration(Class(obo:SO_0000207)) +Declaration(Class(obo:SO_0000248)) +Declaration(Class(obo:SO_0000281)) +Declaration(Class(obo:SO_0000289)) +Declaration(Class(obo:SO_0000337)) +Declaration(Class(obo:SO_0000340)) +Declaration(Class(obo:SO_0000341)) +Declaration(Class(obo:SO_0000577)) +Declaration(Class(obo:SO_0000637)) +Declaration(Class(obo:SO_0000667)) +Declaration(Class(obo:SO_0000694)) +Declaration(Class(obo:SO_0000699)) +Declaration(Class(obo:SO_0000704)) +Declaration(Class(obo:SO_0000771)) +Declaration(Class(obo:SO_0000783)) +Declaration(Class(obo:SO_0000804)) +Declaration(Class(obo:SO_0000830)) +Declaration(Class(obo:SO_0000902)) +Declaration(Class(obo:SO_0001013)) +Declaration(Class(obo:SO_0001019)) +Declaration(Class(obo:SO_0001026)) +Declaration(Class(obo:SO_0001059)) +Declaration(Class(obo:SO_0001218)) +Declaration(Class(obo:SO_0001410)) +Declaration(Class(obo:SO_0001477)) +Declaration(Class(obo:SO_0001478)) +Declaration(Class(obo:SO_0001479)) +Declaration(Class(obo:SO_0001483)) +Declaration(Class(obo:SO_0001500)) +Declaration(Class(obo:SO_0001505)) +Declaration(Class(obo:SO_0001742)) +Declaration(Class(obo:SO_0001743)) +Declaration(Class(obo:SO_0001744)) +Declaration(Class(obo:SO_0001745)) +Declaration(Class(obo:SO_0001746)) +Declaration(Class(obo:SO_0001784)) +Declaration(Class(obo:SO_0001785)) +Declaration(Class(obo:SO_0005836)) +Declaration(Class(obo:SO_1000002)) +Declaration(Class(obo:SO_1000005)) +Declaration(Class(obo:SO_1000008)) +Declaration(Class(obo:SO_1000009)) +Declaration(Class(obo:SO_1000010)) +Declaration(Class(obo:SO_1000011)) +Declaration(Class(obo:SO_1000012)) +Declaration(Class(obo:SO_1000013)) +Declaration(Class(obo:SO_1000014)) +Declaration(Class(obo:SO_1000015)) +Declaration(Class(obo:SO_1000016)) +Declaration(Class(obo:SO_1000017)) +Declaration(Class(obo:SO_1000018)) +Declaration(Class(obo:SO_1000019)) +Declaration(Class(obo:SO_1000020)) +Declaration(Class(obo:SO_1000021)) +Declaration(Class(obo:SO_1000022)) +Declaration(Class(obo:SO_1000023)) +Declaration(Class(obo:SO_1000024)) +Declaration(Class(obo:SO_1000025)) +Declaration(Class(obo:SO_1000026)) +Declaration(Class(obo:SO_1000027)) +Declaration(Class(obo:SO_1000032)) +Declaration(Class(obo:SO_1000035)) +Declaration(Class(obo:SO_1000036)) +Declaration(Class(obo:SO_1000039)) +Declaration(Class(obo:SO_1000040)) +Declaration(Class(obo:SO_1000173)) +Declaration(Class(obo:UBERON_0000105)) +Declaration(Class(obo:UBERON_0001062)) +Declaration(Class(obo:UPHENO_0001001)) +Declaration(Class(obo:WBPhenotype_0000886)) +Declaration(Class(obo:ZP_0000199)) +Declaration(Class(obo:ZP_0000386)) +Declaration(Class(obo:ZP_0000755)) +Declaration(Class(obo:ZP_0005531)) +Declaration(Class(obo:ZP_0005692)) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty(obo:BFO_0000050)) +Declaration(ObjectProperty(obo:BFO_0000051)) +Declaration(ObjectProperty(obo:GENO_0000207)) +Declaration(ObjectProperty(obo:GENO_0000211)) +Declaration(ObjectProperty(obo:GENO_0000220)) +Declaration(ObjectProperty(obo:GENO_0000222)) +Declaration(ObjectProperty(obo:GENO_0000231)) +Declaration(ObjectProperty(obo:GENO_0000239)) +Declaration(ObjectProperty(obo:GENO_0000242)) +Declaration(ObjectProperty(obo:GENO_0000243)) +Declaration(ObjectProperty(obo:GENO_0000244)) +Declaration(ObjectProperty(obo:GENO_0000248)) +Declaration(ObjectProperty(obo:GENO_0000251)) +Declaration(ObjectProperty(obo:GENO_0000252)) +Declaration(ObjectProperty(obo:GENO_0000253)) +Declaration(ObjectProperty(obo:GENO_0000359)) +Declaration(ObjectProperty(obo:GENO_0000368)) +Declaration(ObjectProperty(obo:GENO_0000382)) +Declaration(ObjectProperty(obo:GENO_0000383)) +Declaration(ObjectProperty(obo:GENO_0000385)) +Declaration(ObjectProperty(obo:GENO_0000387)) +Declaration(ObjectProperty(obo:GENO_0000408)) +Declaration(ObjectProperty(obo:GENO_0000410)) +Declaration(ObjectProperty(obo:GENO_0000411)) +Declaration(ObjectProperty(obo:GENO_0000413)) +Declaration(ObjectProperty(obo:GENO_0000414)) +Declaration(ObjectProperty(obo:GENO_0000418)) +Declaration(ObjectProperty(obo:GENO_0000443)) +Declaration(ObjectProperty(obo:GENO_0000445)) +Declaration(ObjectProperty(obo:GENO_0000447)) +Declaration(ObjectProperty(obo:GENO_0000449)) +Declaration(ObjectProperty(obo:GENO_0000486)) +Declaration(ObjectProperty(obo:GENO_0000488)) +Declaration(ObjectProperty(obo:GENO_0000580)) +Declaration(ObjectProperty(obo:GENO_0000608)) +Declaration(ObjectProperty(obo:GENO_0000610)) +Declaration(ObjectProperty(obo:GENO_0000626)) +Declaration(ObjectProperty(obo:GENO_0000634)) +Declaration(ObjectProperty(obo:GENO_0000639)) +Declaration(ObjectProperty(obo:GENO_0000641)) +Declaration(ObjectProperty(obo:GENO_0000650)) +Declaration(ObjectProperty(obo:GENO_0000651)) +Declaration(ObjectProperty(obo:GENO_0000652)) +Declaration(ObjectProperty(obo:GENO_0000653)) +Declaration(ObjectProperty(obo:GENO_0000654)) +Declaration(ObjectProperty(obo:GENO_0000655)) +Declaration(ObjectProperty(obo:GENO_0000661)) +Declaration(ObjectProperty(obo:GENO_0000683)) +Declaration(ObjectProperty(obo:GENO_0000708)) +Declaration(ObjectProperty(obo:GENO_0000726)) +Declaration(ObjectProperty(obo:GENO_0000740)) +Declaration(ObjectProperty(obo:GENO_0000741)) +Declaration(ObjectProperty(obo:GENO_0000742)) +Declaration(ObjectProperty(obo:GENO_0000743)) +Declaration(ObjectProperty(obo:GENO_0000761)) +Declaration(ObjectProperty(obo:GENO_0000767)) +Declaration(ObjectProperty(obo:GENO_0000783)) +Declaration(ObjectProperty(obo:GENO_0000784)) +Declaration(ObjectProperty(obo:GENO_0000790)) +Declaration(ObjectProperty(obo:GENO_0000791)) +Declaration(ObjectProperty(obo:GENO_0000793)) +Declaration(ObjectProperty(obo:GENO_0000794)) +Declaration(ObjectProperty(obo:GENO_0000840)) +Declaration(ObjectProperty(obo:GENO_0000841)) +Declaration(ObjectProperty(obo:GENO_0000842)) +Declaration(ObjectProperty(obo:GENO_0000843)) +Declaration(ObjectProperty(obo:GENO_0000844)) +Declaration(ObjectProperty(obo:GENO_0000845)) +Declaration(ObjectProperty(obo:GENO_0000846)) +Declaration(ObjectProperty(obo:GENO_0000847)) +Declaration(ObjectProperty(obo:GENO_0000849)) +Declaration(ObjectProperty(obo:GENO_0000903)) +Declaration(ObjectProperty(obo:GENO_0000906)) +Declaration(ObjectProperty(obo:GENO_0000957)) +Declaration(ObjectProperty(obo:GENO_0000958)) +Declaration(ObjectProperty(obo:GENO_0000959)) +Declaration(ObjectProperty(obo:GENO_0000966)) +Declaration(ObjectProperty(obo:GENO_0000967)) +Declaration(ObjectProperty(obo:IAO_0000136)) +Declaration(ObjectProperty(obo:IAO_0000219)) +Declaration(ObjectProperty(obo:OBI_0000293)) +Declaration(ObjectProperty(obo:OBI_0000299)) +Declaration(ObjectProperty(obo:RO_0000052)) +Declaration(ObjectProperty(obo:RO_0000053)) +Declaration(ObjectProperty(obo:RO_0000056)) +Declaration(ObjectProperty(obo:RO_0000057)) +Declaration(ObjectProperty(obo:RO_0000059)) +Declaration(ObjectProperty(obo:RO_0000086)) +Declaration(ObjectProperty(obo:RO_0000087)) +Declaration(ObjectProperty(obo:RO_0000091)) +Declaration(ObjectProperty(obo:RO_0001000)) +Declaration(ObjectProperty(obo:RO_0002091)) +Declaration(ObjectProperty(obo:RO_0002093)) +Declaration(ObjectProperty(obo:RO_0002131)) +Declaration(ObjectProperty(obo:RO_0002162)) +Declaration(ObjectProperty(obo:RO_0002200)) +Declaration(ObjectProperty(obo:RO_0002201)) +Declaration(ObjectProperty(obo:RO_0002222)) +Declaration(ObjectProperty(obo:RO_0002233)) +Declaration(ObjectProperty(obo:RO_0002234)) +Declaration(ObjectProperty(obo:RO_0002350)) +Declaration(ObjectProperty(obo:RO_0002351)) +Declaration(ObjectProperty(obo:RO_0002352)) +Declaration(ObjectProperty(obo:RO_0002353)) +Declaration(ObjectProperty(obo:RO_0002354)) +Declaration(ObjectProperty(obo:RO_000244)) +Declaration(ObjectProperty(obo:RO_0002522)) +Declaration(ObjectProperty(obo:RO_0002524)) +Declaration(ObjectProperty(obo:RO_0002525)) +Declaration(ObjectProperty(obo:RO_0002526)) +Declaration(ObjectProperty(obo:RO_0002528)) +Declaration(ObjectProperty(obo:RO_0002529)) +Declaration(ObjectProperty(obo:RO_0003301)) +Declaration(ObjectProperty(obo:RO_0003302)) +Declaration(ObjectProperty(obo:RO_0003303)) +Declaration(ObjectProperty(obo:RO_0003304)) +Declaration(ObjectProperty(obo:RO_0003305)) +Declaration(ObjectProperty(obo:RO_0003306)) +Declaration(ObjectProperty(obo:RO_0003307)) +Declaration(ObjectProperty(obo:RO_0003308)) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(DataProperty()) +Declaration(DataProperty(obo:GENO_0000678)) +Declaration(DataProperty(obo:GENO_0000703)) +Declaration(DataProperty(obo:GENO_0000712)) +Declaration(DataProperty(obo:GENO_0000866)) +Declaration(DataProperty(obo:GENO_0000894)) +Declaration(DataProperty(obo:GENO_0000895)) +Declaration(DataProperty(obo:GENO_0000896)) +Declaration(DataProperty(obo:GENO_0000917)) +Declaration(NamedIndividual(obo:GENO_0000484)) +Declaration(NamedIndividual(obo:GENO_0000514)) +Declaration(AnnotationProperty(obo:GENO_0000834)) +Declaration(AnnotationProperty(obo:GENO_0000867)) +Declaration(AnnotationProperty(obo:GENO_0000905)) +Declaration(AnnotationProperty(obo:GENO_0000909)) +Declaration(AnnotationProperty(obo:IAO_alt_id)) +Declaration(AnnotationProperty(obo:IAO_created_by)) +Declaration(AnnotationProperty(obo:IAO_creation_date)) +Declaration(AnnotationProperty(obo:IAO_id)) +Declaration(AnnotationProperty(obo:IAO_subset)) +Declaration(AnnotationProperty(obo:IAO_xref)) +Declaration(AnnotationProperty(dce:description)) +Declaration(AnnotationProperty(dce:title)) +Declaration(AnnotationProperty(dcterms:license)) +Declaration(AnnotationProperty(dcterms:source)) +############################ +# Annotation Properties +############################ -Import() +# Annotation Property: obo:GENO_0000834 (is_identity_criteria) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000834 "Used to annotation axioms that define identity criteria for instances of a class.") +AnnotationAssertion(rdfs:label obo:GENO_0000834 "is_identity_criteria"@en) +AnnotationPropertyRange(obo:GENO_0000834 xsd:boolean) +# Annotation Property: obo:GENO_0000867 (proabalistic_quantifier) -Annotation(dce:title "GENO ontology") -Annotation(dcterms:license "Unspecified") -Annotation(dce:description "None") +AnnotationAssertion(rdfs:label obo:GENO_0000867 "proabalistic_quantifier"@en) + +# Annotation Property: obo:GENO_0000905 (mixin) + +AnnotationAssertion(rdfs:comment obo:GENO_0000905 "Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models.") +AnnotationAssertion(rdfs:label obo:GENO_0000905 "mixin"@en) +AnnotationPropertyRange(obo:GENO_0000905 xsd:boolean) + +# Annotation Property: obo:GENO_0000909 (gene symbol) -Declaration(Class()) +AnnotationAssertion(rdfs:label obo:GENO_0000909 "gene symbol"@en) ############################ -# Classes +# Object Properties ############################ -# Class: +# Object Property: (begin) + +AnnotationAssertion(rdfs:label "begin"@en) +SubObjectPropertyOf( obo:GENO_0000708) + +# Object Property: (end) + +AnnotationAssertion(rdfs:label "end"@en) +SubObjectPropertyOf( obo:GENO_0000708) + +# Object Property: (location) + +AnnotationAssertion(rdfs:label "location"@en) +SubObjectPropertyOf( obo:GENO_0000708) + +# Object Property: (reference) + +AnnotationAssertion(obo:IAO_0000115 "The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly.") +AnnotationAssertion(rdfs:label "reference") +SubObjectPropertyOf( obo:GENO_0000708) + +# Object Property: obo:BFO_0000050 (is part of) + +AnnotationAssertion(rdfs:label obo:BFO_0000050 "is part of") +SubObjectPropertyOf(obo:BFO_0000050 obo:RO_0002131) +InverseObjectProperties(obo:BFO_0000050 obo:BFO_0000051) +TransitiveObjectProperty(obo:BFO_0000050) + +# Object Property: obo:BFO_0000051 (has part) + +AnnotationAssertion(rdfs:label obo:BFO_0000051 "has part") +SubObjectPropertyOf(obo:BFO_0000051 obo:RO_0002131) +TransitiveObjectProperty(obo:BFO_0000051) + +# Object Property: obo:GENO_0000207 (has_sequence_attribute) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000207 "A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000207 "Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000207 "http://purl.obolibrary.org/obo/so_has_quality") +AnnotationAssertion(rdfs:label obo:GENO_0000207 "has_sequence_attribute") +SubObjectPropertyOf(obo:GENO_0000207 owl:topObjectProperty) +ObjectPropertyDomain(obo:GENO_0000207 ObjectUnionOf(obo:GENO_0000701 obo:GENO_0000702 obo:GENO_0000713)) + +# Object Property: obo:GENO_0000211 (bears_concretization_of) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000211 "A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000211 "materializes") +AnnotationAssertion(rdfs:comment obo:GENO_0000211 "Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence.") +AnnotationAssertion(rdfs:label obo:GENO_0000211 "bears_concretization_of") + +# Object Property: obo:GENO_0000220 (is_genotype_of) + +AnnotationAssertion(rdfs:label obo:GENO_0000220 "is_genotype_of") +InverseObjectProperties(obo:GENO_0000220 obo:GENO_0000222) + +# Object Property: obo:GENO_0000222 (has_genotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000222 "A relationship that holds between a biological entity and some level of genetic variation present in its genome.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000222 "This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype.") +AnnotationAssertion(rdfs:comment obo:GENO_0000222 "The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations.") +AnnotationAssertion(rdfs:label obo:GENO_0000222 "has_genotype") +ObjectPropertyDomain(obo:GENO_0000222 ObjectUnionOf(obo:GENO_0000536 ObjectSomeValuesFrom(obo:BFO_0000050 obo:GENO_0000536))) + +# Object Property: obo:GENO_0000231 (has_proper_part) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000231 "An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO)") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000231 "No proper part relation anymore in RO/BFO?") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000231 "http://semanticscience.org/resource/SIO_000053") +AnnotationAssertion(rdfs:label obo:GENO_0000231 "has_proper_part") +SubObjectPropertyOf(obo:GENO_0000231 obo:BFO_0000051) +InverseObjectProperties(obo:GENO_0000231 obo:GENO_0000248) +TransitiveObjectProperty(obo:GENO_0000231) + +# Object Property: obo:GENO_0000239 (has_sequence) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000239 "A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000239 "has_sequence_component") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000239 "has_state") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000239 "VMC:state") +AnnotationAssertion(rdfs:comment obo:GENO_0000239 "'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule.") +AnnotationAssertion(rdfs:label obo:GENO_0000239 "has_sequence") +InverseObjectProperties(obo:GENO_0000239 obo:GENO_0000251) +ObjectPropertyRange(obo:GENO_0000239 obo:GENO_0000702) + +# Object Property: obo:GENO_0000242 (obsolete_specifies) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000242 "A geno:intrinnsic genotype 'specifies' a SO:genome. +A geno:karyotype 'specifies' a geno:karyotype feature collection.") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000242 "A relationship between an information content entity representing a specification, and the entity it specifies.") +AnnotationAssertion(rdfs:label obo:GENO_0000242 "obsolete_specifies") +SubObjectPropertyOf(obo:GENO_0000242 oboInOwl:ObsoleteProperty) +InverseObjectProperties(obo:GENO_0000242 obo:GENO_0000253) + +# Object Property: obo:GENO_0000243 (obsolete_approximates_sequence) + +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000243 "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. ") +AnnotationAssertion(rdfs:label obo:GENO_0000243 "obsolete_approximates_sequence") +SubObjectPropertyOf(obo:GENO_0000243 oboInOwl:ObsoleteProperty) + +# Object Property: obo:GENO_0000244 (obsolete_resolves_to_sequence) + +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000244 "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. ") +AnnotationAssertion(rdfs:label obo:GENO_0000244 "obsolete_resolves_to_sequence") +SubObjectPropertyOf(obo:GENO_0000244 oboInOwl:ObsoleteProperty) + +# Object Property: obo:GENO_0000248 (is_proper_part_of) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000248 "An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000248 "http://semanticscience.org/resource/SIO_000093") +AnnotationAssertion(rdfs:label obo:GENO_0000248 "is_proper_part_of") +SubObjectPropertyOf(obo:GENO_0000248 obo:BFO_0000050) + +# Object Property: obo:GENO_0000251 (is_sequence_of) + +AnnotationAssertion(rdfs:label obo:GENO_0000251 "is_sequence_of") +ObjectPropertyDomain(obo:GENO_0000251 obo:GENO_0000702) + +# Object Property: obo:GENO_0000252 (is_subject_of) + +AnnotationAssertion(rdfs:label obo:GENO_0000252 "is_subject_of") +InverseObjectProperties(obo:GENO_0000252 obo:IAO_0000136) + +# Object Property: obo:GENO_0000253 (obsolete_is_specified_by) + +AnnotationAssertion(rdfs:label obo:GENO_0000253 "obsolete_is_specified_by") +SubObjectPropertyOf(obo:GENO_0000253 oboInOwl:ObsoleteProperty) + +# Object Property: obo:GENO_0000359 (obsolete_is_phenotype_of_genotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000359 "shortcut relation used to link a phenotype directly to a genotype of an organism") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000359 "is_phenotype_of_organism_with_genotype") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000359 "is_phenotype_with_genotype") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000359 "phenotype_has_genotype") +AnnotationAssertion(rdfs:comment obo:GENO_0000359 "Might expand to something like: + +phenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype)))))))") +AnnotationAssertion(rdfs:label obo:GENO_0000359 "obsolete_is_phenotype_of_genotype") +SubObjectPropertyOf(obo:GENO_0000359 oboInOwl:ObsoleteProperty) +ObjectPropertyDomain(obo:GENO_0000359 obo:UPHENO_0001001) + +# Object Property: obo:GENO_0000368 (obsolete_participates_in_inheritance_process) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000368 "A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000368 "Exploratory/temporary property, as we formalize our phenotypic inheritance model.") +AnnotationAssertion(rdfs:label obo:GENO_0000368 "obsolete_participates_in_inheritance_process") +SubObjectPropertyOf(obo:GENO_0000368 oboInOwl:ObsoleteProperty) +ObjectPropertyRange(obo:GENO_0000368 obo:GENO_0000141) + +# Object Property: obo:GENO_0000382 (has_variant_part) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000382 "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression.") +AnnotationAssertion(rdfs:label obo:GENO_0000382 "has_variant_part"@en) +SubObjectPropertyOf(obo:GENO_0000382 obo:GENO_0000654) +InverseObjectProperties(obo:GENO_0000382 obo:GENO_0000383) +TransitiveObjectProperty(obo:GENO_0000382) + +# Object Property: obo:GENO_0000383 (is_variant_part_of) + +AnnotationAssertion(rdfs:label obo:GENO_0000383 "is_variant_part_of"@en) +SubObjectPropertyOf(obo:GENO_0000383 obo:GENO_0000655) +TransitiveObjectProperty(obo:GENO_0000383) + +# Object Property: obo:GENO_0000385 (has_reference_part) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000385 "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000385 "has_reference_sequence_part") +AnnotationAssertion(rdfs:label obo:GENO_0000385 "has_reference_part") +SubObjectPropertyOf(obo:GENO_0000385 obo:GENO_0000654) +InverseObjectProperties(obo:GENO_0000385 obo:GENO_0000387) +TransitiveObjectProperty(obo:GENO_0000385) + +# Object Property: obo:GENO_0000387 (is_reference_part_of) + +AnnotationAssertion(rdfs:label obo:GENO_0000387 "is_reference_part_of") +SubObjectPropertyOf(obo:GENO_0000387 obo:GENO_0000655) + +# Object Property: obo:GENO_0000408 (is_allele_of) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000408 " is_allele_of the 'danio rerio fgf8a' gene locus.") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000408 "A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000408 "Domain = allele +Range = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation).") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000408 "Note that the allele is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000408 "is_sequence_variant_of") +AnnotationAssertion(rdfs:comment obo:GENO_0000408 "To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size). + +While conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like \"fgf8a is an allele of the Danio rerio fgf8a gene\", and we may create data where fgf8a is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene). + +It is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. + +This departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\\GAL4 gene. + +At the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'.") +AnnotationAssertion(rdfs:label obo:GENO_0000408 "is_allele_of") +SubObjectPropertyOf(obo:GENO_0000408 obo:GENO_0000418) +InverseObjectProperties(obo:GENO_0000408 obo:GENO_0000413) +ObjectPropertyDomain(obo:GENO_0000408 obo:GENO_0000481) + +# Object Property: obo:GENO_0000410 (obsolete_is_genetic_variant_of) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000410 "A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000410 "is_variant_instance_of") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000410 "formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus)") +AnnotationAssertion(rdfs:comment obo:GENO_0000410 "Domain = genomic feature instance +Range = punned gene class IRI") +AnnotationAssertion(rdfs:label obo:GENO_0000410 "obsolete_is_genetic_variant_of") +SubObjectPropertyOf(obo:GENO_0000410 oboInOwl:ObsoleteProperty) +InverseObjectProperties(obo:GENO_0000410 obo:GENO_0000411) + +# Object Property: obo:GENO_0000411 (obsolete_has_genetic_variant) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000411 "A relation linking a gene class to a sequence-varaint or expression-variant of the gene.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000411 "has_variant_instance") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000411 "formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by)") +AnnotationAssertion(rdfs:comment obo:GENO_0000411 "Domain = punned gene class +Range = genomic feature") +AnnotationAssertion(rdfs:label obo:GENO_0000411 "obsolete_has_genetic_variant") +SubObjectPropertyOf(obo:GENO_0000411 oboInOwl:ObsoleteProperty) + +# Object Property: obo:GENO_0000413 (has_allele) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000413 "A relation linking a gene class to one of its sequence-variant alleles.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000413 "Domain = punned gene class +Range = allele") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000413 "has_sequence_variant") +AnnotationAssertion(rdfs:label obo:GENO_0000413 "has_allele") +SubObjectPropertyOf(obo:GENO_0000413 obo:GENO_0000445) + +# Object Property: obo:GENO_0000414 (targets_gene) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000414 "A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets.") +AnnotationAssertion(rdfs:comment obo:GENO_0000414 "This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets.") +AnnotationAssertion(rdfs:label obo:GENO_0000414 "targets_gene") +SubObjectPropertyOf(obo:GENO_0000414 obo:GENO_0000418) +InverseObjectProperties(obo:GENO_0000414 obo:GENO_0000447) + +# Object Property: obo:GENO_0000418 (has_affected_feature) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000418 "A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression.") +AnnotationAssertion(rdfs:comment obo:GENO_0000418 "This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset.") +AnnotationAssertion(rdfs:label obo:GENO_0000418 "has_affected_feature") +InverseObjectProperties(obo:GENO_0000418 obo:GENO_0000445) + +# Object Property: obo:GENO_0000443 (is_expression_variant_of) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000443 "A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000443 "Domain = expression variant feature. +Range = punned gene class") +AnnotationAssertion(rdfs:comment obo:GENO_0000443 "This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class.") +AnnotationAssertion(rdfs:label obo:GENO_0000443 "is_expression_variant_of") +SubObjectPropertyOf(obo:GENO_0000443 obo:GENO_0000418) +InverseObjectProperties(obo:GENO_0000443 obo:GENO_0000449) + +# Object Property: obo:GENO_0000445 (is_feature_affected_by) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000445 "A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000445 "class_to_feature_relation") +AnnotationAssertion(rdfs:comment obo:GENO_0000445 "This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases)") +AnnotationAssertion(rdfs:label obo:GENO_0000445 "is_feature_affected_by") + +# Object Property: obo:GENO_0000447 (is_gene_target_of) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000447 "A relation between a gene class and a gene targeting reagent that targets it.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000447 "is_target_of") +AnnotationAssertion(rdfs:comment obo:GENO_0000447 "Domain = punned gene class +Range = gene knockdown reagent") +AnnotationAssertion(rdfs:label obo:GENO_0000447 "is_gene_target_of") +SubObjectPropertyOf(obo:GENO_0000447 obo:GENO_0000445) + +# Object Property: obo:GENO_0000449 (has_expression_variant) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000449 "A relation linking a gene class to one of an expression-variant of that gene..") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000449 "Domain = punned gene class +Range = expression variant feature") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000449 "has_expression_variant_instance") +AnnotationAssertion(rdfs:label obo:GENO_0000449 "has_expression_variant") +SubObjectPropertyOf(obo:GENO_0000449 obo:GENO_0000445) + +# Object Property: obo:GENO_0000486 (obsolete_is_variant_with) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000486 "A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression.") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000486 "Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property.") +AnnotationAssertion(rdfs:comment obo:GENO_0000486 "This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of.") +AnnotationAssertion(rdfs:label obo:GENO_0000486 "obsolete_is_variant_with"@en) +SubObjectPropertyOf(obo:GENO_0000486 oboInOwl:ObsoleteProperty) + +# Object Property: obo:GENO_0000488 (obsolete_is_expression_variant_with) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000488 "A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways).") +AnnotationAssertion(rdfs:label obo:GENO_0000488 "obsolete_is_expression_variant_with"@en) +SubObjectPropertyOf(obo:GENO_0000488 oboInOwl:ObsoleteProperty) + +# Object Property: obo:GENO_0000580 (has_qualifier) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000580 "A relation used to describe a context or conditions that define and/or identify an entity.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000580 "Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association. + +Used in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000580 "has_qualifying_context") +AnnotationAssertion(rdfs:label obo:GENO_0000580 "has_qualifier") + +# Object Property: obo:GENO_0000608 (has_zygosity) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000608 "a relation to link a single locus complement to its zygosity.") +AnnotationAssertion(rdfs:label obo:GENO_0000608 "has_zygosity"@en) +SubObjectPropertyOf(obo:GENO_0000608 obo:GENO_0000207) +ObjectPropertyDomain(obo:GENO_0000608 obo:GENO_0000516) +ObjectPropertyRange(obo:GENO_0000608 obo:GENO_0000133) + +# Object Property: obo:GENO_0000610 (is_reference_allele_of) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000610 "A relationship between a reference locus/allele and the gene class it is an allele of.") +AnnotationAssertion(rdfs:label obo:GENO_0000610 "is_reference_allele_of"@en) +SubObjectPropertyOf(obo:GENO_0000610 obo:GENO_0000408) +ObjectPropertyDomain(obo:GENO_0000610 obo:GENO_0000036) + +# Object Property: obo:GENO_0000626 (has_staining_intensity) + +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000626 "Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000626 "has_color_value"@en) +AnnotationAssertion(rdfs:comment obo:GENO_0000626 "Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized.") +AnnotationAssertion(rdfs:label obo:GENO_0000626 "has_staining_intensity") +SubObjectPropertyOf(obo:GENO_0000626 obo:GENO_0000207) + +# Object Property: obo:GENO_0000634 (is_targeted_by) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000634 "Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant.") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000634 "relation between an molecular agent and its molecular target") +AnnotationAssertion(rdfs:label obo:GENO_0000634 "is_targeted_by"@en) + +# Object Property: obo:GENO_0000639 (sequence_derives_from) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000639 "1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. + +2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds. + +3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC)") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000639 "Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence.") +AnnotationAssertion(rdfs:label obo:GENO_0000639 "sequence_derives_from"@en) +SubObjectPropertyOf(obo:GENO_0000639 owl:topObjectProperty) + +# Object Property: obo:GENO_0000641 (is_variant_allele_of) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000641 "A relationship between a variant allele and the gene class it is an allele of.") +AnnotationAssertion(rdfs:label obo:GENO_0000641 "is_variant_allele_of"@en) +SubObjectPropertyOf(obo:GENO_0000641 obo:GENO_0000408) +ObjectPropertyDomain(obo:GENO_0000641 obo:GENO_0000002) + +# Object Property: obo:GENO_0000650 (has_sex_agnostic_part) + +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000650 "Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases.") +AnnotationAssertion(rdfs:label obo:GENO_0000650 "has_sex_agnostic_part"@en) +SubObjectPropertyOf(obo:GENO_0000650 obo:GENO_0000654) +InverseObjectProperties(obo:GENO_0000650 obo:GENO_0000661) + +# Object Property: obo:GENO_0000651 (is_mutant_allele_of) + +AnnotationAssertion(rdfs:comment obo:GENO_0000651 "A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of.") +AnnotationAssertion(rdfs:label obo:GENO_0000651 "is_mutant_allele_of"@en) +SubObjectPropertyOf(obo:GENO_0000651 obo:GENO_0000641) +ObjectPropertyDomain(obo:GENO_0000651 obo:GENO_0000491) + +# Object Property: obo:GENO_0000652 (is_polymorphic_allele_of) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000652 "A relationship between a polymorphic allele and the gene class it is an allele of.") +AnnotationAssertion(rdfs:label obo:GENO_0000652 "is_polymorphic_allele_of"@en) +SubObjectPropertyOf(obo:GENO_0000652 obo:GENO_0000641) +ObjectPropertyDomain(obo:GENO_0000652 obo:GENO_0000497) + +# Object Property: obo:GENO_0000653 (is_wild_type_allele_of) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000653 "A relationship between a wild-type allele and the gene class it is an allele of.") +AnnotationAssertion(rdfs:label obo:GENO_0000653 "is_wild_type_allele_of"@en) +SubObjectPropertyOf(obo:GENO_0000653 obo:GENO_0000408) +ObjectPropertyDomain(obo:GENO_0000653 obo:GENO_0000501) + +# Object Property: obo:GENO_0000654 (has_sequence_part) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000654 "An organizational class to hold relations of parthood between sequences/features.") +AnnotationAssertion(rdfs:label obo:GENO_0000654 "has_sequence_part"@en) +SubObjectPropertyOf(obo:GENO_0000654 obo:BFO_0000051) +InverseObjectProperties(obo:GENO_0000654 obo:GENO_0000655) + +# Object Property: obo:GENO_0000655 (is_sequence_part_of) + +AnnotationAssertion(rdfs:label obo:GENO_0000655 "is_sequence_part_of"@en) +SubObjectPropertyOf(obo:GENO_0000655 obo:BFO_0000050) + +# Object Property: obo:GENO_0000661 (is_sex_agnostic_part_of) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000661 "Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases.") +AnnotationAssertion(rdfs:label obo:GENO_0000661 "is_sex_agnostic_part_of"@en) +SubObjectPropertyOf(obo:GENO_0000661 obo:GENO_0000655) + +# Object Property: obo:GENO_0000683 (varies_with) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000683 "A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part).") +AnnotationAssertion(rdfs:comment obo:GENO_0000683 "This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of)") +AnnotationAssertion(rdfs:label obo:GENO_0000683 "varies_with"@en) +SymmetricObjectProperty(obo:GENO_0000683) + +# Object Property: obo:GENO_0000708 (faldo properties) + +AnnotationAssertion(rdfs:comment obo:GENO_0000708 "organizational property to hold imports from faldo.") +AnnotationAssertion(rdfs:label obo:GENO_0000708 "faldo properties"@en) + +# Object Property: obo:GENO_0000726 (has_sequence_feature) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000726 "A relation linking a qualified sequence feature to its component sequence feature.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000726 "has_sequence_feature_component") +AnnotationAssertion(rdfs:comment obo:GENO_0000726 "In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism.") +AnnotationAssertion(rdfs:label obo:GENO_0000726 "has_sequence_feature"@en) +ObjectPropertyDomain(obo:GENO_0000726 ObjectUnionOf(obo:GENO_0000919 obo:GENO_0000920)) +ObjectPropertyRange(obo:GENO_0000726 obo:SO_0000110) + +# Object Property: obo:GENO_0000740 (has_inferred_phenotype) + +AnnotationAssertion(rdfs:label obo:GENO_0000740 "has_inferred_phenotype"@en) +SubObjectPropertyOf(obo:GENO_0000740 obo:RO_0002200) + +# Object Property: obo:GENO_0000741 (obsolete_has_regulatory_part) + +AnnotationAssertion(rdfs:comment obo:GENO_0000741 "Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes.") +AnnotationAssertion(rdfs:label obo:GENO_0000741 "obsolete_has_regulatory_part"@en) +SubObjectPropertyOf(obo:GENO_0000741 oboInOwl:ObsoleteProperty) + +# Object Property: obo:GENO_0000742 (obsolete_is_alteration_within) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000742 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000742 "A relation linking a sequence_alteration to the gene it alters.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000742 "is_within_allele_of") +AnnotationAssertion(rdfs:label obo:GENO_0000742 "obsolete_is_alteration_within"@en) +SubObjectPropertyOf(obo:GENO_0000742 oboInOwl:ObsoleteProperty) + +# Object Property: obo:GENO_0000743 (has_asserted_phenotype) + +AnnotationAssertion(rdfs:label obo:GENO_0000743 "has_asserted_phenotype"@en) +SubObjectPropertyOf(obo:GENO_0000743 obo:RO_0002200) + +# Object Property: obo:GENO_0000761 (is_regulatory_part_of) + +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000761 "Proposal for a property linking regulatory elements to larger features of which they are a part.") +AnnotationAssertion(rdfs:label obo:GENO_0000761 "is_regulatory_part_of"@en) +SubObjectPropertyOf(obo:GENO_0000761 obo:GENO_0000655) + +# Object Property: obo:GENO_0000767 (obsolete_has_position_component) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000767 "A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000767 "For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them.") +AnnotationAssertion(rdfs:label obo:GENO_0000767 "obsolete_has_position_component"@en) +SubObjectPropertyOf(obo:GENO_0000767 oboInOwl:ObsoleteProperty) + +# Object Property: obo:GENO_0000783 (has_sequence_unit) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000783 "A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues)") +AnnotationAssertion(rdfs:label obo:GENO_0000783 "has_sequence_unit"@en) +SubObjectPropertyOf(obo:GENO_0000783 obo:GENO_0000654) + +# Object Property: obo:GENO_0000784 (completely_varies_with) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000784 "A relation between two seqeunces or features that are considered variant with each other along their entire extents.") +AnnotationAssertion(rdfs:label obo:GENO_0000784 "completely_varies_with"@en) +SubObjectPropertyOf(obo:GENO_0000784 obo:GENO_0000683) +SymmetricObjectProperty(obo:GENO_0000784) + +# Object Property: obo:GENO_0000790 (related_condition) + +AnnotationAssertion(rdfs:label obo:GENO_0000790 "related_condition"@en) + +# Object Property: obo:GENO_0000791 (inferred_to_cause_condition) + +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000791 "Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene)") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000791 "The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains. + +Below are the different kinds/paths of propagation we desire: +1. Propagation 'down' a genotype (from larger components to smaller ones) +2. Propagation 'up' a genotype (from smaller components to larger ones) +3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype). +4. From an effective genotype to its intrinsic and extrinsic components. +5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele). +6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this. + +Note that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha/shha [AB] to shha/shha [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition')") +AnnotationAssertion(rdfs:label obo:GENO_0000791 "inferred_to_cause_condition"@en) +SubObjectPropertyOf(obo:GENO_0000791 obo:GENO_0000790) + +# Object Property: obo:GENO_0000793 (inferred_to_contribute_to_condition) + +AnnotationAssertion(rdfs:label obo:GENO_0000793 "inferred_to_contribute_to_condition"@en) +SubObjectPropertyOf(obo:GENO_0000793 obo:GENO_0000790) + +# Object Property: obo:GENO_0000794 (inferred_to_correlate_with_condition) + +AnnotationAssertion(rdfs:label obo:GENO_0000794 "inferred_to_correlate_with_condition"@en) +SubObjectPropertyOf(obo:GENO_0000794 obo:GENO_0000790) + +# Object Property: obo:GENO_0000840 (pathogenic_for_condition) + +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000840 "LOINC:LA6668-3") +AnnotationAssertion(rdfs:label obo:GENO_0000840 "pathogenic_for_condition"@en) +SubObjectPropertyOf(obo:GENO_0000840 obo:RO_0003303) + +# Object Property: obo:GENO_0000841 (likely_pathogenic_for_condition) + +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000841 "LOINC:LA26332-9") +AnnotationAssertion(rdfs:label obo:GENO_0000841 "likely_pathogenic_for_condition"@en) +SubObjectPropertyOf(obo:GENO_0000841 obo:RO_0003303) + +# Object Property: obo:GENO_0000842 (non-causal_for_condition) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000842 "Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to.") +AnnotationAssertion(rdfs:label obo:GENO_0000842 "non-causal_for_condition"@en) +SubObjectPropertyOf(obo:GENO_0000842 obo:GENO_0000790) + +# Object Property: obo:GENO_0000843 (benign_for_condition) + +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000843 "LOINC:LA6675-8") +AnnotationAssertion(rdfs:label obo:GENO_0000843 "benign_for_condition"@en) +SubObjectPropertyOf(obo:GENO_0000843 obo:GENO_0000842) + +# Object Property: obo:GENO_0000844 (likely_benign_for_condition) + +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000844 "LOINC:LA26334-5") +AnnotationAssertion(rdfs:label obo:GENO_0000844 "likely_benign_for_condition"@en) +SubObjectPropertyOf(obo:GENO_0000844 obo:GENO_0000842) + +# Object Property: obo:GENO_0000845 (has_uncertain_significance_for_condition) + +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000845 "LOINC:LA26333-7") +AnnotationAssertion(rdfs:label obo:GENO_0000845 "has_uncertain_significance_for_condition"@en) +SubObjectPropertyOf(obo:GENO_0000845 obo:GENO_0000790) + +# Object Property: obo:GENO_0000846 (has_qualifying_process) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000846 "A relation used to describe a process contextualizing the identity of an entity.") +AnnotationAssertion(rdfs:label obo:GENO_0000846 "has_qualifying_process"@en) +SubObjectPropertyOf(obo:GENO_0000846 obo:GENO_0000580) + +# Object Property: obo:GENO_0000847 (has_qualifying_environment) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000847 "A relation used to describe an environment contextualizing the identity of an entity.") +AnnotationAssertion(rdfs:label obo:GENO_0000847 "has_qualifying_environment"@en) +SubObjectPropertyOf(obo:GENO_0000847 obo:GENO_0000580) + +# Object Property: obo:GENO_0000849 (is_candidate_variant_for) + +AnnotationAssertion(rdfs:label obo:GENO_0000849 "is_candidate_variant_for"@en) +SubObjectPropertyOf(obo:GENO_0000849 obo:GENO_0000790) + +# Object Property: obo:GENO_0000903 (has_location) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000903 "A relation linking a sequence feature to the location it occupies on some reference sequence.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000903 "occupies") +AnnotationAssertion(rdfs:label obo:GENO_0000903 "has_location"@en) +ObjectPropertyDomain(obo:GENO_0000903 obo:SO_0000110) +ObjectPropertyRange(obo:GENO_0000903 obo:GENO_0000815) + +# Object Property: obo:GENO_0000906 (on strand) + +AnnotationAssertion(rdfs:comment obo:GENO_0000906 "Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from.") +AnnotationAssertion(rdfs:label obo:GENO_0000906 "on strand"@en) + +# Object Property: obo:GENO_0000957 (has_defining_location) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000957 "Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement.") +AnnotationAssertion(rdfs:comment obo:GENO_0000957 "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location. + +For copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement.") +AnnotationAssertion(rdfs:label obo:GENO_0000957 "has_defining_location"@en) +ObjectPropertyDomain(obo:GENO_0000957 ObjectUnionOf(obo:GENO_0000961 obo:GENO_0000963)) +ObjectPropertyRange(obo:GENO_0000957 obo:GENO_0000815) + +# Object Property: obo:GENO_0000958 (has_defining_sequence) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000958 "Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement.") +AnnotationAssertion(rdfs:comment obo:GENO_0000958 "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement.") +AnnotationAssertion(rdfs:label obo:GENO_0000958 "has_defining_sequence"@en) +ObjectPropertyDomain(obo:GENO_0000958 ObjectUnionOf(obo:GENO_0000961 obo:GENO_0000963)) +ObjectPropertyRange(obo:GENO_0000958 obo:GENO_0000702) + +# Object Property: obo:GENO_0000959 (has_defining_feature) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000959 "Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement.") +AnnotationAssertion(rdfs:comment obo:GENO_0000959 "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference. + +For copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement.") +AnnotationAssertion(rdfs:label obo:GENO_0000959 "has_defining_feature"@en) +ObjectPropertyDomain(obo:GENO_0000959 ObjectUnionOf(obo:GENO_0000961 obo:GENO_0000963)) +ObjectPropertyRange(obo:GENO_0000959 obo:SO_0000110) + +# Object Property: obo:GENO_0000966 (has_interval) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000966 "Relates a sequence feature location to an interval that defines its start and end position.") +AnnotationAssertion(rdfs:comment obo:GENO_0000966 "Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects.") +AnnotationAssertion(rdfs:label obo:GENO_0000966 "has_interval") +ObjectPropertyDomain(obo:GENO_0000966 obo:GENO_0000815) + +# Object Property: obo:GENO_0000967 (has_reference_sequence) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000967 "Relates a 'sequence feature location' to a sequence that it is anchored to.") +AnnotationAssertion(rdfs:label obo:GENO_0000967 "has_reference_sequence") + +# Object Property: obo:IAO_0000136 (is about) + +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000136 "is_about is a (currently) primitive relation that relates an information artifact to an entity.") +AnnotationAssertion(rdfs:label obo:IAO_0000136 "is about") + +# Object Property: obo:IAO_0000219 (denotes) + +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000219 "Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically") +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000219 "Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of.") +AnnotationAssertion(rdfs:label obo:IAO_0000219 "denotes") +SubObjectPropertyOf(obo:IAO_0000219 obo:IAO_0000136) + +# Object Property: obo:OBI_0000293 (has_specified_input) + +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000293 "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.") +AnnotationAssertion(rdfs:label obo:OBI_0000293 "has_specified_input") +SubObjectPropertyOf(obo:OBI_0000293 obo:RO_0002233) + +# Object Property: obo:OBI_0000299 (has_specified_output) + +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000299 "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.") +AnnotationAssertion(rdfs:label obo:OBI_0000299 "has_specified_output") +SubObjectPropertyOf(obo:OBI_0000299 obo:RO_0002234) + +# Object Property: obo:RO_0000052 (inheres_in) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0000052 "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence") +AnnotationAssertion(rdfs:label obo:RO_0000052 "inheres_in") + +# Object Property: obo:RO_0000053 (bearer of) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0000053 "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence") +AnnotationAssertion(rdfs:label obo:RO_0000053 "bearer of"@en) + +# Object Property: obo:RO_0000056 (participates in) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0000056 "a relation between a continuant and a process, in which the continuant is somehow involved in the process") +AnnotationAssertion(rdfs:label obo:RO_0000056 "participates in") +InverseObjectProperties(obo:RO_0000056 obo:RO_0000057) + +# Object Property: obo:RO_0000057 (has participant) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0000057 "a relation between a process and a continuant, in which the continuant is somehow involved in the process") +AnnotationAssertion(rdfs:label obo:RO_0000057 "has participant") + +# Object Property: obo:RO_0000059 (concretizes) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0000059 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0000059 "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.") +AnnotationAssertion(rdfs:label obo:RO_0000059 "concretizes"@en) + +# Object Property: obo:RO_0000086 (has quality) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0000086 "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence") +AnnotationAssertion(rdfs:label obo:RO_0000086 "has quality") +SubObjectPropertyOf(obo:RO_0000086 obo:RO_0000053) + +# Object Property: obo:RO_0000087 (has_role) + +AnnotationAssertion(rdfs:label obo:RO_0000087 "has_role") +SubObjectPropertyOf(obo:RO_0000087 obo:RO_0000053) + +# Object Property: obo:RO_0000091 (has disposition) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0000091 "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence") +AnnotationAssertion(rdfs:label obo:RO_0000091 "has disposition") +SubObjectPropertyOf(obo:RO_0000091 obo:RO_0000053) + +# Object Property: obo:RO_0001000 (derives from) + +AnnotationAssertion(rdfs:label obo:RO_0001000 "derives from") + +# Object Property: obo:RO_0002091 (starts during) + +AnnotationAssertion(rdfs:label obo:RO_0002091 "starts during") +SubObjectPropertyOf(obo:RO_0002091 obo:RO_0002222) + +# Object Property: obo:RO_0002093 (ends during) + +AnnotationAssertion(rdfs:label obo:RO_0002093 "ends during") +SubObjectPropertyOf(obo:RO_0002093 obo:RO_0002222) + +# Object Property: obo:RO_0002131 (overlaps) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002131 "x overlaps y if and only if there exists some z such that x has part z and z part of y") +AnnotationAssertion(rdfs:label obo:RO_0002131 "overlaps"@en) +SymmetricObjectProperty(obo:RO_0002131) + +# Object Property: obo:RO_0002162 (in taxon) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002162 "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.") +AnnotationAssertion(rdfs:label obo:RO_0002162 "in taxon"@en) + +# Object Property: obo:RO_0002200 (has phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002200 "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).") +AnnotationAssertion(rdfs:label obo:RO_0002200 "has phenotype") +InverseObjectProperties(obo:RO_0002200 obo:RO_0002201) +ObjectPropertyRange(obo:RO_0002200 obo:UPHENO_0001001) + +# Object Property: obo:RO_0002201 (phenotype of) + +AnnotationAssertion(rdfs:label obo:RO_0002201 "phenotype of"@en) +ObjectPropertyDomain(obo:RO_0002201 obo:UPHENO_0001001) + +# Object Property: obo:RO_0002222 (temporally related to) + +AnnotationAssertion(rdfs:label obo:RO_0002222 "temporally related to"@en) + +# Object Property: obo:RO_0002233 (has input) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002233 "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.") +AnnotationAssertion(rdfs:label obo:RO_0002233 "has input"@en) +SubObjectPropertyOf(obo:RO_0002233 obo:RO_0000057) + +# Object Property: obo:RO_0002234 (has output) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002234 "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.") +AnnotationAssertion(rdfs:label obo:RO_0002234 "has output"@en) +SubObjectPropertyOf(obo:RO_0002234 obo:RO_0000057) +InverseObjectProperties(obo:RO_0002234 obo:RO_0002353) + +# Object Property: obo:RO_0002350 (is member of) + +AnnotationAssertion(rdfs:label obo:RO_0002350 "is member of") +SubObjectPropertyOf(obo:RO_0002350 obo:BFO_0000050) +InverseObjectProperties(obo:RO_0002350 obo:RO_0002351) + +# Object Property: obo:RO_0002351 (has member) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0002351 "Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes + +Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002351 "has member is a mereological relation between a collection and an item.") +AnnotationAssertion(rdfs:label obo:RO_0002351 "has member") +SubObjectPropertyOf(obo:RO_0002351 obo:BFO_0000051) + +# Object Property: obo:RO_0002352 (input of) + +AnnotationAssertion(rdfs:label obo:RO_0002352 "input of"@en) +SubObjectPropertyOf(obo:RO_0002352 obo:RO_0000056) + +# Object Property: obo:RO_0002353 (output of) + +AnnotationAssertion(rdfs:label obo:RO_0002353 "output of"@en) +SubObjectPropertyOf(obo:RO_0002353 obo:RO_0000056) + +# Object Property: obo:RO_0002354 (obsolete_formed as result of) + +AnnotationAssertion(rdfs:label obo:RO_0002354 "obsolete_formed as result of"@en) +SubObjectPropertyOf(obo:RO_0002354 oboInOwl:ObsoleteProperty) + +# Object Property: obo:RO_000244 (molecularly controls) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_000244 "Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b") +AnnotationAssertion(rdfs:label obo:RO_000244 "molecularly controls"@en) + +# Object Property: obo:RO_0002522 (bounds sequence of) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002522 "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y") +AnnotationAssertion(obo:IAO_0000117 obo:RO_0002522 "Chris Mungall") +AnnotationAssertion(rdfs:label obo:RO_0002522 "bounds sequence of") +SubObjectPropertyOf(obo:RO_0002522 obo:GENO_0000654) + +# Object Property: obo:RO_0002524 (has subsequence) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002524 "x has subsequence y iff all of the sequence parts of x are sequence parts of y") +AnnotationAssertion(rdfs:label obo:RO_0002524 "has subsequence"@en) +SubObjectPropertyOf(obo:RO_0002524 obo:GENO_0000654) +InverseObjectProperties(obo:RO_0002524 obo:RO_0002525) + +# Object Property: obo:RO_0002525 (is subsequence of) + +AnnotationAssertion(rdfs:label obo:RO_0002525 "is subsequence of"@en) +SubObjectPropertyOf(obo:RO_0002525 obo:GENO_0000655) + +# Object Property: obo:RO_0002526 (overlaps sequence of) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002526 "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.") +AnnotationAssertion(dcterms:source obo:RO_0002526 "http://biorxiv.org/content/early/2014/06/27/006650.abstract") +AnnotationAssertion(rdfs:label obo:RO_0002526 "overlaps sequence of") +SubObjectPropertyOf(obo:RO_0002526 obo:RO_0002131) + +# Object Property: obo:RO_0002528 (is upstream of sequence of) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002528 "inverse of downstream of sequence of") +AnnotationAssertion(rdfs:label obo:RO_0002528 "is upstream of sequence of"@en) + +# Object Property: obo:RO_0002529 (is downstream of sequence of) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002529 "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.") +AnnotationAssertion(rdfs:label obo:RO_0002529 "is downstream of sequence of"@en) + +# Object Property: obo:RO_0003301 (is model of) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0003301 "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.") +AnnotationAssertion(obo:IAO_0000116 obo:RO_0003301 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?") +AnnotationAssertion(obo:IAO_0000117 obo:RO_0003301 "Matthew Brush") +AnnotationAssertion(rdfs:comment obo:RO_0003301 "The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest.") +AnnotationAssertion(rdfs:label obo:RO_0003301 "is model of"@en) + +# Object Property: obo:RO_0003302 (causes or contributes to condition) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0003302 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. + +An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0003302 "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition.") +AnnotationAssertion(obo:IAO_0000116 obo:RO_0003302 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.") +AnnotationAssertion(rdfs:comment obo:RO_0003302 "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.") +AnnotationAssertion(rdfs:label obo:RO_0003302 "causes or contributes to condition"@en) +SubObjectPropertyOf(obo:RO_0003302 obo:GENO_0000790) + +# Object Property: obo:RO_0003303 (causes condition) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0003303 "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition.") +AnnotationAssertion(rdfs:label obo:RO_0003303 "causes condition"@en) +SubObjectPropertyOf(obo:RO_0003303 obo:RO_0003302) + +# Object Property: obo:RO_0003304 (contributes to condition) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0003304 "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition.") +AnnotationAssertion(rdfs:label obo:RO_0003304 "contributes to condition"@en) +SubObjectPropertyOf(obo:RO_0003304 obo:RO_0003302) + +# Object Property: obo:RO_0003305 (contributes to severity of condition) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0003305 "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual.") +AnnotationAssertion(obo:IAO_0000118 obo:RO_0003305 "contributes to expressivity of condition") +AnnotationAssertion(rdfs:label obo:RO_0003305 "contributes to severity of condition"@en) +SubObjectPropertyOf(obo:RO_0003305 obo:RO_0003304) + +# Object Property: obo:RO_0003306 (contributes to frequency of condition) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0003306 "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population.") +AnnotationAssertion(obo:IAO_0000118 obo:RO_0003306 "contributes to penetrance of condition") +AnnotationAssertion(rdfs:label obo:RO_0003306 "contributes to frequency of condition"@en) +SubObjectPropertyOf(obo:RO_0003306 obo:RO_0003304) + +# Object Property: obo:RO_0003307 (is preventative for condition) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0003307 "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition.") +AnnotationAssertion(rdfs:comment obo:RO_0003307 "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.") +AnnotationAssertion(rdfs:label obo:RO_0003307 "is preventative for condition"@en) +SubObjectPropertyOf(obo:RO_0003307 obo:GENO_0000790) + +# Object Property: obo:RO_0003308 (correlated with condition) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0003308 "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.") +AnnotationAssertion(rdfs:label obo:RO_0003308 "correlated with condition"@en) +SubObjectPropertyOf(obo:RO_0003308 obo:GENO_0000790) + +# Object Property: (association has object) + +AnnotationAssertion(rdfs:label "association has object"@en) + +# Object Property: (association has predicate) + +AnnotationAssertion(rdfs:label "association has predicate"@en) + +# Object Property: (association has subject) + +AnnotationAssertion(rdfs:label "association has subject"@en) + + +############################ +# Data Properties +############################ + +# Data Property: (position) + +AnnotationAssertion(rdfs:comment "The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is.") +AnnotationAssertion(rdfs:label "position"@en) + +# Data Property: obo:GENO_0000678 (has_extent) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000678 "Property linking a sequence or sequence feature to an integer representing its length in terms of the number of units in the sequence.") +AnnotationAssertion(rdfs:label obo:GENO_0000678 "has_extent"@en) +DataPropertyRange(obo:GENO_0000678 xsd:int) + +# Data Property: obo:GENO_0000703 (has_sequence_string) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000703 "Shortcut relation linking a sequence feature directly to a string representing the 'state' of its sequence - i.e. the ordering of units that comprise it (e.g. 'atgcagctagctaccgtcgatcg').") +AnnotationAssertion(rdfs:label obo:GENO_0000703 "has_sequence_string"@en) +DataPropertyDomain(obo:GENO_0000703 obo:SO_0000110) +DataPropertyRange(obo:GENO_0000703 xsd:string) + +# Data Property: obo:GENO_0000712 (ObsoleteDataProperty) + +AnnotationAssertion(rdfs:label obo:GENO_0000712 "ObsoleteDataProperty"@en) + +# Data Property: obo:GENO_0000866 (has_quantifier) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000866 "The 'rank' quantifier in Bgee gene-anatomy associations, that indicates the imporatnace/specificity of a gene expression in a given anatommy relative to expressionin other anatomies for the same gene.") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000866 "Property to link an assertion or association with some value quantifying its relevance or ranking.") +AnnotationAssertion(rdfs:label obo:GENO_0000866 "has_quantifier"@en) + +# Data Property: obo:GENO_0000894 (start_position) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000894 "The starting position of a sequence feature or interval.") +AnnotationAssertion(rdfs:label obo:GENO_0000894 "start_position") + +# Data Property: obo:GENO_0000895 (end_position) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000895 "The ending position of a sequence feature or interval.") +AnnotationAssertion(rdfs:label obo:GENO_0000895 "end_position") + +# Data Property: obo:GENO_0000896 (has_string) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000896 "Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg').") +AnnotationAssertion(rdfs:label obo:GENO_0000896 "has_string") +DataPropertyDomain(obo:GENO_0000896 obo:GENO_0000702) +DataPropertyRange(obo:GENO_0000896 xsd:string) + +# Data Property: obo:GENO_0000917 (has_member_count) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000917 "Describes the number of members in some set.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000917 "has_count") +AnnotationAssertion(rdfs:comment obo:GENO_0000917 "In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'.") +AnnotationAssertion(rdfs:label obo:GENO_0000917 "has_member_count"@en) + + + +############################ +# Classes +############################ + +# Class: (Both strands) + +AnnotationAssertion(rdfs:label "Both strands"@en) +SubClassOf( ) + +# Class: (Exact position) + +AnnotationAssertion(obo:IAO_0000115 "A position that is exactly known.") +AnnotationAssertion(rdfs:label "Exact position"@en) +SubClassOf( ) + +# Class: (Positive strand) + +AnnotationAssertion(rdfs:label "Positive strand"@en) +SubClassOf( ) + +# Class: (Position) + +AnnotationAssertion(obo:IAO_0000115 "Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate.") +AnnotationAssertion(obo:IAO_0000116 "We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region).") +AnnotationAssertion(obo:IAO_0000412 "FALDO") +AnnotationAssertion(rdfs:label "Position"@en) +SubClassOf( obo:GENO_0000902) + +# Class: (Region) + +AnnotationAssertion(obo:IAO_0000115 "A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene.") +AnnotationAssertion(obo:IAO_0000116 "From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence.") +AnnotationAssertion(rdfs:label "Region"@en) +SubClassOf( obo:SO_0000110) +SubClassOf( ObjectIntersectionOf(ObjectExactCardinality(1 ) ObjectExactCardinality(1 ))) + +# Class: (Negative strand) + +AnnotationAssertion(rdfs:label "Negative strand"@en) +SubClassOf( ) + +# Class: (Stranded position) + +AnnotationAssertion(rdfs:comment "Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'.") +AnnotationAssertion(rdfs:label "Stranded position"@en) +SubClassOf( ) + +# Class: obo:BFO_0000001 (entity) + +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000001 "Julius Caesar"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000001 "Verdi’s Requiem"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000001 "the Second World War"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000001 "your body mass index"@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000001 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000001 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"@en) +AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000001 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000001 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000001 "entity"@en) + +# Class: obo:BFO_0000002 (continuant) + +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000002 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000002 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en) +AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000002 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000002 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000002 "continuant") +AnnotationAssertion(rdfs:label obo:BFO_0000002 "continuant"@en) +SubClassOf(obo:BFO_0000002 obo:BFO_0000001) +DisjointClasses(obo:BFO_0000002 obo:BFO_0000003) + +# Class: obo:BFO_0000003 (occurrent) + +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000003 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000003 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000003 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process."@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000003 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.") +AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000003 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000003 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000003 "occurrent") +AnnotationAssertion(rdfs:label obo:BFO_0000003 "occurrent"@en) +SubClassOf(obo:BFO_0000003 obo:BFO_0000001) + +# Class: obo:BFO_0000004 (independent continuant) + +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000004 "a chair"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000004 "a heart"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000004 "a leg"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000004 "a molecule"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000004 "a spatial region"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000004 "an atom"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000004 "an orchestra."@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000004 "an organism"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000004 "the bottom right portion of a human torso"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000004 "the interior of your mouth"@en) +AnnotationAssertion(obo:IAO_0000115 obo:BFO_0000004 "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000004 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000004 "independent continuant") +AnnotationAssertion(rdfs:label obo:BFO_0000004 "independent continuant"@en) +SubClassOf(obo:BFO_0000004 obo:BFO_0000002) + +# Class: obo:BFO_0000015 (process) + +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000015 "a process of cell-division, \\ a beating of the heart"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000015 "a process of meiosis"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000015 "a process of sleeping"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000015 "the course of a disease"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000015 "the flight of a bird"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000015 "the life of an organism"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000015 "your process of aging."@en) +AnnotationAssertion(obo:IAO_0000115 obo:BFO_0000015 "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000015 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000015 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000015 "process") +AnnotationAssertion(rdfs:label obo:BFO_0000015 "process"@en) +SubClassOf(obo:BFO_0000015 obo:BFO_0000003) + +# Class: obo:BFO_0000016 (disposition) + +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000016 "an atom of element X has the disposition to decay to an atom of element Y"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000016 "certain people have a predisposition to colon cancer"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000016 "children are innately disposed to categorize objects in certain ways."@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000016 "the cell wall is disposed to filter chemicals in endocitosis and exocitosis"@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000016 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89"@en) +AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000016 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000016 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000016 "disposition") +AnnotationAssertion(rdfs:label obo:BFO_0000016 "disposition"@en) +SubClassOf(obo:BFO_0000016 obo:BFO_0000017) +DisjointClasses(obo:BFO_0000016 obo:BFO_0000023) + +# Class: obo:BFO_0000017 (realizable entity) + +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000017 "the disposition of this piece of metal to conduct electricity."@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000017 "the disposition of your blood to coagulate"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000017 "the function of your reproductive organs"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000017 "the role of being a doctor"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000017 "the role of this boundary to delineate where Utah and Colorado meet"@en) +AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000017 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000017 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000017 "realizable entity") +AnnotationAssertion(rdfs:label obo:BFO_0000017 "realizable entity"@en) +SubClassOf(obo:BFO_0000017 obo:BFO_0000020) +DisjointClasses(obo:BFO_0000017 obo:BFO_0000019) + +# Class: obo:BFO_0000019 (quality) + +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000019 "the ambient temperature of this portion of air"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000019 "the color of a tomato"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000019 "the length of the circumference of your waist"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000019 "the mass of this piece of gold."@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000019 "the shape of your nose"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000019 "the shape of your nostril"@en) +AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000019 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000019 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000019 "quality") +AnnotationAssertion(rdfs:label obo:BFO_0000019 "quality"@en) +SubClassOf(obo:BFO_0000019 obo:BFO_0000020) + +# Class: obo:BFO_0000020 (specifically dependent continuant) + +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "of one-sided specifically dependent continuants: the mass of this tomato"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "the disposition of this fish to decay"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "the function of this heart: to pump blood"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "the pink color of a medium rare piece of grilled filet mignon at its center"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "the role of being a doctor"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "the shape of this hole."@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "the smell of this portion of mozzarella"@en) +AnnotationAssertion(obo:IAO_0000115 obo:BFO_0000020 "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])"@en) +AnnotationAssertion(obo:IAO_0000115 obo:BFO_0000020 "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000020 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000020 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000020 "specifically dependent continuant") +AnnotationAssertion(rdfs:label obo:BFO_0000020 "specifically dependent continuant"@en) +SubClassOf(obo:BFO_0000020 obo:BFO_0000002) + +# Class: obo:BFO_0000023 (role) + +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000023 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000023 "the priest role"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000023 "the role of a boundary to demarcate two neighboring administrative territories"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000023 "the role of a building in serving as a military target"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000023 "the role of a stone in marking a property boundary"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000023 "the role of subject in a clinical trial"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000023 "the student role"@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000023 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) +AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000023 "b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000023 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000023 "role") +AnnotationAssertion(rdfs:label obo:BFO_0000023 "role"@en) +SubClassOf(obo:BFO_0000023 obo:BFO_0000017) + +# Class: obo:BFO_0000031 (generically dependent continuant) + +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000031 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000031 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000031 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) +AnnotationAssertion(obo:IAO_0000115 obo:BFO_0000031 "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000031 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000031 "generically dependent continuant") +AnnotationAssertion(rdfs:label obo:BFO_0000031 "generically dependent continuant"@en) +SubClassOf(obo:BFO_0000031 obo:BFO_0000002) + +# Class: obo:BFO_0000034 (function) + +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000034 "the function of a hammer to drive in nails"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000034 "the function of a heart pacemaker to regulate the beating of a heart through electricity"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000034 "the function of amylase in saliva to break down starch into sugar"@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000034 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc."@en) +AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000034 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000034 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000034 "function"@en) +SubClassOf(obo:BFO_0000034 obo:BFO_0000016) + +# Class: obo:BFO_0000040 (material entity) + +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "a flame"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "a forest fire"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "a human being"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "a hurricane"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "a photon"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "a puff of smoke"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "a sea wave"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "a tornado"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "an aggregate of human beings."@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "an energy wave"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "an epidemic"@en) +AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "the undetached arm of a human being"@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000040 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000040 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."@en) +AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000040 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."@en) +AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000040 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"@en) +AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000040 obo:bfo.owl) +AnnotationAssertion(rdfs:label obo:BFO_0000040 "material entity") +AnnotationAssertion(rdfs:label obo:BFO_0000040 "material entity"@en) +SubClassOf(obo:BFO_0000040 obo:BFO_0000004) + +# Class: obo:CHEBI_23367 (molecular entity) + +AnnotationAssertion(obo:IAO_0000116 obo:CHEBI_23367 "Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology.") +AnnotationAssertion(rdfs:label obo:CHEBI_23367 "molecular entity") +SubClassOf(obo:CHEBI_23367 obo:BFO_0000040) + +# Class: obo:CHEBI_33696 (nucleic acid) + +AnnotationAssertion(rdfs:label obo:CHEBI_33696 "nucleic acid") +SubClassOf(obo:CHEBI_33696 obo:CHEBI_23367) + +# Class: obo:CLO_0000031 (cell line) + +AnnotationAssertion(obo:IAO_0000115 obo:CLO_0000031 "A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).") +AnnotationAssertion(rdfs:label obo:CLO_0000031 "cell line"@en) +SubClassOf(obo:CLO_0000031 obo:BFO_0000040) +SubClassOf(obo:CLO_0000031 ObjectSomeValuesFrom(obo:RO_0001000 obo:OBI_0100026)) + +# Class: obo:CL_0000000 (cell) + +AnnotationAssertion(rdfs:comment obo:CL_0000000 "Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies.") +AnnotationAssertion(rdfs:label obo:CL_0000000 "cell") +SubClassOf(obo:CL_0000000 obo:UBERON_0001062) + +# Class: obo:ENVO_01000254 (environmental system) + +AnnotationAssertion(obo:IAO_0000116 obo:ENVO_01000254 "1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions. + +2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity).") +AnnotationAssertion(rdfs:comment obo:ENVO_01000254 "In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class \"system\". The relation \"environed_by\" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.") +AnnotationAssertion(rdfs:label obo:ENVO_01000254 "environmental system") +SubClassOf(obo:ENVO_01000254 obo:BFO_0000040) + +# Class: obo:ERO_0000007 (technique) + +AnnotationAssertion(obo:IAO_0000115 obo:ERO_0000007 "A technique is a planned process used to accomplish a specific activity or task.") +AnnotationAssertion(rdfs:label obo:ERO_0000007 "technique"@en) +SubClassOf(obo:ERO_0000007 obo:OBI_0000011) + +# Class: obo:ERO_0002002 (embryonic stem cell line) + +AnnotationAssertion(obo:IAO_0000115 obo:ERO_0002002 "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo.") +AnnotationAssertion(rdfs:label obo:ERO_0002002 "embryonic stem cell line"@en) +SubClassOf(obo:ERO_0002002 obo:ERO_0002003) + +# Class: obo:ERO_0002003 (stem cell line) + +AnnotationAssertion(obo:IAO_0000115 obo:ERO_0002003 "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types.") +AnnotationAssertion(rdfs:label obo:ERO_0002003 "stem cell line"@en) +SubClassOf(obo:ERO_0002003 obo:CLO_0000031) + +# Class: obo:GENO_0000000 (genomic genotype (sex-agnostic)) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000000 "Example zebrafish intrinsic genotype: + +Genotype = fgf8a; shha (AB) +reference component (genomic background) = AB +variant component ('genomic variation complement') = fgf8a; shha + +. . . and within this variant component, there are two 'variant single locus complements' represented: + +allele complement 1 = fgf8a +allele complement 2 = shha + +and within each of these 'variant single locus complements' there is one or more variant gene locus member: + +in complement 1: fgf8a +in complement 2: shha") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000000 "A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement)") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000000 "This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). + +Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000000 "genotype") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000000 "organismal genotype") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000000 "sex-agnostic intrinsic genotype") +AnnotationAssertion(rdfs:comment obo:GENO_0000000 "In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances).") +AnnotationAssertion(rdfs:label obo:GENO_0000000 "genomic genotype (sex-agnostic)") +SubClassOf(obo:GENO_0000000 obo:GENO_0000899) + +# Class: obo:GENO_0000002 (variant allele) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000002 "An allele that varies in it sequence from what is considered the reference or canonical sequence at that location.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000002 "The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000002 "alternate allele") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000002 "sequence-variant feature") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000002 "variant feature") +AnnotationAssertion(rdfs:comment obo:GENO_0000002 "Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another. + +A variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence.") +AnnotationAssertion(rdfs:label obo:GENO_0000002 "variant allele") +EquivalentClasses(obo:GENO_0000002 ObjectIntersectionOf(obo:GENO_0000512 ObjectSomeValuesFrom(obo:GENO_0000683 obo:GENO_0000036))) +SubClassOf(obo:GENO_0000002 ObjectUnionOf(obo:SO_0001059 ObjectSomeValuesFrom(obo:RO_0002524 obo:SO_0001059))) + +# Class: obo:GENO_0000009 (genomic variation complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000009 "A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000009 "Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases.") +AnnotationAssertion(rdfs:comment obo:GENO_0000009 "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation. + +In model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)).") +AnnotationAssertion(rdfs:label obo:GENO_0000009 "genomic variation complement") +EquivalentClasses(obo:GENO_0000009 ObjectIntersectionOf(obo:GENO_0000660 ObjectSomeValuesFrom(obo:GENO_0000382 obo:GENO_0000030))) + +# Class: obo:GENO_0000010 (background genome) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000010 "The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB)") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000010 "A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000010 "Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000010 "genomic background") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000010 "OBI:genetic population background information") +AnnotationAssertion(rdfs:label obo:GENO_0000010 "background genome") +SubClassOf(obo:GENO_0000010 obo:GENO_0000914) + +# Class: obo:GENO_0000014 (gene allele) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000014 "The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The \"mn004Gt\" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome. + +http://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722 + +http://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000014 "A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene)") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000014 "Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment). + +This design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000014 "http://purl.obolibrary.org/obo/SO_0001023 ! allele") +AnnotationAssertion(rdfs:comment obo:GENO_0000014 "In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion. + +A genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene.") +AnnotationAssertion(rdfs:label obo:GENO_0000014 "gene allele") +SubClassOf(obo:GENO_0000014 obo:GENO_0000512) +SubClassOf(obo:GENO_0000014 ObjectSomeValuesFrom(obo:GENO_0000408 obo:SO_0000704)) + +# Class: obo:GENO_0000017 (reference sequence) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000017 "A sequence that serves as a standard against which other sequences at the same location are compared.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000017 "The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000017 "reference sequence") +AnnotationAssertion(rdfs:comment obo:GENO_0000017 "A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence.") +AnnotationAssertion(rdfs:label obo:GENO_0000017 "reference sequence") +EquivalentClasses(obo:GENO_0000017 ObjectIntersectionOf(obo:GENO_0000702 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000152))) + +# Class: obo:GENO_0000019 (obsolete_sequence feature collection) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000019 "a collection more than one sequence features (ie a collection of discontinuous sequence features)") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000019 "perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one)") +AnnotationAssertion(rdfs:comment obo:GENO_0000019 "1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions.") +AnnotationAssertion(rdfs:label obo:GENO_0000019 "obsolete_sequence feature collection") +SubClassOf(obo:GENO_0000019 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000022 (obsolete_genomic feature collection) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000022 "A sequence feature collection comprised of discontiguous sequences from a single genome") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000022 "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000022 "genomic feature collection") +AnnotationAssertion(rdfs:comment obo:GENO_0000022 "Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection.") +AnnotationAssertion(rdfs:label obo:GENO_0000022 "obsolete_genomic feature collection") +SubClassOf(obo:GENO_0000022 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000029 (obsolete_reference single locus complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000029 "A single locus complement that serves as a standard against which 'variant' sequences are compared") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000029 "reference allelic complement") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000029 "reference single locus feature complement") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000029 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class axiom: +'single locus complement' + and (has_sequence_attribute some reference) + +SC axioms: +'has member' exactly 0 'variant allele' +'has member' only 'reference genomic feature' +'has member' some 'reference genomic feature'") +AnnotationAssertion(rdfs:label obo:GENO_0000029 "obsolete_reference single locus complement") +SubClassOf(obo:GENO_0000029 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000030 (variant single locus complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000030 "A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000030 "variant allelic complement"@en) +AnnotationAssertion(rdfs:comment obo:GENO_0000030 "Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members. + +Note that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant.") +AnnotationAssertion(rdfs:label obo:GENO_0000030 "variant single locus complement") +EquivalentClasses(obo:GENO_0000030 ObjectIntersectionOf(obo:GENO_0000516 ObjectSomeValuesFrom(obo:GENO_0000382 obo:GENO_0000002))) + +# Class: obo:GENO_0000033 (variant genome) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000033 "A genome that varies at one or more loci from the sequence of some reference genome.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000033 "http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here)") +AnnotationAssertion(rdfs:label obo:GENO_0000033 "variant genome") +EquivalentClasses(obo:GENO_0000033 ObjectIntersectionOf(obo:SO_0001026 ObjectSomeValuesFrom(obo:GENO_0000683 obo:GENO_0000914))) +SubClassOf(obo:GENO_0000033 ObjectSomeValuesFrom(obo:GENO_0000382 obo:SO_0001059)) + +# Class: obo:GENO_0000036 (reference allele) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000036 "An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome.") +AnnotationAssertion(rdfs:comment obo:GENO_0000036 "Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population. + +In model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared.") +AnnotationAssertion(rdfs:label obo:GENO_0000036 "reference allele") +EquivalentClasses(obo:GENO_0000036 ObjectIntersectionOf(obo:GENO_0000512 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000152))) + +# Class: obo:GENO_0000037 (obsolete_unspecified feature) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000037 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000037 "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus).") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000037 "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '.") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000037 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class def: 'genomic feature' + and (has_sequence_attribute some unspecified)") +AnnotationAssertion(rdfs:comment obo:GENO_0000037 "An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele).") +AnnotationAssertion(rdfs:label obo:GENO_0000037 "obsolete_unspecified feature") +SubClassOf(obo:GENO_0000037 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000042 (obsolete_reference junction) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000042 "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000042 "hemizygous reference junction") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000042 "Eliminating unecessary defined/organizational classes. Former logical def: + +junction + and (has_sequence_attribute some reference) + +Subclass axiom: +is_variant_with some insertion") +AnnotationAssertion(rdfs:comment obo:GENO_0000042 "In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. + +The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation.") +AnnotationAssertion(rdfs:label obo:GENO_0000042 "obsolete_reference junction") +SubClassOf(obo:GENO_0000042 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000047 (danio rerio gene) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000047 "A gene that originates from the genome of a danio rerio.") +AnnotationAssertion(rdfs:label obo:GENO_0000047 "danio rerio gene") +EquivalentClasses(obo:GENO_0000047 ObjectIntersectionOf(obo:SO_0000704 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_7955))) + +# Class: obo:GENO_0000054 (homo sapiens gene) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000054 "A gene that originates from the genome of a homo sapiens.") +AnnotationAssertion(rdfs:label obo:GENO_0000054 "homo sapiens gene") +EquivalentClasses(obo:GENO_0000054 ObjectIntersectionOf(obo:SO_0000704 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_9606))) + +# Class: obo:GENO_0000057 (mus musculus gene) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000057 "A gene that originates from the genome of a mus musculus.") +AnnotationAssertion(rdfs:label obo:GENO_0000057 "mus musculus gene") +EquivalentClasses(obo:GENO_0000057 ObjectIntersectionOf(obo:SO_0000704 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_10090))) + +# Class: obo:GENO_0000060 (obsolete_reference gene allele) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000060 "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development. +http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690 + +Note that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000060 "A version/allele of a gene that serves as a standard against which variant genes are compared.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000060 "reference gene") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000060 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class axiom: +'gene allele' + and (has_sequence_attribute some reference) + +SC axioms: +is_variant_with some 'gene allele' +is_reference_allele_of some gene") +AnnotationAssertion(rdfs:comment obo:GENO_0000060 "Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. + +In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared.") +AnnotationAssertion(rdfs:label obo:GENO_0000060 "obsolete_reference gene allele") +SubClassOf(obo:GENO_0000060 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000091 (obsolete_experimental insertion) + +AnnotationAssertion(rdfs:label obo:GENO_0000091 "obsolete_experimental insertion") +SubClassOf(obo:GENO_0000091 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000092 (gene trap insertion) + +AnnotationAssertion(rdfs:label obo:GENO_0000092 "gene trap insertion") +SubClassOf(obo:GENO_0000092 obo:SO_0000667) +SubClassOf(obo:GENO_0000092 ObjectSomeValuesFrom(obo:RO_0002353 obo:GENO_0000172)) + +# Class: obo:GENO_0000093 (integrated transgene) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000093 "A transgene that has been integrated into a chrromosome in the host genome.") +AnnotationAssertion(rdfs:comment obo:GENO_0000093 "An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion. + +An 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome.") +AnnotationAssertion(rdfs:label obo:GENO_0000093 "integrated transgene") +SubClassOf(obo:GENO_0000093 obo:SO_0000902) +SubClassOf(obo:GENO_0000093 ObjectSomeValuesFrom(obo:BFO_0000050 obo:SO_0001218)) + +# Class: obo:GENO_0000106 (genomic material) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000106 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000106 "A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000106 "1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. + +2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way.") +AnnotationAssertion(rdfs:comment obo:GENO_0000106 "1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. + +2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms.") +AnnotationAssertion(rdfs:label obo:GENO_0000106 "genomic material") +SubClassOf(obo:GENO_0000106 obo:GENO_0000482) +SubClassOf(obo:GENO_0000106 ObjectSomeValuesFrom(obo:BFO_0000050 obo:GENO_0000108)) +SubClassOf(obo:GENO_0000106 ObjectSomeValuesFrom(obo:GENO_0000248 ObjectUnionOf(obo:CL_0000000 obo:NCBITaxon_10239))) +SubClassOf(obo:GENO_0000106 ObjectSomeValuesFrom(obo:RO_0000091 obo:GENO_0000139)) + +# Class: obo:GENO_0000108 (material genome) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000108 "A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000108 "physical genome") +AnnotationAssertion(rdfs:comment obo:GENO_0000108 "A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements. + +Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome.") +AnnotationAssertion(rdfs:label obo:GENO_0000108 "material genome") +SubClassOf(obo:GENO_0000108 obo:BFO_0000040) + +# Class: obo:GENO_0000111 (human population) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000111 "a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000111 "Consider http://semanticscience.org/resource/SIO_001062 ! human population (\"A human population refers to a collection of human beings\").") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000111 "homo sapiens population") +AnnotationAssertion(rdfs:label obo:GENO_0000111 "human population") +SubClassOf(obo:GENO_0000111 obo:OBI_0000181) + +# Class: obo:GENO_0000112 (strain or breed) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000112 "A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000112 "organism strain or breed") +AnnotationAssertion(rdfs:comment obo:GENO_0000112 "Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR)") +AnnotationAssertion(rdfs:label obo:GENO_0000112 "strain or breed") +SubClassOf(obo:GENO_0000112 obo:GENO_0000113) +SubClassOf(obo:GENO_0000112 ObjectSomeValuesFrom(obo:RO_0002162 obo:OBI_0100026)) + +# Class: obo:GENO_0000113 (taxonomic group) + +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000113 "A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon)") +AnnotationAssertion(rdfs:label obo:GENO_0000113 "taxonomic group") +SubClassOf(obo:GENO_0000113 obo:PCO_0000000) + +# Class: obo:GENO_0000118 (mus musculus strain) + +AnnotationAssertion(rdfs:label obo:GENO_0000118 "mus musculus strain") +SubClassOf(obo:GENO_0000118 obo:GENO_0000112) + +# Class: obo:GENO_0000119 (danio rerio strain) + +AnnotationAssertion(rdfs:label obo:GENO_0000119 "danio rerio strain") +SubClassOf(obo:GENO_0000119 obo:GENO_0000112) +SubClassOf(obo:GENO_0000119 ObjectSomeValuesFrom(obo:RO_0002351 obo:NCBITaxon_7955)) +SubClassOf(obo:GENO_0000119 ObjectAllValuesFrom(obo:RO_0002351 obo:NCBITaxon_7955)) + +# Class: obo:GENO_0000125 (obsolete_sequence feature collection attribute) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000125 "sequence attribute that can inhere only in a collection of more than one sequence features") +AnnotationAssertion(rdfs:label obo:GENO_0000125 "obsolete_sequence feature collection attribute") +SubClassOf(obo:GENO_0000125 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000131 (in cis) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000131 "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes).") +AnnotationAssertion(rdfs:label obo:GENO_0000131 "in cis") +SubClassOf(obo:GENO_0000131 obo:GENO_0000886) + +# Class: obo:GENO_0000132 (in trans) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000132 "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes).") +AnnotationAssertion(rdfs:label obo:GENO_0000132 "in trans") +SubClassOf(obo:GENO_0000132 obo:GENO_0000886) + +# Class: obo:GENO_0000133 (zygosity) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000133 "An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000133 "allelic state") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000133 "derived from https://en.wikipedia.org/wiki/Zygosity") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000133 "http://semanticscience.org/resource/SIO_001263") +AnnotationAssertion(rdfs:label obo:GENO_0000133 "zygosity") +SubClassOf(obo:GENO_0000133 obo:GENO_0000875) +SubClassOf(obo:GENO_0000133 ObjectSomeValuesFrom(obo:RO_0000052 obo:GENO_0000516)) + +# Class: obo:GENO_0000134 (hemizygous) + +AnnotationAssertion(rdfs:label obo:GENO_0000134 "hemizygous") +SubClassOf(obo:GENO_0000134 obo:GENO_0000391) + +# Class: obo:GENO_0000135 (heterozygous) + +AnnotationAssertion(rdfs:label obo:GENO_0000135 "heterozygous") +SubClassOf(obo:GENO_0000135 obo:GENO_0000391) + +# Class: obo:GENO_0000136 (homozygous) + +AnnotationAssertion(rdfs:label obo:GENO_0000136 "homozygous") +SubClassOf(obo:GENO_0000136 obo:GENO_0000391) + +# Class: obo:GENO_0000137 (unspecified zygosity) + +AnnotationAssertion(Annotation(rdfs:comment "MGI uses this term when zygosity is not known.") obo:IAO_0000118 obo:GENO_0000137 "indeterminite zygosity") +AnnotationAssertion(Annotation(rdfs:comment "(this is how the GVF10 format/standard refers to loci without enough data to make an accurate call . . . see http://www.sequenceontology.org/resources/gvf.html#quick_gvf_examples)") obo:IAO_0000118 obo:GENO_0000137 "no-call zygosity") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000137 "unknown zygosity") +AnnotationAssertion(rdfs:label obo:GENO_0000137 "unspecified zygosity") +SubClassOf(obo:GENO_0000137 obo:GENO_0000133) + +# Class: obo:GENO_0000138 (heritabililty) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000138 "The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event.") +AnnotationAssertion(rdfs:comment obo:GENO_0000138 "We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells). + +We can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms.") +AnnotationAssertion(rdfs:label obo:GENO_0000138 "heritabililty") +SubClassOf(obo:GENO_0000138 obo:BFO_0000016) + +# Class: obo:GENO_0000139 (heritable) + +AnnotationAssertion(rdfs:label obo:GENO_0000139 "heritable") +SubClassOf(obo:GENO_0000139 obo:GENO_0000138) + +# Class: obo:GENO_0000140 (non-heritable) + +AnnotationAssertion(rdfs:label obo:GENO_0000140 "non-heritable") +SubClassOf(obo:GENO_0000140 obo:GENO_0000138) + +# Class: obo:GENO_0000141 (inheritance pattern) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000141 "The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000141 "The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000141 "mode of inheritance") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000141 "phenotypic inheritance pattern") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000141 "http://purl.obolibrary.org/obo/HP_0000005") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000141 "http://purl.obolibrary.org/obo/NCIT_C45827") +AnnotationAssertion(rdfs:comment obo:GENO_0000141 "An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, \"genetic context\" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. + +These genetic and environmental \"interactions\" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y.") +AnnotationAssertion(rdfs:label obo:GENO_0000141 "inheritance pattern") +SubClassOf(obo:GENO_0000141 obo:BFO_0000016) + +# Class: obo:GENO_0000142 (obsolete_dominant inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000142 "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000142 "Triage until decide if want to define this as grouping class that would result in multiple-inheritance.") +AnnotationAssertion(rdfs:label obo:GENO_0000142 "obsolete_dominant inheritance") +SubClassOf(obo:GENO_0000142 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000143 (co-dominant autosomal inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000143 "An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.") +AnnotationAssertion(rdfs:label obo:GENO_0000143 "co-dominant autosomal inheritance") +SubClassOf(obo:GENO_0000143 obo:GENO_0000147) + +# Class: obo:GENO_0000144 (complete autosomal dominant inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000144 "An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000144 "pure dominant inheritance") +AnnotationAssertion(rdfs:label obo:GENO_0000144 "complete autosomal dominant inheritance") +SubClassOf(obo:GENO_0000144 obo:GENO_0000147) + +# Class: obo:GENO_0000145 (incomplete autosomal dominant inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000145 "An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000145 "intermediate dominant autosomal inheritance") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000145 "semi-dominant autosomal inheritance") +AnnotationAssertion(rdfs:label obo:GENO_0000145 "incomplete autosomal dominant inheritance") +SubClassOf(obo:GENO_0000145 obo:GENO_0000147) + +# Class: obo:GENO_0000146 (X-linked dominant inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000146 "An X-linked inheritance pattern wherein the trait manifests in heterozygotes.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000146 "http://purl.obolibrary.org/obo/HP_0001423") +AnnotationAssertion(rdfs:label obo:GENO_0000146 "X-linked dominant inheritance") +SubClassOf(obo:GENO_0000146 obo:GENO_0000936) + +# Class: obo:GENO_0000147 (autosomal dominant inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000147 "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000147 "vertical inheritance") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000147 "http://purl.obolibrary.org/obo/HP_0000006") +AnnotationAssertion(rdfs:label obo:GENO_0000147 "autosomal dominant inheritance") +SubClassOf(obo:GENO_0000147 obo:GENO_0000934) + +# Class: obo:GENO_0000148 (autosomal recessive inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000148 "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals.") +AnnotationAssertion(rdfs:label obo:GENO_0000148 "autosomal recessive inheritance") +SubClassOf(obo:GENO_0000148 obo:GENO_0000934) + +# Class: obo:GENO_0000149 (X-linked recessive inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000149 "An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000149 "http://purl.obolibrary.org/obo/HP_0001419") +AnnotationAssertion(rdfs:label obo:GENO_0000149 "X-linked recessive inheritance"@en) +SubClassOf(obo:GENO_0000149 obo:GENO_0000936) + +# Class: obo:GENO_0000150 (obsolete_autosomal recessive inheritance) + +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000150 "duplicate term, use GENO:0000148") +AnnotationAssertion(rdfs:label obo:GENO_0000150 "obsolete_autosomal recessive inheritance") +SubClassOf(obo:GENO_0000150 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000152 (reference) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000152 "An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared.") +AnnotationAssertion(rdfs:comment obo:GENO_0000152 "Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another.") +AnnotationAssertion(rdfs:label obo:GENO_0000152 "reference") +SubClassOf(obo:GENO_0000152 obo:GENO_0000773) + +# Class: obo:GENO_0000160 (unspecified life cycle stage) + +AnnotationAssertion(rdfs:label obo:GENO_0000160 "unspecified life cycle stage") +SubClassOf(obo:GENO_0000160 obo:UBERON_0000105) + +# Class: obo:GENO_0000164 (genetic insertion technique) + +AnnotationAssertion(rdfs:comment obo:GENO_0000164 "objective is to insert some specified sequence into the genome of a cell or virus") +AnnotationAssertion(rdfs:label obo:GENO_0000164 "genetic insertion technique") +SubClassOf(obo:GENO_0000164 obo:OBI_0600043) + +# Class: obo:GENO_0000165 (mutagen treatment technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000165 "mutagen treatment technique") +SubClassOf(obo:GENO_0000165 obo:OBI_0600043) + +# Class: obo:GENO_0000166 (targeted gene mutation technique) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000166 "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping).") +AnnotationAssertion(rdfs:comment obo:GENO_0000166 "This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created.") +AnnotationAssertion(rdfs:label obo:GENO_0000166 "targeted gene mutation technique") +SubClassOf(obo:GENO_0000166 obo:OBI_0600043) +SubClassOf(obo:GENO_0000166 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) + +# Class: obo:GENO_0000169 (random genetic insertion technique) + +AnnotationAssertion(rdfs:comment obo:GENO_0000169 "Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination.") +AnnotationAssertion(rdfs:label obo:GENO_0000169 "random genetic insertion technique") +SubClassOf(obo:GENO_0000169 obo:GENO_0000164) + +# Class: obo:GENO_0000170 (targeted genetic insertion technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000170 "targeted genetic insertion technique") +SubClassOf(obo:GENO_0000170 obo:GENO_0000164) +SubClassOf(obo:GENO_0000170 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) + +# Class: obo:GENO_0000171 (enhancer trapping technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000171 "enhancer trapping technique") +SubClassOf(obo:GENO_0000171 obo:GENO_0000170) +SubClassOf(obo:GENO_0000171 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) + +# Class: obo:GENO_0000172 (gene trapping technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000172 "gene trapping technique") +SubClassOf(obo:GENO_0000172 obo:GENO_0000170) +SubClassOf(obo:GENO_0000172 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) + +# Class: obo:GENO_0000173 (promoter trapping technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000173 "promoter trapping technique") +SubClassOf(obo:GENO_0000173 obo:GENO_0000170) +SubClassOf(obo:GENO_0000173 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) + +# Class: obo:GENO_0000174 (targeted knock-in technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000174 "targeted knock-in technique") +SubClassOf(obo:GENO_0000174 obo:GENO_0000170) +SubClassOf(obo:GENO_0000174 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) + +# Class: obo:GENO_0000175 (random transgene insertion technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000175 "random transgene insertion technique") +SubClassOf(obo:GENO_0000175 obo:GENO_0000169) + +# Class: obo:GENO_0000324 (obsolete_chromosome complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000324 "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome") +AnnotationAssertion(rdfs:label obo:GENO_0000324 "obsolete_chromosome complement") +SubClassOf(obo:GENO_0000324 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000338 (gained aneusomic chromosome) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000338 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000338 "A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000338 "duplicate chromosome") +AnnotationAssertion(rdfs:comment obo:GENO_0000338 "This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome.") +AnnotationAssertion(rdfs:label obo:GENO_0000338 "gained aneusomic chromosome") +SubClassOf(obo:GENO_0000338 obo:GENO_0000346) +SubClassOf(obo:GENO_0000338 ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000685)) + +# Class: obo:GENO_0000339 (lost aneusomic chromosome) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000339 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000339 "A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000339 "This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as \"the point at which one or more contiguous nucleotides were excised\".") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000339 "absent aneusomic chromosome") +AnnotationAssertion(rdfs:label obo:GENO_0000339 "lost aneusomic chromosome") +SubClassOf(obo:GENO_0000339 obo:GENO_0000346) +SubClassOf(obo:GENO_0000339 DataHasValue(obo:GENO_0000678 "0"^^xsd:integer)) + +# Class: obo:GENO_0000343 (aneusomic chromosomal part) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000343 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000343 "A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000343 "Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000343 "aneuploid chromosomal segment") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000343 "aneusomic chromosomal subregion/segment") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000343 "partial aneusomic chromosomal element") +AnnotationAssertion(rdfs:comment obo:GENO_0000343 "Aneusomic chromosomal parts are examples of \"partial aneuploidy\" as described in http://en.wikipedia.org/wiki/Aneuploidy: \"The terms \"partial monosomy\" and \"partial trisomy\" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome.\"") +AnnotationAssertion(rdfs:label obo:GENO_0000343 "aneusomic chromosomal part") +SubClassOf(obo:GENO_0000343 obo:SO_0001059) +SubClassOf(obo:GENO_0000343 ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000513)) +SubClassOf(obo:GENO_0000343 ObjectSomeValuesFrom(obo:GENO_0000248 obo:SO_0000340)) + +# Class: obo:GENO_0000344 (gained aneusomic chromosomal segment) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000344 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000344 "A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000344 "duplicate partial aneuploid chromosomal element") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000344 "translocated duplicate chromosomal element") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000344 "translocated duplicate chromosomal segment") +AnnotationAssertion(rdfs:comment obo:GENO_0000344 "Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location.") +AnnotationAssertion(rdfs:label obo:GENO_0000344 "gained aneusomic chromosomal segment") +SubClassOf(obo:GENO_0000344 obo:GENO_0000343) + +# Class: obo:GENO_0000345 (lost aneusomic chromosomal segment) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000345 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000345 "A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000345 "In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000345 "dropped partial anneuploid chromosomal element") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000345 "translocated absent chromosomal segment") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000345 "truncated chromosome terminus") +AnnotationAssertion(rdfs:comment obo:GENO_0000345 "This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome. + +Loss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus.") +AnnotationAssertion(rdfs:label obo:GENO_0000345 "lost aneusomic chromosomal segment") +SubClassOf(obo:GENO_0000345 obo:GENO_0000343) +SubClassOf(obo:GENO_0000345 DataHasValue(obo:GENO_0000678 "0"^^xsd:integer)) + +# Class: obo:GENO_0000346 (aneusomic chromosome) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000346 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000346 "A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000346 "complete aneusomic chromosome") +AnnotationAssertion(rdfs:comment obo:GENO_0000346 "Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism. + +Similarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication.") +AnnotationAssertion(rdfs:label obo:GENO_0000346 "aneusomic chromosome") +SubClassOf(obo:GENO_0000346 obo:SO_0000340) +SubClassOf(obo:GENO_0000346 obo:SO_0001059) +SubClassOf(obo:GENO_0000346 ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000513)) + +# Class: obo:GENO_0000351 (biological process) + +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000351 "Stub class to serve as root of hierarchy for imports of biological processes from GO-BP.") +AnnotationAssertion(rdfs:label obo:GENO_0000351 "biological process") +SubClassOf(obo:GENO_0000351 obo:BFO_0000015) + +# Class: obo:GENO_0000391 (disomic zygosity) + +AnnotationAssertion(rdfs:label obo:GENO_0000391 "disomic zygosity") +SubClassOf(obo:GENO_0000391 obo:GENO_0000133) + +# Class: obo:GENO_0000392 (aneusomic zygosity) + +AnnotationAssertion(rdfs:label obo:GENO_0000392 "aneusomic zygosity") +SubClassOf(obo:GENO_0000392 obo:GENO_0000133) + +# Class: obo:GENO_0000393 (trisomic homozygous) + +AnnotationAssertion(rdfs:label obo:GENO_0000393 "trisomic homozygous") +SubClassOf(obo:GENO_0000393 obo:GENO_0000392) + +# Class: obo:GENO_0000394 (trisomic heterozygous) + +AnnotationAssertion(rdfs:label obo:GENO_0000394 "trisomic heterozygous") +SubClassOf(obo:GENO_0000394 obo:GENO_0000392) + +# Class: obo:GENO_0000402 (compound heterozygous) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000402 "A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a/fgf8a)") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000402 "trans-heterozygous") +AnnotationAssertion(rdfs:label obo:GENO_0000402 "compound heterozygous") +SubClassOf(obo:GENO_0000402 obo:GENO_0000135) + +# Class: obo:GENO_0000415 (obsolete_reagent sequence feature) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000415 "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000415 "replaced with SO:engineered_region") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000415 "extra-genomic sequence") +AnnotationAssertion(rdfs:label obo:GENO_0000415 "obsolete_reagent sequence feature") +SubClassOf(obo:GENO_0000415 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000458 (simple heterozygous) + +AnnotationAssertion(rdfs:comment obo:GENO_0000458 "a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a)") +AnnotationAssertion(rdfs:label obo:GENO_0000458 "simple heterozygous") +SubClassOf(obo:GENO_0000458 obo:GENO_0000135) + +# Class: obo:GENO_0000460 (transgene part) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000460 "A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc)") +AnnotationAssertion(rdfs:label obo:GENO_0000460 "transgene part") +EquivalentClasses(obo:GENO_0000460 ObjectIntersectionOf(obo:GENO_0000666 ObjectSomeValuesFrom(obo:RO_0002525 obo:SO_0000902))) + +# Class: obo:GENO_0000476 (variant) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000476 "An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level") +AnnotationAssertion(rdfs:label obo:GENO_0000476 "variant"@en) +SubClassOf(obo:GENO_0000476 obo:GENO_0000773) + +# Class: obo:GENO_0000477 (polymorphic) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000477 "An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant.") +AnnotationAssertion(rdfs:label obo:GENO_0000477 "polymorphic"@en) +SubClassOf(obo:GENO_0000477 obo:GENO_0000773) + +# Class: obo:GENO_0000480 (mutant) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000480 "An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence.") +AnnotationAssertion(rdfs:label obo:GENO_0000480 "mutant"@en) +SubClassOf(obo:GENO_0000480 obo:GENO_0000773) + +# Class: obo:GENO_0000481 (genomic feature) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000481 "A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000481 "This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology.") +AnnotationAssertion(rdfs:comment obo:GENO_0000481 "1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. + +2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). + +3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome.") +AnnotationAssertion(rdfs:label obo:GENO_0000481 "genomic feature"@en) +EquivalentClasses(obo:GENO_0000481 ObjectIntersectionOf(obo:SO_0000110 ObjectSomeValuesFrom(obo:GENO_0000903 obo:GENO_0000902))) +SubClassOf(obo:GENO_0000481 ObjectSomeValuesFrom(obo:BFO_0000050 obo:SO_0001026)) +SubClassOf(obo:GENO_0000481 ObjectSomeValuesFrom(obo:GENO_0000239 obo:GENO_0000960)) +SubClassOf(obo:GENO_0000481 ObjectSomeValuesFrom(obo:RO_0002162 obo:OBI_0100026)) + +# Class: obo:GENO_0000482 (genetic material) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000482 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000482 "A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion).") +AnnotationAssertion(rdfs:comment obo:GENO_0000482 "This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material.") +AnnotationAssertion(rdfs:label obo:GENO_0000482 "genetic material"@en) +SubClassOf(obo:GENO_0000482 obo:CHEBI_33696) + +# Class: obo:GENO_0000491 (obsolete_mutant allele) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000491 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000491 "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000491 "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000491 "Not required for any specific use case at this point so removed for simplicity. +Formely asserted as allele and inferred as varaint allele. +Eq class definition: +allele + and (mutation or ('has subsequence' some mutation))") +AnnotationAssertion(rdfs:comment obo:GENO_0000491 "'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line.") +AnnotationAssertion(rdfs:label obo:GENO_0000491 "obsolete_mutant allele") +SubClassOf(obo:GENO_0000491 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000492 (mutation) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000492 "A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain.") +AnnotationAssertion(rdfs:label obo:GENO_0000492 "mutation"@en) +SubClassOf(obo:GENO_0000492 obo:SO_0001059) +SubClassOf(obo:GENO_0000492 ObjectSomeValuesFrom(obo:GENO_0000683 obo:GENO_0000501)) + +# Class: obo:GENO_0000494 (extrachromosomal replicon) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000494 "A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon)") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000494 "Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000494 "episomal replicon") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000494 "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'.") +AnnotationAssertion(rdfs:label obo:GENO_0000494 "extrachromosomal replicon"@en) +EquivalentClasses(obo:GENO_0000494 ObjectIntersectionOf(obo:GENO_0000481 ObjectComplementOf(ObjectSomeValuesFrom(obo:GENO_0000248 obo:SO_0000340)) ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000139))) + +# Class: obo:GENO_0000495 (expression construct) + +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000495 "expression construct feature") +AnnotationAssertion(rdfs:label obo:GENO_0000495 "expression construct"@en) +SubClassOf(obo:GENO_0000495 obo:GENO_0000856) + +# Class: obo:GENO_0000497 (polymorphic allele) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000497 "An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000497 "PMID: 25741868 ACMG Guidelines") +AnnotationAssertion(rdfs:comment obo:GENO_0000497 "Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%).") +AnnotationAssertion(rdfs:label obo:GENO_0000497 "polymorphic allele") +SubClassOf(obo:GENO_0000497 obo:GENO_0000512) + +# Class: obo:GENO_0000498 (major polymorphic allele) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000498 "A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000498 "major allele"@en) +AnnotationAssertion(rdfs:label obo:GENO_0000498 "major polymorphic allele") +SubClassOf(obo:GENO_0000498 obo:GENO_0000497) + +# Class: obo:GENO_0000499 (minor polymorphic allele) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000499 "A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000499 "minor allele"@en) +AnnotationAssertion(rdfs:label obo:GENO_0000499 "minor polymorphic allele") +SubClassOf(obo:GENO_0000499 obo:GENO_0000497) + +# Class: obo:GENO_0000500 (ancestral polymorphic allele) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000500 "A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000500 "ancestral allele"@en) +AnnotationAssertion(rdfs:label obo:GENO_0000500 "ancestral polymorphic allele") +SubClassOf(obo:GENO_0000500 obo:GENO_0000497) + +# Class: obo:GENO_0000501 (wild-type allele) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000501 "An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000501 "wild-type allele") +AnnotationAssertion(rdfs:comment obo:GENO_0000501 "'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain. + +The notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis.") +AnnotationAssertion(rdfs:label obo:GENO_0000501 "wild-type allele") +SubClassOf(obo:GENO_0000501 obo:GENO_0000512) +SubClassOf(obo:GENO_0000501 ObjectSomeValuesFrom(obo:GENO_0000683 obo:GENO_0000481)) + +# Class: obo:GENO_0000502 (wild-type gene) + +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000502 "wild-type gene allele"@en) +AnnotationAssertion(rdfs:comment obo:GENO_0000502 "A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation.") +AnnotationAssertion(rdfs:label obo:GENO_0000502 "wild-type gene") +SubClassOf(obo:GENO_0000502 obo:GENO_0000501) +SubClassOf(obo:GENO_0000502 obo:SO_0000704) + +# Class: obo:GENO_0000504 (reagent targeted gene) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000504 "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.") +AnnotationAssertion(rdfs:comment obo:GENO_0000504 "The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position.") +AnnotationAssertion(rdfs:label obo:GENO_0000504 "reagent targeted gene"@en) +SubClassOf(obo:GENO_0000504 obo:GENO_0000529) +SubClassOf(obo:GENO_0000504 ObjectSomeValuesFrom(obo:GENO_0000231 obo:GENO_0000534)) +SubClassOf(obo:GENO_0000504 ObjectSomeValuesFrom(obo:GENO_0000447 obo:GENO_0000533)) + +# Class: obo:GENO_0000506 (transiently-expressed transgene) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000506 "A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000506 "experimentally-expressed transgene") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000506 "extrinsic transgene"@en) +AnnotationAssertion(rdfs:label obo:GENO_0000506 "transiently-expressed transgene") +SubClassOf(obo:GENO_0000506 obo:GENO_0000529) + +# Class: obo:GENO_0000511 (wild-type) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000511 "An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared.") +AnnotationAssertion(rdfs:label obo:GENO_0000511 "wild-type"@en) +SubClassOf(obo:GENO_0000511 obo:GENO_0000773) + +# Class: obo:GENO_0000512 (allele) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000512 "One of a set of sequence features known to exist at a particular genomic location.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000512 "A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene. + +To be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene. + +[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17) +[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17) +[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17) +[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17) +[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17) +[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17) +[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483 +[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17) +[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17) +[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17) +[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17) +[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000512 "variable feature"@en) +AnnotationAssertion(rdfs:comment obo:GENO_0000512 "An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). + +Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence).") +AnnotationAssertion(rdfs:label obo:GENO_0000512 "allele") +EquivalentClasses(obo:GENO_0000512 ObjectIntersectionOf(obo:GENO_0000481 ObjectSomeValuesFrom(obo:GENO_0000683 obo:GENO_0000481))) + +# Class: obo:GENO_0000513 (aneusomic) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000513 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000513 "a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation.") +AnnotationAssertion(rdfs:label obo:GENO_0000513 "aneusomic"@en) +SubClassOf(obo:GENO_0000513 obo:GENO_0000773) + +# Class: obo:GENO_0000515 (variant gene allele) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000515 "An allele of a gene that contains some sequence alteration.") +AnnotationAssertion(rdfs:comment obo:GENO_0000515 "A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset.") +AnnotationAssertion(rdfs:label obo:GENO_0000515 "variant gene allele") +EquivalentClasses(obo:GENO_0000515 ObjectIntersectionOf(obo:GENO_0000014 ObjectSomeValuesFrom(obo:GENO_0000683 obo:GENO_0000036))) +SubClassOf(obo:GENO_0000515 ObjectSomeValuesFrom(obo:GENO_0000382 obo:SO_0001059)) +SubClassOf(obo:GENO_0000515 ObjectSomeValuesFrom(obo:GENO_0000641 obo:SO_0000704)) + +# Class: obo:GENO_0000516 (single locus complement) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000516 "The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a. + +The collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome.") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000516 "A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000516 "TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000516 "allelic complement") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000516 "homologous allele complement") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000516 "single locus feature complement") +AnnotationAssertion(rdfs:comment obo:GENO_0000516 "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes. + +The fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus.") +AnnotationAssertion(rdfs:label obo:GENO_0000516 "single locus complement") +SubClassOf(obo:GENO_0000516 obo:GENO_0000660) + +# Class: obo:GENO_0000524 (extrinsic genotype) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000524 "In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as: + + shha; shhb + +This notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct.") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000524 "A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000524 "We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. + +Our rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. + +Finally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000524 "experimental genotype") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000524 "expression genotype") +AnnotationAssertion(rdfs:comment obo:GENO_0000524 "An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment. + +The 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations.") +AnnotationAssertion(rdfs:label obo:GENO_0000524 "extrinsic genotype"@en) +SubClassOf(obo:GENO_0000524 obo:GENO_0000536) + +# Class: obo:GENO_0000525 (effective genotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000525 "A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs).") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000525 "Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"") +AnnotationAssertion(rdfs:comment obo:GENO_0000525 "An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment.") +AnnotationAssertion(rdfs:label obo:GENO_0000525 "effective genotype"@en) +SubClassOf(obo:GENO_0000525 obo:GENO_0000536) +SubClassOf(obo:GENO_0000525 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GENO_0000524)) +SubClassOf(obo:GENO_0000525 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GENO_0000719)) + +# Class: obo:GENO_0000527 (reagent-targeted gene complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000527 "A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes).") +AnnotationAssertion(rdfs:comment obo:GENO_0000527 "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment.") +AnnotationAssertion(rdfs:label obo:GENO_0000527 "reagent-targeted gene complement"@en) +SubClassOf(obo:GENO_0000527 obo:GENO_0000715) +SubClassOf(obo:GENO_0000527 ObjectSomeValuesFrom(obo:RO_0002351 obo:GENO_0000504)) + +# Class: obo:GENO_0000528 (transiently-expressed transgene complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000528 "The set of all transgenes trransiently expressed in a biological system in the context of a given experiment.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000528 "experimental transgene complement"@en) +AnnotationAssertion(rdfs:label obo:GENO_0000528 "transiently-expressed transgene complement") +SubClassOf(obo:GENO_0000528 obo:GENO_0000715) +SubClassOf(obo:GENO_0000528 ObjectSomeValuesFrom(obo:GENO_0000382 obo:GENO_0000506)) + +# Class: obo:GENO_0000529 (expression-variant gene) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000529 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes).") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000529 "A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism).") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000529 "See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000529 "expression allele") +AnnotationAssertion(rdfs:comment obo:GENO_0000529 "Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism). + +The identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system.") +AnnotationAssertion(rdfs:label obo:GENO_0000529 "expression-variant gene"@en) +SubClassOf(obo:GENO_0000529 obo:GENO_0000737) +SubClassOf(obo:GENO_0000529 ObjectSomeValuesFrom(obo:GENO_0000443 obo:SO_0000704)) + +# Class: obo:GENO_0000533 (gene knockdown reagent) + +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000533 "gene targeting reagent") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000533 "sequence targeting reagent") +AnnotationAssertion(rdfs:label obo:GENO_0000533 "gene knockdown reagent"@en) +SubClassOf(obo:GENO_0000533 obo:SO_0000804) + +# Class: obo:GENO_0000534 (reagent-targeted gene subregion) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000534 "A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000534 "targeted gene segment"@en) +AnnotationAssertion(rdfs:label obo:GENO_0000534 "reagent-targeted gene subregion") +SubClassOf(obo:GENO_0000534 obo:GENO_0000737) + +# Class: obo:GENO_0000536 (genotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000536 "A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000536 "As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000536 "Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). +Note however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO.") +AnnotationAssertion(rdfs:comment obo:GENO_0000536 "1. Scope of 'Genetic State': +'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs. + +2. Genotype Subtypes: +In GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. + +Two more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features. + +3. The Genotype Partonomy: +'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype \"fgf8a; fgf3[AB]\", described at zfin.org/ZDB-FISH-150901-9362, include the following elements: + + - GVC: fgf8a; fgf3 (total intrinsic variation in the genome) + - Genomic Background: AB (the reference against which the GVC is variant) + - VSLC1: fgf8a (homozygous complement of gene alleles at one known variant locus) + - VSLC2: fgf3 (heterozygous complement of gene alleles at another known variant locus) + - Allele 1: fgf8a (variant version of the fgf8a gene, present in two copies) + - Allele 2: fgf3 (variant version of the fgf3 gene, present in one copy) + - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy) + - Sequence Alteration1: (the specific mutation within the fgf8a gene that makes it variant) + - Sequence Alteration2: (the specific mutation within the fgf3 gene that makes it variant) + +A graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md + +One reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to \"propagate phenotypes\" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data.") +AnnotationAssertion(rdfs:label obo:GENO_0000536 "genotype"@en) +SubClassOf(obo:GENO_0000536 obo:IAO_0000030) +SubClassOf(obo:GENO_0000536 ObjectSomeValuesFrom(obo:IAO_0000219 ObjectUnionOf(obo:GENO_0000660 obo:GENO_0000715))) + +# Class: obo:GENO_0000575 (zebrafish phenotype) + +AnnotationAssertion(rdfs:comment obo:GENO_0000575 "ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl +This ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes.") +AnnotationAssertion(rdfs:label obo:GENO_0000575 "zebrafish phenotype") +SubClassOf(obo:GENO_0000575 obo:UPHENO_0001001) + +# Class: obo:GENO_0000602 (homoplasmic) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000602 "an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism.") +AnnotationAssertion(rdfs:label obo:GENO_0000602 "homoplasmic"@en) +SubClassOf(obo:GENO_0000602 obo:GENO_0000918) + +# Class: obo:GENO_0000603 (heteroplasmic) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000603 "an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism.") +AnnotationAssertion(rdfs:label obo:GENO_0000603 "heteroplasmic"@en) +SubClassOf(obo:GENO_0000603 obo:GENO_0000918) + +# Class: obo:GENO_0000604 (hemizygous X-linked) + +AnnotationAssertion(rdfs:label obo:GENO_0000604 "hemizygous X-linked"@en) +SubClassOf(obo:GENO_0000604 obo:GENO_0000134) + +# Class: obo:GENO_0000605 (hemizygous Y-linked) + +AnnotationAssertion(rdfs:label obo:GENO_0000605 "hemizygous Y-linked"@en) +SubClassOf(obo:GENO_0000605 obo:GENO_0000134) + +# Class: obo:GENO_0000606 (hemizygous insertion-linked) + +AnnotationAssertion(rdfs:label obo:GENO_0000606 "hemizygous insertion-linked"@en) +SubClassOf(obo:GENO_0000606 obo:GENO_0000134) + +# Class: obo:GENO_0000611 (genomic background) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000611 "A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000611 "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000611 "background genotype") +AnnotationAssertion(rdfs:label obo:GENO_0000611 "genomic background"@en) +EquivalentClasses(obo:GENO_0000611 ObjectIntersectionOf(obo:GENO_0000899 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000152))) +SubClassOf(obo:GENO_0000611 ObjectSomeValuesFrom(obo:IAO_0000219 obo:GENO_0000010)) + +# Class: obo:GENO_0000614 (chromosomal region) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000614 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\".") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000614 "An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000614 "New term request for SO.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000614 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band") +AnnotationAssertion(rdfs:label obo:GENO_0000614 "chromosomal region"@en) +SubClassOf(obo:GENO_0000614 obo:SO_0000830) +SubClassOf(obo:GENO_0000614 ObjectSomeValuesFrom(obo:BFO_0000050 obo:SO_0000105)) + +# Class: obo:GENO_0000616 (chromosome sub-band) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000616 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\".") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000616 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band") +AnnotationAssertion(rdfs:label obo:GENO_0000616 "chromosome sub-band"@en) +SubClassOf(obo:GENO_0000616 obo:SO_0000830) +SubClassOf(obo:GENO_0000616 ObjectSomeValuesFrom(obo:BFO_0000050 obo:SO_0000341)) +SubClassOf(obo:GENO_0000616 ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000618)) + +# Class: obo:GENO_0000618 (chromosomal band intensity) + +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000618 "chromosomal band brightness") +AnnotationAssertion(rdfs:label obo:GENO_0000618 "chromosomal band intensity"@en) +SubClassOf(obo:GENO_0000618 obo:GENO_0000788) + +# Class: obo:GENO_0000619 (gpos) + +AnnotationAssertion(rdfs:label obo:GENO_0000619 "gpos"@en) +SubClassOf(obo:GENO_0000619 obo:GENO_0000618) + +# Class: obo:GENO_0000620 (gneg) + +AnnotationAssertion(rdfs:label obo:GENO_0000620 "gneg"@en) +SubClassOf(obo:GENO_0000620 obo:GENO_0000618) + +# Class: obo:GENO_0000621 (gvar) + +AnnotationAssertion(rdfs:label obo:GENO_0000621 "gvar"@en) +SubClassOf(obo:GENO_0000621 obo:GENO_0000618) + +# Class: obo:GENO_0000622 (gpos100) + +AnnotationAssertion(rdfs:label obo:GENO_0000622 "gpos100"@en) +SubClassOf(obo:GENO_0000622 obo:GENO_0000619) + +# Class: obo:GENO_0000623 (gpos75) + +AnnotationAssertion(rdfs:label obo:GENO_0000623 "gpos75"@en) +SubClassOf(obo:GENO_0000623 obo:GENO_0000619) + +# Class: obo:GENO_0000624 (gpos50) + +AnnotationAssertion(rdfs:label obo:GENO_0000624 "gpos50"@en) +SubClassOf(obo:GENO_0000624 obo:GENO_0000619) + +# Class: obo:GENO_0000625 (gpos25) + +AnnotationAssertion(rdfs:label obo:GENO_0000625 "gpos25"@en) +SubClassOf(obo:GENO_0000625 obo:GENO_0000619) + +# Class: obo:GENO_0000628 (short chromosome arm) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000628 "A chromosome arm that is the shorter of the two arms of a given chromosome.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000628 "p-arm") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000628 "stalk") +AnnotationAssertion(rdfs:label obo:GENO_0000628 "short chromosome arm"@en) +SubClassOf(obo:GENO_0000628 obo:SO_0000105) + +# Class: obo:GENO_0000629 (long chromosome arm) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000629 "A chromosome arm that is the longer of the two arms of a given chromosome.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000629 "q-arm") +AnnotationAssertion(rdfs:label obo:GENO_0000629 "long chromosome arm"@en) +SubClassOf(obo:GENO_0000629 obo:SO_0000105) + +# Class: obo:GENO_0000632 (gpos66) + +AnnotationAssertion(rdfs:label obo:GENO_0000632 "gpos66") +SubClassOf(obo:GENO_0000632 obo:GENO_0000619) + +# Class: obo:GENO_0000633 (gpos33) + +AnnotationAssertion(rdfs:label obo:GENO_0000633 "gpos33") +SubClassOf(obo:GENO_0000633 obo:GENO_0000619) + +# Class: obo:GENO_0000637 (regulatory transgene region) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000637 "A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed.") +AnnotationAssertion(rdfs:label obo:GENO_0000637 "regulatory transgene region"@en) +SubClassOf(obo:GENO_0000637 obo:SO_0005836) +SubClassOf(obo:GENO_0000637 ObjectSomeValuesFrom(obo:RO_0002525 obo:SO_0000902)) + +# Class: obo:GENO_0000638 (expressed transgene region) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000638 "A transgene part whose sequence is expressed in a gene product through transcription and/or translation.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000638 "coding transgene feature") +AnnotationAssertion(rdfs:label obo:GENO_0000638 "expressed transgene region"@en) +SubClassOf(obo:GENO_0000638 obo:GENO_0000460) +SubClassOf(obo:GENO_0000638 ObjectSomeValuesFrom(obo:RO_0002525 obo:SO_0000902)) + +# Class: obo:GENO_0000640 (reporter region) + +AnnotationAssertion(rdfs:label obo:GENO_0000640 "reporter region"@en) +SubClassOf(obo:GENO_0000640 obo:GENO_0000638) + +# Class: obo:GENO_0000642 (selectable marker transgene) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000642 "A transgene whose product is used as a selectable marker.") +AnnotationAssertion(rdfs:label obo:GENO_0000642 "selectable marker transgene"@en) +EquivalentClasses(obo:GENO_0000642 ObjectIntersectionOf(obo:SO_0000902 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000911))) +SubClassOf(obo:GENO_0000642 ObjectSomeValuesFrom(obo:GENO_0000207 obo:SO_0000783)) + +# Class: obo:GENO_0000644 (karyotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000644 "A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000644 "Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28)") +AnnotationAssertion(rdfs:comment obo:GENO_0000644 "Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). + +A base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation).") +AnnotationAssertion(rdfs:label obo:GENO_0000644 "karyotype"@en) +SubClassOf(obo:GENO_0000644 obo:GENO_0000899) +SubClassOf(obo:GENO_0000644 ObjectSomeValuesFrom(obo:IAO_0000219 obo:SO_0001026)) + +# Class: obo:GENO_0000645 (genomic genotype (sex-qualified)) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000645 "A genomic genotype where the genomic background specifies a male or female sex chromosome complement.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000645 "This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). + +In the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000645 "intrinsic genotype (sex-specific)") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000645 "sex-qualified genotype") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000645 "sex-qualified intrinsic genotype") +AnnotationAssertion(rdfs:comment obo:GENO_0000645 "We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances. + +Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome.") +AnnotationAssertion(rdfs:label obo:GENO_0000645 "genomic genotype (sex-qualified)"@en) +SubClassOf(obo:GENO_0000645 obo:GENO_0000899) +SubClassOf(obo:GENO_0000645 ObjectSomeValuesFrom(obo:GENO_0000650 obo:GENO_0000000)) + +# Class: obo:GENO_0000646 (male intrinsic genotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000646 "A genomic genotype here the genomic background specifies a male sex chromosome complement.") +AnnotationAssertion(rdfs:label obo:GENO_0000646 "male intrinsic genotype"@en) +SubClassOf(obo:GENO_0000646 obo:GENO_0000645) + +# Class: obo:GENO_0000647 (female intrinsic genotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000647 "A genomic genotype here the genomic background specifies a female sex chromosome complement.") +AnnotationAssertion(rdfs:label obo:GENO_0000647 "female intrinsic genotype"@en) +SubClassOf(obo:GENO_0000647 obo:GENO_0000645) + +# Class: obo:GENO_0000649 (unspecified genomic background) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000649 "A background genotype whose sequence or identity is not known or specified.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000649 "unspecified background genotype") +AnnotationAssertion(rdfs:label obo:GENO_0000649 "unspecified genomic background"@en) +SubClassOf(obo:GENO_0000649 obo:GENO_0000611) + +# Class: obo:GENO_0000659 (sequence feature set) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000659 "1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus + +2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele. + +3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y}") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000659 "A set of sequence features.") +AnnotationAssertion(rdfs:comment obo:GENO_0000659 "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature). + +The notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3]. + +[1] https://www.snpedia.com/index.php/APOE-%CE%B54 +[2] https://www.snpedia.com/index.php/APOE-%CE%B52 +[3] https://www.snpedia.com/index.php/Gs270") +AnnotationAssertion(rdfs:label obo:GENO_0000659 "sequence feature set"@en) +SubClassOf(obo:GENO_0000659 obo:GENO_0000701) +SubClassOf(obo:GENO_0000659 ObjectSomeValuesFrom(obo:RO_0002351 obo:SO_0000110)) +SubClassOf(obo:GENO_0000659 DataSomeValuesFrom(obo:GENO_0000917 xsd:int)) + +# Class: obo:GENO_0000660 (genomic feature set) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000660 "A set of genomic features (i.e. sequence features that are of genomic origin).") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000660 "In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000660 "genomic locus complement") +AnnotationAssertion(rdfs:comment obo:GENO_0000660 "A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature. + +The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside.") +AnnotationAssertion(rdfs:label obo:GENO_0000660 "genomic feature set"@en) +SubClassOf(obo:GENO_0000660 obo:GENO_0000659) +SubClassOf(obo:GENO_0000660 ObjectSomeValuesFrom(obo:RO_0002162 obo:OBI_0100026)) +SubClassOf(obo:GENO_0000660 ObjectSomeValuesFrom(obo:RO_0002351 obo:GENO_0000481)) + +# Class: obo:GENO_0000666 (gene part) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000666 "A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000666 "defined gene part") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000666 "SO:0000831 (gene member region)") +AnnotationAssertion(rdfs:label obo:GENO_0000666 "gene part") +EquivalentClasses(obo:GENO_0000666 ObjectIntersectionOf(obo:GENO_0000481 ObjectSomeValuesFrom(obo:RO_0002525 obo:GENO_0000014))) + +# Class: obo:GENO_0000667 (reporter transgene) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000667 "A transgene that codes for a product used as a reporter of gene expression or activity.") +AnnotationAssertion(rdfs:label obo:GENO_0000667 "reporter transgene"@en) +EquivalentClasses(obo:GENO_0000667 ObjectIntersectionOf(obo:SO_0000902 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000910))) +SubClassOf(obo:GENO_0000667 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GENO_0000640)) +SubClassOf(obo:GENO_0000667 ObjectSomeValuesFrom(obo:GENO_0000207 obo:SO_0000783)) + +# Class: obo:GENO_0000680 (obsolete_null feature) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000680 "A junction between bases, a deletion variant, a terminus at the end of a chromosome.") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000680 "A genomic feature that has an extent of zero.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000680 "Former logical def: +'genomic feature' + and (has_extent value 0)") +AnnotationAssertion(rdfs:label obo:GENO_0000680 "obsolete_null feature"@en) +SubClassOf(obo:GENO_0000680 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000681 (novel extrachromosomal replicon) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000681 "An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000681 "aberrant extrachromosomal replicon") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000681 "exogenous extrachromosomal replicon") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000681 "transgenic extrachromosomal replicon"@en) +AnnotationAssertion(rdfs:comment obo:GENO_0000681 "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'.") +AnnotationAssertion(rdfs:label obo:GENO_0000681 "novel extrachromosomal replicon") +SubClassOf(obo:GENO_0000681 obo:GENO_0000684) +SubClassOf(obo:GENO_0000681 ObjectComplementOf(ObjectSomeValuesFrom(obo:GENO_0000248 obo:SO_0000340))) +SubClassOf(obo:GENO_0000681 ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000139)) +SubClassOf(obo:GENO_0000681 ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000685)) + +# Class: obo:GENO_0000684 (novel replicon) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000684 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000684 "A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000684 "This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature.") +AnnotationAssertion(rdfs:comment obo:GENO_0000684 "Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles.") +AnnotationAssertion(rdfs:label obo:GENO_0000684 "novel replicon"@en) +SubClassOf(obo:GENO_0000684 obo:SO_0001059) +SubClassOf(obo:GENO_0000684 ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000685)) + +# Class: obo:GENO_0000685 (novel) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000685 "An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome.") +AnnotationAssertion(rdfs:label obo:GENO_0000685 "novel"@en) +SubClassOf(obo:GENO_0000685 obo:GENO_0000773) + +# Class: obo:GENO_0000688 (terminus) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000688 "A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide).") +AnnotationAssertion(rdfs:label obo:GENO_0000688 "terminus"@en) +SubClassOf(obo:GENO_0000688 obo:SO_0000110) + +# Class: obo:GENO_0000701 (sequence feature or set) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000701 "A sequence feature or a set of such features.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000701 "sequence feature or collection") +AnnotationAssertion(rdfs:comment obo:GENO_0000701 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.") +AnnotationAssertion(rdfs:label obo:GENO_0000701 "sequence feature or set"@en) +EquivalentClasses(obo:GENO_0000701 ObjectUnionOf(obo:GENO_0000701 obo:SO_0000110)) +SubClassOf(obo:GENO_0000701 obo:BFO_0000031) + +# Class: obo:GENO_0000702 (biological sequence) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000702 "A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides).") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000702 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000702 "biomacromolecular sequence") +AnnotationAssertion(Annotation(obo:IAO_0000116 "In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele.") obo:IAO_0000118 obo:GENO_0000702 "state") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000702 "VMC:State") +AnnotationAssertion(rdfs:comment obo:GENO_0000702 "'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome.") +AnnotationAssertion(rdfs:label obo:GENO_0000702 "biological sequence"@en) +SubClassOf(obo:GENO_0000702 obo:GENO_0000921) +SubClassOf(Annotation(obo:GENO_0000834 "true"^^xsd:boolean) obo:GENO_0000702 DataSomeValuesFrom(obo:GENO_0000896 xsd:string)) +DisjointClasses(obo:GENO_0000702 obo:GENO_0000815) +DisjointClasses(obo:GENO_0000702 obo:SO_0000110) + +# Class: obo:GENO_0000713 (qualified sequence feature or collection) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000713 "A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification.") +AnnotationAssertion(rdfs:label obo:GENO_0000713 "qualified sequence feature or collection"@en) +SubClassOf(obo:GENO_0000713 obo:BFO_0000031) + +# Class: obo:GENO_0000714 (qualified genomic feature) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000714 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes).") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000714 "A qualified sequence feature that carries sequence derived from the genome of a cell or organism.") +AnnotationAssertion(rdfs:label obo:GENO_0000714 "qualified genomic feature"@en) +SubClassOf(obo:GENO_0000714 obo:GENO_0000919) +SubClassOf(Annotation(obo:GENO_0000834 "true"^^xsd:boolean) Annotation(rdfs:comment "This axiom is an initial attempt to formalize the identity criteria of an extrinnsic context that separates qualified sequence features from sequence features (i.e. the context of its material bearer). As we further develop our efforts here this will get refined and more precise.") obo:GENO_0000714 ObjectSomeValuesFrom(obo:GENO_0000580 owl:Thing)) +SubClassOf(Annotation(obo:GENO_0000834 "true"^^xsd:boolean) Annotation(rdfs:comment "Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position).") obo:GENO_0000714 ObjectSomeValuesFrom(obo:GENO_0000726 obo:GENO_0000481)) +SubClassOf(obo:GENO_0000714 ObjectSomeValuesFrom(obo:RO_0002162 obo:OBI_0100026)) + +# Class: obo:GENO_0000715 (qualified genomic feature set) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000715 "A set of qualified sequence features that carry genomic sequence.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000715 "Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member.") +AnnotationAssertion(rdfs:comment obo:GENO_0000715 "A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele. + +A complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome.") +AnnotationAssertion(rdfs:label obo:GENO_0000715 "qualified genomic feature set"@en) +SubClassOf(obo:GENO_0000715 obo:GENO_0000920) +SubClassOf(obo:GENO_0000715 ObjectSomeValuesFrom(obo:GENO_0000726 obo:GENO_0000660)) +SubClassOf(obo:GENO_0000715 ObjectSomeValuesFrom(obo:RO_0002162 obo:OBI_0100026)) +SubClassOf(obo:GENO_0000715 ObjectSomeValuesFrom(obo:RO_0002351 obo:GENO_0000714)) + +# Class: obo:GENO_0000719 (intrinsic genotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000719 "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000719 "Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome.") +AnnotationAssertion(rdfs:comment obo:GENO_0000719 "1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. + +2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons.") +AnnotationAssertion(rdfs:label obo:GENO_0000719 "intrinsic genotype"@en) +SubClassOf(obo:GENO_0000719 obo:GENO_0000536) +SubClassOf(obo:GENO_0000719 ObjectSomeValuesFrom(obo:IAO_0000219 ObjectUnionOf(obo:GENO_0000516 obo:SO_0001026))) + +# Class: obo:GENO_0000720 (DNA sequence) + +AnnotationAssertion(rdfs:label obo:GENO_0000720 "DNA sequence"@en) +EquivalentClasses(obo:GENO_0000720 ObjectIntersectionOf(obo:GENO_0000702 ObjectSomeValuesFrom(obo:GENO_0000783 obo:GENO_0000780) ObjectAllValuesFrom(obo:GENO_0000783 obo:GENO_0000780))) + +# Class: obo:GENO_0000721 (RNA sequence) + +AnnotationAssertion(rdfs:label obo:GENO_0000721 "RNA sequence"@en) +EquivalentClasses(obo:GENO_0000721 ObjectIntersectionOf(obo:GENO_0000702 ObjectSomeValuesFrom(obo:GENO_0000783 obo:GENO_0000781) ObjectAllValuesFrom(obo:GENO_0000783 obo:GENO_0000781))) + +# Class: obo:GENO_0000722 (amino acid sequence) + +AnnotationAssertion(rdfs:label obo:GENO_0000722 "amino acid sequence"@en) +EquivalentClasses(obo:GENO_0000722 ObjectIntersectionOf(obo:GENO_0000702 ObjectSomeValuesFrom(obo:GENO_0000783 obo:GENO_0000782) ObjectAllValuesFrom(obo:GENO_0000783 obo:GENO_0000782))) + +# Class: obo:GENO_0000724 (obsolete_biological sequence or collection) + +AnnotationAssertion(rdfs:label obo:GENO_0000724 "obsolete_biological sequence or collection"@en) +SubClassOf(obo:GENO_0000724 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000725 (obsolete_biological sequence collection) + +AnnotationAssertion(rdfs:label obo:GENO_0000725 "obsolete_biological sequence collection"@en) +SubClassOf(obo:GENO_0000725 obo:GENO_0000724) + +# Class: obo:GENO_0000736 (location-qualified sequence feature) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000736 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000736 "A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature.") +AnnotationAssertion(rdfs:comment obo:GENO_0000736 "As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell).") +AnnotationAssertion(rdfs:label obo:GENO_0000736 "location-qualified sequence feature"@en) +SubClassOf(obo:GENO_0000736 obo:GENO_0000714) + +# Class: obo:GENO_0000737 (expression-qualified sequence feature) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000737 "A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct)") +AnnotationAssertion(rdfs:label obo:GENO_0000737 "expression-qualified sequence feature"@en) +SubClassOf(obo:GENO_0000737 obo:GENO_0000714) + +# Class: obo:GENO_0000768 (obsolete_genomic position) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000768 "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000768 "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000768 "genomic coordinates"@en) +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000768 "remodeling notion of sequence feature position around the idea of a 'genomic locus'") +AnnotationAssertion(rdfs:label obo:GENO_0000768 "obsolete_genomic position") +SubClassOf(obo:GENO_0000768 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000770 (phenotypic inheritance process) + +AnnotationAssertion(rdfs:label obo:GENO_0000770 "phenotypic inheritance process"@en) +SubClassOf(obo:GENO_0000770 obo:GENO_0000351) + +# Class: obo:GENO_0000772 (obsolete_unspecified) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000772 "A sequence attribute inhering in a feature whose identity is not specified.") +AnnotationAssertion(rdfs:label obo:GENO_0000772 "obsolete_unspecified"@en) +SubClassOf(obo:GENO_0000772 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000773 (variation attribute) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000773 "An attribute describing a type of variation inhering in a sequence feature or collection.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000773 "allele attribute") +AnnotationAssertion(rdfs:label obo:GENO_0000773 "variation attribute"@en) +SubClassOf(obo:GENO_0000773 obo:GENO_0000788) + +# Class: obo:GENO_0000777 (variant genomic genotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000777 "An intrinsic genotype that specifies variation from a defined reference genome.") +AnnotationAssertion(rdfs:label obo:GENO_0000777 "variant genomic genotype"@en) +EquivalentClasses(obo:GENO_0000777 ObjectIntersectionOf(obo:GENO_0000899 ObjectSomeValuesFrom(obo:IAO_0000219 obo:GENO_0000033))) + +# Class: obo:GENO_0000778 (obsolete_sequence information entity) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000778 "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities.") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000778 "eliminating classes that are not necessary or add uneeded complexity.") +AnnotationAssertion(rdfs:label obo:GENO_0000778 "obsolete_sequence information entity"@en) +SubClassOf(obo:GENO_0000778 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000779 (biological sequence unit) + +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000779 "biological sequence residue") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000779 "monomeric residue") +AnnotationAssertion(rdfs:label obo:GENO_0000779 "biological sequence unit"@en) +EquivalentClasses(obo:GENO_0000779 ObjectIntersectionOf(obo:GENO_0000702 DataHasValue(obo:GENO_0000678 "1"^^xsd:integer))) + +# Class: obo:GENO_0000780 (DNA residue) + +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000780 "deoxyribonucleic acid residue") +AnnotationAssertion(rdfs:label obo:GENO_0000780 "DNA residue"@en) +SubClassOf(obo:GENO_0000780 obo:GENO_0000779) + +# Class: obo:GENO_0000781 (RNA residue) + +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000781 "ribonucleic acid residue") +AnnotationAssertion(rdfs:label obo:GENO_0000781 "RNA residue"@en) +SubClassOf(obo:GENO_0000781 obo:GENO_0000779) + +# Class: obo:GENO_0000782 (amino acid residue) + +AnnotationAssertion(rdfs:label obo:GENO_0000782 "amino acid residue"@en) +SubClassOf(obo:GENO_0000782 obo:GENO_0000779) + +# Class: obo:GENO_0000788 (sequence feature attribute) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000788 "An attribute, quality, or state of a sequence feature or collection.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000788 "http://purl.obolibrary.org/obo/SO_0000400") +AnnotationAssertion(rdfs:comment obo:GENO_0000788 "Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity.") +AnnotationAssertion(rdfs:label obo:GENO_0000788 "sequence feature attribute") +SubClassOf(obo:GENO_0000788 obo:BFO_0000020) + +# Class: obo:GENO_0000815 (sequence feature location) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000815 "The location of a sequence feature as defined by its start and end position on some reference coordinate system.") +AnnotationAssertion(rdfs:comment obo:GENO_0000815 "1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). + +2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there.") +AnnotationAssertion(rdfs:label obo:GENO_0000815 "sequence feature location"@en) +SubClassOf(obo:GENO_0000815 obo:BFO_0000031) +DisjointClasses(obo:GENO_0000815 obo:SO_0000110) + +# Class: obo:GENO_0000818 (modification-qualified sequence feature) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000818 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000818 "A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature)") +AnnotationAssertion(rdfs:label obo:GENO_0000818 "modification-qualified sequence feature"@en) +SubClassOf(obo:GENO_0000818 obo:GENO_0000714) + +# Class: obo:GENO_0000823 (allelic genotype) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000823 "1. The zebrafish \"fgf8a/fgf8a<+>\" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state). + +2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308. + + ##fileformat=VCFv4.2 + ##FORMAT= + #CHROM POS REF ALT FILTER FORMAT SAMP001 + 20 2300608 C T PASS GT 0/1 + 20 2301308 T G PASS GT 1/1 + (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html) + +3. Some allelic genotype formats encode the genotype as a single string - e.g. \"GRCh38 Chr12:258635(A;T)\" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12.") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000823 "A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000823 "single locus genotype") +AnnotationAssertion(rdfs:comment obo:GENO_0000823 "An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location. + +This contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background.") +AnnotationAssertion(rdfs:label obo:GENO_0000823 "allelic genotype"@en) +EquivalentClasses(obo:GENO_0000823 ObjectIntersectionOf(obo:GENO_0000719 ObjectSomeValuesFrom(obo:IAO_0000219 obo:GENO_0000516))) + +# Class: obo:GENO_0000833 (genotype-phenotype association) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000833 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000833 "Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each.") +AnnotationAssertion(rdfs:label obo:GENO_0000833 "genotype-phenotype association"@en) +SubClassOf(obo:GENO_0000833 ) +SubClassOf(Annotation(obo:GENO_0000834 "true"^^xsd:boolean) obo:GENO_0000833 ObjectSomeValuesFrom(obo:GENO_0000580 obo:ENVO_01000254)) +SubClassOf(Annotation(obo:GENO_0000834 "true"^^xsd:boolean) obo:GENO_0000833 ObjectSomeValuesFrom(obo:GENO_0000580 ObjectIntersectionOf(obo:GO_0032502 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:RO_0002091 obo:UBERON_0000105) ObjectSomeValuesFrom(obo:RO_0002093 obo:UBERON_0000105))))) +SubClassOf(Annotation(obo:GENO_0000834 "true"^^xsd:boolean) obo:GENO_0000833 ObjectSomeValuesFrom( obo:UPHENO_0001001)) +SubClassOf(Annotation(obo:GENO_0000834 "true"^^xsd:boolean) obo:GENO_0000833 ObjectSomeValuesFrom( ObjectUnionOf(obo:GENO_0000536 ObjectSomeValuesFrom(obo:BFO_0000050 obo:GENO_0000536)))) + +# Class: obo:GENO_0000839 (knockdown reagent targeted gene complement) + +AnnotationAssertion(rdfs:label obo:GENO_0000839 "knockdown reagent targeted gene complement"@en) +SubClassOf(obo:GENO_0000839 obo:GENO_0000527) +SubClassOf(obo:GENO_0000839 ObjectSomeValuesFrom(obo:GENO_0000382 obo:GENO_0000504)) + +# Class: obo:GENO_0000848 (obsolete_coding sequence alteration) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000848 obo:GENO_0000484) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000848 "A sequence alteration within the coding sequence of a gene.") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000848 "Not required at this poitn, so marked exploratory and obsoleted. +Asserted under sequence_alteration.") +AnnotationAssertion(rdfs:label obo:GENO_0000848 "obsolete_coding sequence alteration"@en) +SubClassOf(obo:GENO_0000848 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000850 (P-element construct) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000850 "A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome.") +AnnotationAssertion(rdfs:label obo:GENO_0000850 "P-element construct"@en) +SubClassOf(obo:GENO_0000850 obo:GENO_0000856) + +# Class: obo:GENO_0000856 (engineered genetic construct) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000856 "An engineered region that is used to transfer foreign genetic material into a host cell.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000856 "engineered_genetic_vector") +AnnotationAssertion(rdfs:comment obo:GENO_0000856 "Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. + +Constructs are typically packaged as part of delivery systems such as plasmids or viral vectors.") +AnnotationAssertion(rdfs:label obo:GENO_0000856 "engineered genetic construct"@en) +SubClassOf(obo:GENO_0000856 obo:SO_0000804) + +# Class: obo:GENO_0000861 (extra-chromosomal transgene) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000861 "A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000861 "non-integrated transgene") +AnnotationAssertion(rdfs:label obo:GENO_0000861 "extra-chromosomal transgene"@en) +SubClassOf(obo:GENO_0000861 obo:SO_0000902) + +# Class: obo:GENO_0000870 (obsolete_sequence feature collection) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000870 "A collection of more than one sequence feature.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000870 "http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection") +AnnotationAssertion(rdfs:label obo:GENO_0000870 "obsolete_sequence feature collection"@en) +SubClassOf(obo:GENO_0000870 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000871 (haplotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000871 "A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000871 "Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block. + +Instead, we can create an 'allele set' class as the haplotype parent?") +AnnotationAssertion(dcterms:source obo:GENO_0000871 "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype.") +AnnotationAssertion(rdfs:comment obo:GENO_0000871 "A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. + +As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': + +1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. + +2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). \"Star alleles\" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/). + +3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. + +Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations.") +AnnotationAssertion(rdfs:label obo:GENO_0000871 "haplotype"@en) +SubClassOf(obo:GENO_0000871 obo:GENO_0000660) +SubClassOf(obo:GENO_0000871 ObjectSomeValuesFrom(obo:RO_0002351 obo:GENO_0000512)) + +# Class: obo:GENO_0000872 (genomic sequence set) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000872 "A set of genomic sequences (a biological sequence that is of genomic origin).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000872 "copy number complement") +AnnotationAssertion(rdfs:comment obo:GENO_0000872 "A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location.") +AnnotationAssertion(rdfs:label obo:GENO_0000872 "genomic sequence set"@en) +SubClassOf(obo:GENO_0000872 obo:GENO_0000922) + +# Class: obo:GENO_0000873 (microsatellite alteration) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000873 "A relation used to describe an environment contextualizing the identity of an entity.") +AnnotationAssertion(rdfs:label obo:GENO_0000873 "microsatellite alteration"@en) +SubClassOf(obo:GENO_0000873 obo:GENO_0000874) + +# Class: obo:GENO_0000874 (repeat region alteration) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000874 "A relation used to describe a process contextualizing the identity of an entity.") +AnnotationAssertion(rdfs:label obo:GENO_0000874 "repeat region alteration"@en) +SubClassOf(obo:GENO_0000874 obo:SO_0001059) + +# Class: obo:GENO_0000875 (allelic state) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000875 "A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism") +AnnotationAssertion(rdfs:label obo:GENO_0000875 "allelic state"@en) +SubClassOf(obo:GENO_0000875 obo:GENO_0000788) + +# Class: obo:GENO_0000876 (obsolete_genetic dosage) + +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000876 "allelic dosage") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000876 "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000876 "gene dosage") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000876 "Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute.") +AnnotationAssertion(rdfs:comment obo:GENO_0000876 "Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. + +Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found.") +AnnotationAssertion(rdfs:label obo:GENO_0000876 "obsolete_genetic dosage"@en) +SubClassOf(obo:GENO_0000876 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000877 (allele origin) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000877 "A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000877 "genetic origin") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000877 "variant origin") +AnnotationAssertion(rdfs:label obo:GENO_0000877 "allele origin"@en) +SubClassOf(obo:GENO_0000877 obo:GENO_0000788) + +# Class: obo:GENO_0000878 (maternal allele origin) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000878 "Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000878 "maternally inherited") +AnnotationAssertion(rdfs:label obo:GENO_0000878 "maternal allele origin"@en) +SubClassOf(obo:GENO_0000878 obo:GENO_0000888) + +# Class: obo:GENO_0000879 (paternal allele origin) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000879 "Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000879 "paternally inherited") +AnnotationAssertion(rdfs:label obo:GENO_0000879 "paternal allele origin"@en) +SubClassOf(obo:GENO_0000879 obo:GENO_0000888) + +# Class: obo:GENO_0000880 (de novo allele origin) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000880 "Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000880 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation") +AnnotationAssertion(rdfs:comment obo:GENO_0000880 "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. + +De novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder.") +AnnotationAssertion(rdfs:label obo:GENO_0000880 "de novo allele origin"@en) +SubClassOf(obo:GENO_0000880 obo:GENO_0000877) + +# Class: obo:GENO_0000881 (unknown allele origin) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000881 "Describes an allele whose origin is not known.") +AnnotationAssertion(rdfs:label obo:GENO_0000881 "unknown allele origin"@en) +SubClassOf(obo:GENO_0000881 obo:GENO_0000877) + +# Class: obo:GENO_0000882 (somatic allele origin) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000882 "Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000882 "acquired") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000882 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation") +AnnotationAssertion(rdfs:comment obo:GENO_0000882 "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells. + +These acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations.") +AnnotationAssertion(rdfs:label obo:GENO_0000882 "somatic allele origin"@en) +SubClassOf(obo:GENO_0000882 obo:GENO_0000877) + +# Class: obo:GENO_0000883 (obsolete_gametic) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000883 "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000883 "germ-line") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000883 "replaced by GENO:0000900 ! 'germline'") +AnnotationAssertion(rdfs:label obo:GENO_0000883 "obsolete_gametic"@en) +SubClassOf(obo:GENO_0000883 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000885 (diplotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000885 "An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement') + +Alt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome.") +AnnotationAssertion(rdfs:comment obo:GENO_0000885 "\"Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes.\" +From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/ +https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/") +AnnotationAssertion(rdfs:label obo:GENO_0000885 "diplotype"@en) +EquivalentClasses(obo:GENO_0000885 ObjectIntersectionOf(obo:GENO_0000823 ObjectSomeValuesFrom(obo:IAO_0000219 ObjectIntersectionOf(obo:GENO_0000516 ObjectExactCardinality(2 obo:RO_0002351 obo:GENO_0000512))))) + +# Class: obo:GENO_0000886 (allelic phase) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000886 "A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes.") +AnnotationAssertion(rdfs:label obo:GENO_0000886 "allelic phase") +SubClassOf(obo:GENO_0000886 obo:GENO_0000788) + +# Class: obo:GENO_0000887 (oryzias latipes strain) + +AnnotationAssertion(rdfs:label obo:GENO_0000887 "oryzias latipes strain") +SubClassOf(obo:GENO_0000887 obo:GENO_0000112) +SubClassOf(obo:GENO_0000887 ObjectSomeValuesFrom(obo:RO_0002351 obo:NCBITaxon_8090)) +SubClassOf(obo:GENO_0000887 ObjectAllValuesFrom(obo:RO_0002351 obo:NCBITaxon_8090)) + +# Class: obo:GENO_0000888 (germline allele origin) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000888 "Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000888 "hereditary") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000888 "parental origin") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000888 "parentally inherited") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000888 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation") +AnnotationAssertion(rdfs:comment obo:GENO_0000888 "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells.") +AnnotationAssertion(rdfs:label obo:GENO_0000888 "germline allele origin"@en) +SubClassOf(obo:GENO_0000888 obo:GENO_0000877) + +# Class: obo:GENO_0000889 (undetermined inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000889 "An inheritance pattern that is not determined or not known.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000889 "unknown inheritance") +AnnotationAssertion(rdfs:label obo:GENO_0000889 "undetermined inheritance") +SubClassOf(obo:GENO_0000889 obo:GENO_0000141) + +# Class: obo:GENO_0000890 (obsolete_canonical allele) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000890 "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”.") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000890 "One of a set of sequence features or haplotypes that exist at a particular genetic locus. ") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000890 "The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000890 "http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000890 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.") +AnnotationAssertion(dcterms:source obo:GENO_0000890 "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)") +AnnotationAssertion(rdfs:comment obo:GENO_0000890 "As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. + +In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references)") +AnnotationAssertion(rdfs:label obo:GENO_0000890 "obsolete_canonical allele") +SubClassOf(obo:GENO_0000890 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000891 (obsolete_contextual allele) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000891 "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000891 "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000891 "http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000891 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. + +Former axiom: denotes some 'obsolete_canonical allele'") +AnnotationAssertion(dcterms:source obo:GENO_0000891 "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)") +AnnotationAssertion(rdfs:comment obo:GENO_0000891 "The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene.") +AnnotationAssertion(rdfs:label obo:GENO_0000891 "obsolete_contextual allele") +SubClassOf(obo:GENO_0000891 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000892 (heteroplasmic mitochondrial inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000892 "A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not.") +AnnotationAssertion(rdfs:label obo:GENO_0000892 "heteroplasmic mitochondrial inheritance") +SubClassOf(obo:GENO_0000892 obo:GENO_0000949) + +# Class: obo:GENO_0000893 (homoplasmic mitochondrial inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000893 "A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited.") +AnnotationAssertion(rdfs:label obo:GENO_0000893 "homoplasmic mitochondrial inheritance") +SubClassOf(obo:GENO_0000893 obo:GENO_0000949) + +# Class: obo:GENO_0000897 (genomic entity) + +AnnotationAssertion(obo:GENO_0000905 obo:GENO_0000897 "true"^^xsd:boolean) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000897 "An generically dependent continuant that carries biological sequence that is part of or derived from a genome.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000897 "An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities.") +AnnotationAssertion(rdfs:label obo:GENO_0000897 "genomic entity"@en) +EquivalentClasses(obo:GENO_0000897 ObjectUnionOf(obo:GENO_0000481 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GENO_0000481) ObjectSomeValuesFrom(obo:GENO_0000726 ObjectUnionOf(obo:GENO_0000481 obo:GENO_0000660)) ObjectSomeValuesFrom(obo:IAO_0000219 ObjectUnionOf(obo:GENO_0000481 obo:GENO_0000660 obo:GENO_0000715)))) +SubClassOf(obo:GENO_0000897 obo:BFO_0000031) +SubClassOf(obo:GENO_0000897 ObjectSomeValuesFrom(obo:RO_0002162 obo:OBI_0100026)) + +# Class: obo:GENO_0000898 (haplotype block) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000898 "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000898 "Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as +\"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.\" Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location. + +Current definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000898 "Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424.") +AnnotationAssertion(rdfs:comment obo:GENO_0000898 "A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.") +AnnotationAssertion(rdfs:label obo:GENO_0000898 "haplotype block"@en) +SubClassOf(obo:GENO_0000898 obo:GENO_0000481) + +# Class: obo:GENO_0000899 (genomic genotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000899 "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000899 "'Genomic Genotype' vs 'Genome' in GENO: +A genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000899 "complete genotype") +AnnotationAssertion(rdfs:comment obo:GENO_0000899 "1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. + +2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons.") +AnnotationAssertion(rdfs:label obo:GENO_0000899 "genomic genotype"@en) +EquivalentClasses(obo:GENO_0000899 ObjectIntersectionOf(obo:GENO_0000719 ObjectSomeValuesFrom(obo:IAO_0000219 obo:SO_0001026))) +SubClassOf(obo:GENO_0000899 ObjectSomeValuesFrom(obo:GENO_0000385 obo:GENO_0000611)) + +# Class: obo:GENO_0000901 (obsolete_allele cellular context) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000901 "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000901 "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin") +AnnotationAssertion(rdfs:comment obo:GENO_0000901 "Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others.") +AnnotationAssertion(rdfs:label obo:GENO_0000901 "obsolete_allele cellular context") +SubClassOf(obo:GENO_0000901 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000902 (genomic feature location) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000902 "The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000902 "In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. + +We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000902 "In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. + +For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000902 "genomic location") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000902 "genomic locus") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000902 "VMC:Location") +AnnotationAssertion(rdfs:comment obo:GENO_0000902 "1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. + +2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. + +3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there.") +AnnotationAssertion(rdfs:label obo:GENO_0000902 "genomic feature location"@en) +SubClassOf(obo:GENO_0000902 obo:GENO_0000815) + +# Class: obo:GENO_0000904 (organismal entity) + +AnnotationAssertion(obo:GENO_0000905 obo:GENO_0000904 "true"^^xsd:boolean) +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000904 "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc).") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000904 "useful organizational term to collect entities that have genomes/genotypes.") +AnnotationAssertion(rdfs:label obo:GENO_0000904 "organismal entity"@en) +EquivalentClasses(obo:GENO_0000904 ObjectUnionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0001000 obo:OBI_0100026) ObjectSomeValuesFrom(obo:RO_0002351 obo:OBI_0100026))) +SubClassOf(obo:GENO_0000904 obo:BFO_0000040) + +# Class: obo:GENO_0000907 (gene product) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000907 "The molecular product resulting from transcription of a single gene (either a protein or RNA molecule)") +AnnotationAssertion(rdfs:label obo:GENO_0000907 "gene product"@en) +SubClassOf(obo:GENO_0000907 obo:SO_0000110) + +# Class: obo:GENO_0000910 (reporter role) + +AnnotationAssertion(rdfs:label obo:GENO_0000910 "reporter role"@en) +SubClassOf(obo:GENO_0000910 obo:OBI_0000086) + +# Class: obo:GENO_0000911 (selectable marker role) + +AnnotationAssertion(rdfs:label obo:GENO_0000911 "selectable marker role"@en) +SubClassOf(obo:GENO_0000911 obo:OBI_0000086) + +# Class: obo:GENO_0000912 (selectable marker region) + +AnnotationAssertion(rdfs:label obo:GENO_0000912 "selectable marker region"@en) +SubClassOf(obo:GENO_0000912 obo:GENO_0000638) + +# Class: obo:GENO_0000914 (reference genome) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000914 "A genome whose sequence is identical to that of a genome sequence considered to be the reference.") +AnnotationAssertion(rdfs:label obo:GENO_0000914 "reference genome"@en) +SubClassOf(obo:GENO_0000914 obo:SO_0001026) +SubClassOf(obo:GENO_0000914 ObjectSomeValuesFrom(obo:GENO_0000239 obo:SO_0001505)) + +# Class: obo:GENO_0000915 (obsolete_haplotype) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000915 "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000915 "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000915 "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype.") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000915 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. + +Former SC axioms: +- is_allele_of some 'haplotype block' +- 'has part' some sequence_alteration") +AnnotationAssertion(rdfs:comment obo:GENO_0000915 "1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene). + +2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. + +GENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. + +3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': + +a. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. +b. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. +c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. + +The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations.") +AnnotationAssertion(rdfs:label obo:GENO_0000915 "obsolete_haplotype"@en) +SubClassOf(obo:GENO_0000915 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000916 (obsolete_haplotype block) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000916 "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000916 "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block.") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000916 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.") +AnnotationAssertion(rdfs:comment obo:GENO_0000916 "A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. + +The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. + +----------------------- + +* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces.") +AnnotationAssertion(rdfs:label obo:GENO_0000916 "obsolete_haplotype block"@en) +SubClassOf(obo:GENO_0000916 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000918 (organellar plasmy) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000918 "An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell.") +AnnotationAssertion(rdfs:comment obo:GENO_0000918 "Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene.") +AnnotationAssertion(rdfs:label obo:GENO_0000918 "organellar plasmy"@en) +SubClassOf(obo:GENO_0000918 obo:GENO_0000875) + +# Class: obo:GENO_0000919 (qualified sequence feature) + +AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000919 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes).") +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000919 "A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification.") +AnnotationAssertion(rdfs:comment obo:GENO_0000919 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern).") +AnnotationAssertion(rdfs:comment obo:GENO_0000919 "Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes.") +AnnotationAssertion(rdfs:label obo:GENO_0000919 "qualified sequence feature"@en) +SubClassOf(obo:GENO_0000919 obo:GENO_0000713) + +# Class: obo:GENO_0000920 (qualified sequence feature set) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000920 "A set of qualified seqeunce features.") +AnnotationAssertion(rdfs:comment obo:GENO_0000920 "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'.") +AnnotationAssertion(rdfs:label obo:GENO_0000920 "qualified sequence feature set"@en) +SubClassOf(obo:GENO_0000920 obo:GENO_0000713) +SubClassOf(obo:GENO_0000920 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GENO_0000919)) +SubClassOf(obo:GENO_0000920 ObjectSomeValuesFrom(obo:GENO_0000726 obo:GENO_0000659)) + +# Class: obo:GENO_0000921 (biological sequence or set) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000921 "A biolocical sequence, or set of such sequences.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000921 "biological sequence or collection") +AnnotationAssertion(rdfs:label obo:GENO_0000921 "biological sequence or set"@en) +SubClassOf(obo:GENO_0000921 obo:BFO_0000031) + +# Class: obo:GENO_0000922 (biological sequence set) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000922 "A set of biological sequences.") +AnnotationAssertion(rdfs:comment obo:GENO_0000922 "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. + +A set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence.") +AnnotationAssertion(rdfs:label obo:GENO_0000922 "biological sequence set"@en) +SubClassOf(obo:GENO_0000922 obo:GENO_0000921) + +# Class: obo:GENO_0000923 (obsolete_functional copy number complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000923 "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000923 "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000923 "functional feature complement") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000923 "genetic dosage"@en) +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000923 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963.") +AnnotationAssertion(rdfs:comment obo:GENO_0000923 "As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage).") +AnnotationAssertion(rdfs:comment obo:GENO_0000923 "The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage.") +AnnotationAssertion(rdfs:label obo:GENO_0000923 "obsolete_functional copy number complement") +SubClassOf(obo:GENO_0000923 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000924 (obsolete_intrinsic sequence feature attribute) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000924 "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form.") +AnnotationAssertion(rdfs:label obo:GENO_0000924 "obsolete_intrinsic sequence feature attribute"@en) +SubClassOf(obo:GENO_0000924 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000925 (obsolete_extrinsic sequence feature attribute) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000925 "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)") +AnnotationAssertion(rdfs:label obo:GENO_0000925 "obsolete_extrinsic sequence feature attribute"@en) +SubClassOf(obo:GENO_0000925 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000926 (allelic cellular distribution) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000926 "A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism).") +AnnotationAssertion(rdfs:label obo:GENO_0000926 "allelic cellular distribution"@en) +SubClassOf(obo:GENO_0000926 obo:GENO_0000788) + +# Class: obo:GENO_0000927 (constitutional) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000927 "A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin.") +AnnotationAssertion(rdfs:label obo:GENO_0000927 "constitutional"@en) +SubClassOf(obo:GENO_0000927 obo:GENO_0000926) + +# Class: obo:GENO_0000928 (clonal) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000928 "A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin.") +AnnotationAssertion(rdfs:label obo:GENO_0000928 "clonal"@en) +SubClassOf(obo:GENO_0000928 obo:GENO_0000926) + +# Class: obo:GENO_0000929 (multifactorial inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000929 "An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000929 "complex inherritance") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000929 "multi-factorial inheritance") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000929 "multi-genic inheritance") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000929 "multi-locus inheritance") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000929 "multigenic inheritance") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000929 "http://purl.obolibrary.org/obo/HP_0001426") +AnnotationAssertion(rdfs:comment obo:GENO_0000929 "Diseases inherited in this manner are termed 'complex diseases'.") +AnnotationAssertion(rdfs:label obo:GENO_0000929 "multifactorial inheritance"@en) +SubClassOf(obo:GENO_0000929 obo:GENO_0000141) + +# Class: obo:GENO_0000930 (digenic inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000930 "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000930 "http://purl.obolibrary.org/obo/HP_0010984") +AnnotationAssertion(rdfs:label obo:GENO_0000930 "digenic inheritance"@en) +SubClassOf(obo:GENO_0000930 obo:GENO_0000929) + +# Class: obo:GENO_0000931 (oligogenic inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000931 "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000931 "http://purl.obolibrary.org/obo/HP_0010983") +AnnotationAssertion(rdfs:comment obo:GENO_0000931 "It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform.") +AnnotationAssertion(rdfs:label obo:GENO_0000931 "oligogenic inheritance"@en) +SubClassOf(obo:GENO_0000931 obo:GENO_0000929) + +# Class: obo:GENO_0000932 (polygenic inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000932 "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000932 "http://purl.obolibrary.org/obo/HP_0010982") +AnnotationAssertion(rdfs:comment obo:GENO_0000932 "Typically used for traits/conditions governed by more than three gene loci.") +AnnotationAssertion(rdfs:label obo:GENO_0000932 "polygenic inheritance"@en) +SubClassOf(obo:GENO_0000932 obo:GENO_0000929) + +# Class: obo:GENO_0000933 (monogenic inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000933 "An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000933 "single-gene inheritance") +AnnotationAssertion(rdfs:label obo:GENO_0000933 "monogenic inheritance"@en) +SubClassOf(obo:GENO_0000933 obo:GENO_0000141) + +# Class: obo:GENO_0000934 (autosomal inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000934 "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome.") +AnnotationAssertion(rdfs:label obo:GENO_0000934 "autosomal inheritance"@en) +SubClassOf(obo:GENO_0000934 obo:GENO_0000933) + +# Class: obo:GENO_0000935 (allosomal inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000935 "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000935 "gonosomal inheritance") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000935 "http://purl.obolibrary.org/obo/HP_0010985") +AnnotationAssertion(rdfs:label obo:GENO_0000935 "allosomal inheritance"@en) +SubClassOf(obo:GENO_0000935 obo:GENO_0000933) + +# Class: obo:GENO_0000936 (X-linked inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000936 "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000936 "http://purl.obolibrary.org/obo/HP_0001417") +AnnotationAssertion(rdfs:label obo:GENO_0000936 "X-linked inheritance"@en) +SubClassOf(obo:GENO_0000936 obo:GENO_0000935) + +# Class: obo:GENO_0000937 (complete X-linked dominant inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000937 "An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.") +AnnotationAssertion(rdfs:label obo:GENO_0000937 "complete X-linked dominant inheritance"@en) +SubClassOf(obo:GENO_0000937 obo:GENO_0000146) + +# Class: obo:GENO_0000938 (incomplete X-linked dominant inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000938 "An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000938 "semi-dominant X-linked inheritance") +AnnotationAssertion(rdfs:label obo:GENO_0000938 "incomplete X-linked dominant inheritance"@en) +SubClassOf(obo:GENO_0000938 obo:GENO_0000146) + +# Class: obo:GENO_0000939 (co-dominant X-linked inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000939 "An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.") +AnnotationAssertion(rdfs:label obo:GENO_0000939 "co-dominant X-linked inheritance"@en) +SubClassOf(obo:GENO_0000939 obo:GENO_0000146) + +# Class: obo:GENO_0000941 (Y-linked inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000941 "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000941 "holandric inheritance") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000941 "http://purl.obolibrary.org/obo/HP_0001450") +AnnotationAssertion(rdfs:label obo:GENO_0000941 "Y-linked inheritance"@en) +SubClassOf(obo:GENO_0000941 obo:GENO_0000935) + +# Class: obo:GENO_0000942 (Z-linked inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000942 "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome.") +AnnotationAssertion(rdfs:label obo:GENO_0000942 "Z-linked inheritance"@en) +SubClassOf(obo:GENO_0000942 obo:GENO_0000935) + +# Class: obo:GENO_0000943 (Z-linked dominant inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000943 "A Z-linked inheritance pattern wherein the trait manifests in heterozygotes.") +AnnotationAssertion(rdfs:label obo:GENO_0000943 "Z-linked dominant inheritance"@en) +SubClassOf(obo:GENO_0000943 obo:GENO_0000942) + +# Class: obo:GENO_0000944 (complete Z-linked dominant inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000944 "A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.") +AnnotationAssertion(rdfs:label obo:GENO_0000944 "complete Z-linked dominant inheritance"@en) +SubClassOf(obo:GENO_0000944 obo:GENO_0000943) + +# Class: obo:GENO_0000945 (incomplete Z-linked dominant inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000945 "A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000945 "semi-dominant Z-linked inheritance") +AnnotationAssertion(rdfs:label obo:GENO_0000945 "incomplete Z-linked dominant inheritance"@en) +SubClassOf(obo:GENO_0000945 obo:GENO_0000943) + +# Class: obo:GENO_0000946 (co-dominant Z-linked inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000946 "An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.") +AnnotationAssertion(rdfs:label obo:GENO_0000946 "co-dominant Z-linked inheritance"@en) +SubClassOf(obo:GENO_0000946 obo:GENO_0000943) + +# Class: obo:GENO_0000947 (Z-linked reccessive inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000947 "A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals.") +AnnotationAssertion(rdfs:label obo:GENO_0000947 "Z-linked reccessive inheritance"@en) +SubClassOf(obo:GENO_0000947 obo:GENO_0000942) + +# Class: obo:GENO_0000948 (W-linked inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000948 "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome.") +AnnotationAssertion(rdfs:label obo:GENO_0000948 "W-linked inheritance"@en) +SubClassOf(obo:GENO_0000948 obo:GENO_0000935) + +# Class: obo:GENO_0000949 (mitochondrial inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000949 "An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome.") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000949 "http://purl.obolibrary.org/obo/HP_0001427") +AnnotationAssertion(rdfs:comment obo:GENO_0000949 "Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy).") +AnnotationAssertion(rdfs:label obo:GENO_0000949 "mitochondrial inheritance"@en) +SubClassOf(obo:GENO_0000949 obo:GENO_0000141) + +# Class: obo:GENO_0000952 (sex-limited autosomal dominant inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000952 "An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females).") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000952 "http://purl.obolibrary.org/obo/HP_0001470") +AnnotationAssertion(rdfs:label obo:GENO_0000952 "sex-limited autosomal dominant inheritance"@en) +SubClassOf(obo:GENO_0000952 obo:GENO_0000147) + +# Class: obo:GENO_0000953 (sex-limited autosomal recessive inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000953 "An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females).") +AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000953 "http://purl.obolibrary.org/obo/HP_0031362") +AnnotationAssertion(rdfs:label obo:GENO_0000953 "sex-limited autosomal recessive inheritance"@en) +SubClassOf(obo:GENO_0000953 obo:GENO_0000148) + +# Class: obo:GENO_0000954 (allele set) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000954 "A set of discrete alleles within a particular genome.") +AnnotationAssertion(rdfs:comment obo:GENO_0000954 "'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An \"Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'.") +AnnotationAssertion(rdfs:label obo:GENO_0000954 "allele set"@en) +SubClassOf(obo:GENO_0000954 obo:GENO_0000660) + +# Class: obo:GENO_0000955 (obsolete_variant copy number complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000955 "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s).") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000955 "copy number variation"@en) +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000955 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level.") +AnnotationAssertion(rdfs:comment obo:GENO_0000955 "In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). + +Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class.") +AnnotationAssertion(rdfs:label obo:GENO_0000955 "obsolete_variant copy number complement") +SubClassOf(obo:GENO_0000955 obo:GENO_0000956) + +# Class: obo:GENO_0000956 (obsolete_copy number complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000956 "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger.") +AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000956 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961.") +AnnotationAssertion(rdfs:comment obo:GENO_0000956 "1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. + +2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. + +3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members.") +AnnotationAssertion(rdfs:label obo:GENO_0000956 "obsolete_copy number complement"@en) +SubClassOf(obo:GENO_0000956 oboInOwl:ObsoleteClass) + +# Class: obo:GENO_0000960 (genomic sequence) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000960 "A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism).") +AnnotationAssertion(rdfs:comment obo:GENO_0000960 "A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome.") +AnnotationAssertion(rdfs:label obo:GENO_0000960 "genomic sequence"@en) +EquivalentClasses(obo:GENO_0000960 ObjectSomeValuesFrom(obo:GENO_0000251 obo:GENO_0000481)) +SubClassOf(obo:GENO_0000960 obo:GENO_0000702) + +# Class: obo:GENO_0000961 (copy number complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000961 "A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome.") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000961 "The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome. + +We represent the notion of copy number at the \"sequence level\" (as opposed to the \"sequence feature level\") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The \"sequence level\" representation here supports this use case. By contrast, a \"feature level\" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity).") +AnnotationAssertion(rdfs:comment obo:GENO_0000961 "The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result. + +A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. + +The fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus.") +AnnotationAssertion(rdfs:comment obo:GENO_0000961 "The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence.") +AnnotationAssertion(rdfs:label obo:GENO_0000961 "copy number complement"@en) +SubClassOf(obo:GENO_0000961 obo:GENO_0000872) + +# Class: obo:GENO_0000962 (variant copy number complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000962 "A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s).") +AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000962 "Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a \"sequence feature level\" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred). + +For example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains.") +AnnotationAssertion(rdfs:comment obo:GENO_0000962 "'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome.") +AnnotationAssertion(rdfs:label obo:GENO_0000962 "variant copy number complement"@en) +SubClassOf(obo:GENO_0000962 obo:GENO_0000961) + +# Class: obo:GENO_0000963 (functional copy complement) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000963 "A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome.") +AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000963 "functional genetic dosage") +AnnotationAssertion(rdfs:comment obo:GENO_0000963 "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence. + +'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. + +As we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele.") +AnnotationAssertion(rdfs:label obo:GENO_0000963 "functional copy complement"@en) +SubClassOf(obo:GENO_0000963 obo:GENO_0000872) + +# Class: obo:GENO_0000964 (mosaic) + +AnnotationAssertion(rdfs:comment obo:GENO_0000964 "A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type.") +AnnotationAssertion(rdfs:label obo:GENO_0000964 "mosaic"@en) +SubClassOf(obo:GENO_0000964 obo:GENO_0000928) + +# Class: obo:GENO_0000965 (sequence interval) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000965 "A pair of integers representing start and end position of a location on a sequence coordinate system.") +AnnotationAssertion(rdfs:label obo:GENO_0000965 "sequence interval") +SubClassOf(obo:GENO_0000965 obo:IAO_0000030) + +# Class: obo:GO_0003674 (molecular function) + +AnnotationAssertion(rdfs:label obo:GO_0003674 "molecular function") +SubClassOf(obo:GO_0003674 obo:BFO_0000034) + +# Class: obo:GO_0032502 (developmental process) + +AnnotationAssertion(obo:IAO_0000115 obo:GO_0032502 "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete]") +AnnotationAssertion(rdfs:label obo:GO_0032502 "developmental process"@en) +SubClassOf(obo:GO_0032502 obo:GENO_0000351) + +# Class: obo:HP_0000118 (human phenotypic abnormality) + +AnnotationAssertion(rdfs:comment obo:HP_0000118 "pulling in HP 'phenotypic abnormality' root here"^^xsd:string) +AnnotationAssertion(rdfs:label obo:HP_0000118 "human phenotypic abnormality"^^xsd:string) +SubClassOf(obo:HP_0000118 obo:UPHENO_0001001) + +# Class: obo:HsapDv_0000000 (human life cycle stage) + +AnnotationAssertion(obo:IAO_0000116 obo:HsapDv_0000000 "Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology.") +AnnotationAssertion(obo:IAO_0000119 obo:HsapDv_0000000 "A spatiotemporal region encompassing some part of the life cycle of an organism.") +AnnotationAssertion(rdfs:label obo:HsapDv_0000000 "human life cycle stage"@en) +SubClassOf(obo:HsapDv_0000000 obo:GENO_0000351) + +# Class: obo:IAO_0000030 (information content entity) + +AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000030 "information content entity"@en) +AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000030 "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en) +AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000030 obo:IAO_0000125) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000030 "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity"@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000030 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000030 "PERSON: Chris Stoeckert"@en) +AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000030 "OBI_0000142"@en) +AnnotationAssertion(rdfs:label obo:IAO_0000030 "information content entity") +AnnotationAssertion(rdfs:label obo:IAO_0000030 "information content entity"@en) +SubClassOf(obo:IAO_0000030 obo:BFO_0000031) + +# Class: obo:IAO_0000102 (data about an ontology part) + +AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000102 "ontology metadata") +AnnotationAssertion(rdfs:label obo:IAO_0000102 "data about an ontology part") +SubClassOf(obo:IAO_0000102 obo:IAO_0000030) + +# Class: obo:MP_0000001 (mammalian phenotype) + +AnnotationAssertion(rdfs:comment obo:MP_0000001 "where to place this depends on if we take the organismal view or the quality centric view.") +AnnotationAssertion(rdfs:label obo:MP_0000001 "mammalian phenotype"^^xsd:string) +SubClassOf(obo:MP_0000001 obo:UPHENO_0001001) + +# Class: obo:NCBITaxon_10090 (Mus musculus) + +AnnotationAssertion(rdfs:label obo:NCBITaxon_10090 "Mus musculus") +SubClassOf(obo:NCBITaxon_10090 obo:OBI_0100026) + +# Class: obo:NCBITaxon_10239 (Viruses) + +AnnotationAssertion(rdfs:comment obo:NCBITaxon_10239 "Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies.") +AnnotationAssertion(rdfs:label obo:NCBITaxon_10239 "Viruses") +SubClassOf(obo:NCBITaxon_10239 obo:OBI_0100026) + +# Class: obo:NCBITaxon_7955 (Danio rerio) + +AnnotationAssertion(rdfs:label obo:NCBITaxon_7955 "Danio rerio") +SubClassOf(obo:NCBITaxon_7955 obo:OBI_0100026) + +# Class: obo:NCBITaxon_8090 (Oryzias latipes) + +AnnotationAssertion(rdfs:label obo:NCBITaxon_8090 "Oryzias latipes") +SubClassOf(obo:NCBITaxon_8090 obo:OBI_0100026) + +# Class: obo:NCBITaxon_9606 (Homo sapiens) + +AnnotationAssertion(rdfs:label obo:NCBITaxon_9606 "Homo sapiens") +SubClassOf(obo:NCBITaxon_9606 obo:OBI_0100026) + +# Class: obo:OBI_0000011 (planned process) + +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000011 "A processual entity that realizes a plan which is the concretization of a plan specification.") +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000011 "Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO.") +AnnotationAssertion(rdfs:label obo:OBI_0000011 "planned process") +SubClassOf(obo:OBI_0000011 obo:BFO_0000015) + +# Class: obo:OBI_0000086 (reagent role) + +AnnotationAssertion(rdfs:label obo:OBI_0000086 "reagent role"@en) +SubClassOf(obo:OBI_0000086 obo:BFO_0000023) + +# Class: obo:OBI_0000181 (population) + +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000181 "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area") +AnnotationAssertion(rdfs:label obo:OBI_0000181 "population"@en) +SubClassOf(obo:OBI_0000181 obo:GENO_0000113) + +# Class: obo:OBI_0000435 (genotyping assay) + +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000435 "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.") +AnnotationAssertion(rdfs:label obo:OBI_0000435 "genotyping assay") +SubClassOf(obo:OBI_0000435 obo:ERO_0000007) + +# Class: obo:OBI_0001148 (targeted gene knock-out technique) + +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001148 "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.") +AnnotationAssertion(rdfs:comment obo:OBI_0001148 "A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a \"targeted\" insertion.") +AnnotationAssertion(rdfs:label obo:OBI_0001148 "targeted gene knock-out technique") +SubClassOf(obo:OBI_0001148 obo:GENO_0000166) + +# Class: obo:OBI_0001149 (targeted gene knock-in technique) + +AnnotationAssertion(rdfs:label obo:OBI_0001149 "targeted gene knock-in technique"@en) +SubClassOf(obo:OBI_0001149 obo:GENO_0000166) + +# Class: obo:OBI_0100026 (organism) + +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0100026 "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy.") +AnnotationAssertion(rdfs:label obo:OBI_0100026 "organism") +SubClassOf(obo:OBI_0100026 obo:BFO_0000040) + +# Class: obo:OBI_0600043 (genetic modification technique) + +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0600043 "the introduction. alteration or integration of genetic material into a cell or organism") +AnnotationAssertion(rdfs:label obo:OBI_0600043 "genetic modification technique") +SubClassOf(obo:OBI_0600043 obo:ERO_0000007) +SubClassOf(obo:OBI_0600043 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectIntersectionOf(obo:GENO_0000106 ObjectSomeValuesFrom(obo:GENO_0000211 obo:GENO_0000002)))) + +# Class: obo:PATO_0000016 (obsolete_color brightness) + +AnnotationAssertion(obo:IAO_0000116 obo:PATO_0000016 "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html") +AnnotationAssertion(obo:IAO_0000116 obo:PATO_0000016 "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute.") +AnnotationAssertion(obo:IAO_0000118 obo:PATO_0000016 "color value") +AnnotationAssertion(rdfs:label obo:PATO_0000016 "obsolete_color brightness"@en) +SubClassOf(obo:PATO_0000016 oboInOwl:ObsoleteClass) + +# Class: obo:PATO_0000383 (female) + +AnnotationAssertion(rdfs:label obo:PATO_0000383 "female") +SubClassOf(obo:PATO_0000383 obo:PATO_0001894) + +# Class: obo:PATO_0000384 (male) + +AnnotationAssertion(rdfs:label obo:PATO_0000384 "male") +SubClassOf(obo:PATO_0000384 obo:PATO_0001894) + +# Class: obo:PATO_0001894 (phenotypic sex) + +AnnotationAssertion(rdfs:label obo:PATO_0001894 "phenotypic sex"@en) +SubClassOf(obo:PATO_0001894 obo:BFO_0000019) + +# Class: obo:PCO_0000000 (collection of organisms) + +AnnotationAssertion(obo:IAO_0000115 obo:PCO_0000000 "A material entity that consists of two or more organisms, viruses, or viroids.") +AnnotationAssertion(rdfs:comment obo:PCO_0000000 "A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role).") +AnnotationAssertion(rdfs:label obo:PCO_0000000 "collection of organisms") +SubClassOf(obo:PCO_0000000 obo:BFO_0000040) +SubClassOf(obo:PCO_0000000 ObjectSomeValuesFrom(obo:RO_0002351 obo:OBI_0100026)) + +# Class: obo:PCO_0000020 (family) + +AnnotationAssertion(obo:IAO_0000115 obo:PCO_0000020 "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.") +AnnotationAssertion(rdfs:label obo:PCO_0000020 "family") +SubClassOf(obo:PCO_0000020 obo:PCO_0000000) + +# Class: obo:SO_0000034 (morpholino_oligo) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000034 "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.") +AnnotationAssertion(rdfs:label obo:SO_0000034 "morpholino_oligo") +SubClassOf(obo:SO_0000034 obo:GENO_0000533) + +# Class: obo:SO_0000105 (chromosome arm) + +AnnotationAssertion(obo:IAO_0000112 obo:SO_0000105 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\".") +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000105 "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.") +AnnotationAssertion(obo:IAO_0000116 obo:SO_0000105 "Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term.") +AnnotationAssertion(obo:IAO_0000119 obo:SO_0000105 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band") +AnnotationAssertion(rdfs:label obo:SO_0000105 "chromosome arm"@en) +SubClassOf(obo:SO_0000105 obo:SO_0000830) +SubClassOf(obo:SO_0000105 ObjectSomeValuesFrom(obo:BFO_0000050 obo:SO_0000830)) + +# Class: obo:SO_0000110 (sequence_feature) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000110 "Any extent of continuous biological sequence.") +AnnotationAssertion(obo:IAO_0000116 obo:SO_0000110 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern).") +AnnotationAssertion(rdfs:comment obo:SO_0000110 "A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome.") +AnnotationAssertion(rdfs:label obo:SO_0000110 "sequence_feature") +SubClassOf(obo:SO_0000110 obo:GENO_0000701) +SubClassOf(Annotation(obo:GENO_0000834 "true"^^xsd:boolean) Annotation(rdfs:comment "Formalizes the first identity criteria for a sequence feature of its sequence.") obo:SO_0000110 ObjectSomeValuesFrom(obo:GENO_0000239 obo:GENO_0000702)) +SubClassOf(Annotation(obo:GENO_0000834 "true"^^xsd:boolean) Annotation(rdfs:comment "Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property).") obo:SO_0000110 ObjectSomeValuesFrom(obo:GENO_0000903 obo:GENO_0000815)) + +# Class: obo:SO_0000143 (obsolete_assembly_component) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000143 "A region of known length which may be used to manufacture a longer region.") +AnnotationAssertion(rdfs:label obo:SO_0000143 "obsolete_assembly_component"@en) +SubClassOf(obo:SO_0000143 obo:SO_0001410) + +# Class: obo:SO_0000149 (obsolete_contig) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000149 "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.") +AnnotationAssertion(rdfs:label obo:SO_0000149 "obsolete_contig"@en) +SubClassOf(obo:SO_0000149 obo:SO_0000143) + +# Class: obo:SO_0000159 (deletion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000159 "The point at which one or more contiguous nucleotides were excised."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000159 "deleted_sequence"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000159 "nucleotide deletion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000159 "nucleotide_deletion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0000159 obo:so.owl) +AnnotationAssertion(obo:IAO_alt_id obo:SO_0000159 "SO:1000033"^^xsd:string) +AnnotationAssertion(obo:IAO_id obo:SO_0000159 "SO:0000159"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0000159 "SOFA"^^xsd:string) +AnnotationAssertion(obo:IAO_xref obo:SO_0000159 "http://en.wikipedia.org/wiki/Nucleotide_deletion"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0000159 "deletion"^^xsd:string) +SubClassOf(obo:SO_0000159 obo:SO_0001059) +SubClassOf(obo:SO_0000159 DataHasValue(obo:GENO_0000678 "0"^^xsd:integer)) + +# Class: obo:SO_0000165 (enhancer) + +AnnotationAssertion(rdfs:label obo:SO_0000165 "enhancer") +SubClassOf(obo:SO_0000165 obo:SO_0005836) + +# Class: obo:SO_0000167 (promoter) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000167 "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.") +AnnotationAssertion(rdfs:label obo:SO_0000167 "promoter") +SubClassOf(obo:SO_0000167 obo:SO_0005836) + +# Class: obo:SO_0000199 (translocation) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000199 "A region of nucleotide sequence that has translocated to a new position."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000199 "transchr"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000199 "translocated sequence"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0000199 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_0000199 "SO:0000199"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0000199 "DBVAR"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0000199 "translocation"^^xsd:string) +SubClassOf(obo:SO_0000199 obo:SO_0001059) + +# Class: obo:SO_0000207 (simple_sequence_length_variation) + +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000207 "SSLP"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000207 "simple sequence length polymorphism"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000207 "simple sequence length variation"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0000207 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_0000207 "SO:0000207"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0000207 "simple_sequence_length_variation"^^xsd:string) +SubClassOf(obo:SO_0000207 obo:SO_0000248) + +# Class: obo:SO_0000248 (sequence_length_variation) + +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000248 "sequence length variation"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0000248 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_0000248 "SO:0000248"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0000248 "sequence_length_variation"^^xsd:string) +SubClassOf(obo:SO_0000248 obo:SO_1000002) + +# Class: obo:SO_0000281 (engineered_foreign_gene) + +AnnotationAssertion(obo:IAO_0000116 obo:SO_0000281 "See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25. + +Includes things like loxP sites, inducible promoters, ires elements, etc.") +AnnotationAssertion(rdfs:label obo:SO_0000281 "engineered_foreign_gene") +SubClassOf(obo:SO_0000281 obo:SO_0000704) +SubClassOf(obo:SO_0000281 ObjectSomeValuesFrom(obo:GENO_0000207 obo:SO_0000783)) + +# Class: obo:SO_0000289 (microsatellite) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000289 "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.") +AnnotationAssertion(obo:IAO_0000119 obo:SO_0000289 "http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29") +AnnotationAssertion(rdfs:comment obo:SO_0000289 "A defined feature that includes any type of VNTR or SSLP locus.") +AnnotationAssertion(rdfs:label obo:SO_0000289 "microsatellite") +SubClassOf(obo:SO_0000289 obo:GENO_0000481) + +# Class: obo:SO_0000337 (RNAi_reagent) + +AnnotationAssertion(rdfs:label obo:SO_0000337 "RNAi_reagent"@en) +SubClassOf(obo:SO_0000337 obo:GENO_0000533) + +# Class: obo:SO_0000340 (chromosome) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000340 "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.") +AnnotationAssertion(rdfs:comment obo:SO_0000340 "A complete chromosome sequence.") +AnnotationAssertion(rdfs:label obo:SO_0000340 "chromosome") +SubClassOf(obo:SO_0000340 obo:GENO_0000481) + +# Class: obo:SO_0000341 (chromosome band) + +AnnotationAssertion(obo:IAO_0000112 obo:SO_0000341 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\".") +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000341 "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.") +AnnotationAssertion(obo:IAO_0000119 obo:SO_0000341 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band +") +AnnotationAssertion(rdfs:comment obo:SO_0000341 "\"Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band.") +AnnotationAssertion(rdfs:label obo:SO_0000341 "chromosome band"@en) +SubClassOf(obo:SO_0000341 obo:SO_0000830) +SubClassOf(obo:SO_0000341 ObjectSomeValuesFrom(obo:BFO_0000050 obo:GENO_0000614)) +SubClassOf(obo:SO_0000341 ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000618)) + +# Class: obo:SO_0000577 (centromere) + +AnnotationAssertion(rdfs:label obo:SO_0000577 "centromere"@en) +SubClassOf(obo:SO_0000577 obo:SO_0000830) + +# Class: obo:SO_0000637 (obsolete_engineered_plasmid) + +AnnotationAssertion(obo:IAO_0000116 obo:SO_0000637 "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct.") +AnnotationAssertion(rdfs:label obo:SO_0000637 "obsolete_engineered_plasmid"@en) +SubClassOf(obo:SO_0000637 oboInOwl:ObsoleteClass) + +# Class: obo:SO_0000667 (insertion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000667 "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000667 "insertion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000667 "nucleotide insertion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000667 "nucleotide_insertion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0000667 obo:so.owl) +AnnotationAssertion(obo:IAO_alt_id obo:SO_0000667 "SO:1000034"^^xsd:string) +AnnotationAssertion(obo:IAO_id obo:SO_0000667 "SO:0000667"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0000667 "DBVAR"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0000667 "SOFA"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0000667 "insertion"^^xsd:string) +SubClassOf(obo:SO_0000667 obo:SO_0001059) + +# Class: obo:SO_0000694 (SNP) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000694 "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000694 "single nucleotide polymorphism"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0000694 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_0000694 "SO:0000694"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0000694 "SOFA"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0000694 "SNP"^^xsd:string) +SubClassOf(obo:SO_0000694 obo:SO_0001483) + +# Class: obo:SO_0000699 (junction) + +AnnotationAssertion(rdfs:comment obo:SO_0000699 "A junction is a boundary between regions. A boundary has an extent of zero.") +AnnotationAssertion(rdfs:label obo:SO_0000699 "junction"@en) +SubClassOf(obo:SO_0000699 obo:SO_0000110) + +# Class: obo:SO_0000704 (gene) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000704 "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.") +AnnotationAssertion(obo:IAO_0000116 obo:SO_0000704 "Regarding the distinction between a 'gene' and a 'gene allele': +Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment).") +AnnotationAssertion(rdfs:comment obo:SO_0000704 "A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion.") +AnnotationAssertion(rdfs:label obo:SO_0000704 "gene") +SubClassOf(obo:SO_0000704 obo:GENO_0000481) + +# Class: obo:SO_0000771 (QTL) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000771 "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.") +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000771 "quantitative trait locus") +AnnotationAssertion(rdfs:label obo:SO_0000771 "QTL") +SubClassOf(obo:SO_0000771 obo:GENO_0000481) + +# Class: obo:SO_0000783 (engineered) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000783 "An attribute to describe a region that was modified in vitro.") +AnnotationAssertion(rdfs:label obo:SO_0000783 "engineered") +SubClassOf(obo:SO_0000783 obo:GENO_0000788) + +# Class: obo:SO_0000804 (engineered_region) + +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000804 "construct") +AnnotationAssertion(rdfs:label obo:SO_0000804 "engineered_region"@en) +EquivalentClasses(obo:SO_0000804 ObjectIntersectionOf(obo:SO_0000110 ObjectSomeValuesFrom(obo:GENO_0000207 obo:SO_0000783))) + +# Class: obo:SO_0000830 (chromosome part) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000830 "An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'.") +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000830 "chromosomal feature") +AnnotationAssertion(obo:IAO_0000118 obo:SO_0000830 "gross chromosomal part") +AnnotationAssertion(rdfs:label obo:SO_0000830 "chromosome part") +EquivalentClasses(obo:SO_0000830 ObjectIntersectionOf(obo:GENO_0000481 ObjectSomeValuesFrom(obo:GENO_0000248 obo:SO_0000340))) + +# Class: obo:SO_0000902 (transgene) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0000902 "A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome).") +AnnotationAssertion(rdfs:comment obo:SO_0000902 "On the relationship between 'transgenic insertions', 'transgenes', and 'alleles' +Transgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete. + +In addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. + +For the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach.") +AnnotationAssertion(rdfs:comment obo:SO_0000902 "Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism). + +Note that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome.") +AnnotationAssertion(rdfs:label obo:SO_0000902 "transgene"@en) +SubClassOf(obo:SO_0000902 obo:SO_0000704) + +# Class: obo:SO_0001013 (MNP) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001013 "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001013 "multiple nucleotide polymorphism"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001013 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_0001013 "SO:0001013"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0001013 "MNP"^^xsd:string) +SubClassOf(obo:SO_0001013 obo:SO_1000002) + +# Class: obo:SO_0001019 (copy_number_variation) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001019 "A variation that increases or decreases the copy number of a given region."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001019 "CNP"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001019 "CNV"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001019 "copy number polymorphism"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001019 "copy number variation"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001019 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_0001019 "SO:0001019"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0001019 "SOFA"^^xsd:string) +AnnotationAssertion(obo:IAO_xref obo:SO_0001019 "http://en.wikipedia.org/wiki/Copy_number_variation"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0001019 "copy_number_variation"^^xsd:string) +SubClassOf(obo:SO_0001019 obo:SO_0001059) + +# Class: obo:SO_0001026 (genome) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001026 "A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny)") +AnnotationAssertion(obo:IAO_0000116 obo:SO_0001026 "Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence.") +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001026 "'genome sequence'") +AnnotationAssertion(rdfs:comment obo:SO_0001026 "A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'.") +AnnotationAssertion(rdfs:label obo:SO_0001026 "genome") +SubClassOf(obo:SO_0001026 obo:GENO_0000660) +SubClassOf(obo:SO_0001026 ObjectSomeValuesFrom(obo:RO_0002162 obo:OBI_0100026)) + +# Class: obo:SO_0001059 (sequence_alteration) + +AnnotationAssertion(obo:IAO_0000112 obo:SO_0001059 "A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': + +1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871. + +2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112. + +3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112.") +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001059 "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001059 "sequence variation"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001059 obo:so.owl) +AnnotationAssertion(obo:IAO_alt_id obo:SO_0001059 "SO:1000004"^^xsd:string) +AnnotationAssertion(obo:IAO_alt_id obo:SO_0001059 "SO:1000007"^^xsd:string) +AnnotationAssertion(obo:IAO_id obo:SO_0001059 "SO:0001059"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0001059 "SOFA"^^xsd:string) +AnnotationAssertion(rdfs:comment obo:SO_0001059 "1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. + +Alleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part. + +2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. + +For a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference. + +3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism.") +AnnotationAssertion(rdfs:label obo:SO_0001059 "sequence_alteration"^^xsd:string) +EquivalentClasses(obo:SO_0001059 ObjectIntersectionOf(obo:GENO_0000512 ObjectSomeValuesFrom(obo:GENO_0000784 obo:GENO_0000481))) + +# Class: obo:SO_0001218 (transgenic_insertion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001218 "An insertion that derives from another organism, via the use of recombinant DNA technology."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001218 "transgenic insertion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001218 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_0001218 "SO:0001218"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0001218 "transgenic_insertion"^^xsd:string) +SubClassOf(obo:SO_0001218 obo:SO_0000667) +SubClassOf(obo:SO_0001218 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GENO_0000093)) + +# Class: obo:SO_0001410 (obsolete_experimental_feature) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001410 "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.") +AnnotationAssertion(obo:IAO_0000231 obo:SO_0001410 "not currently needed to support modeling use cases. can re-introduce if becomes necessary.") +AnnotationAssertion(rdfs:label obo:SO_0001410 "obsolete_experimental_feature"@en) +SubClassOf(obo:SO_0001410 oboInOwl:ObsoleteClass) + +# Class: obo:SO_0001477 (gene_trap_construct) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001477 "A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker.") +AnnotationAssertion(rdfs:label obo:SO_0001477 "gene_trap_construct"@en) +SubClassOf(obo:SO_0001477 obo:GENO_0000856) + +# Class: obo:SO_0001478 (promoter_trap_construct) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001478 "A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic.") +AnnotationAssertion(rdfs:label obo:SO_0001478 "promoter_trap_construct"@en) +SubClassOf(obo:SO_0001478 obo:GENO_0000856) + +# Class: obo:SO_0001479 (enhancer_trap_construct) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001479 "A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic.") +AnnotationAssertion(rdfs:label obo:SO_0001479 "enhancer_trap_construct"@en) +SubClassOf(obo:SO_0001479 obo:GENO_0000856) + +# Class: obo:SO_0001483 (SNV) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001483 "SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001483 "single nucleotide variant"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001483 obo:so.owl) +AnnotationAssertion(obo:IAO_created_by obo:SO_0001483 "kareneilbeck"^^xsd:string) +AnnotationAssertion(obo:IAO_creation_date obo:SO_0001483 "Thu Oct 08 11:37:49 PDT 2009"^^xsd:string) +AnnotationAssertion(obo:IAO_id obo:SO_0001483 "SO:0001483"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0001483 "SOFA"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0001483 "SNV"^^xsd:string) +SubClassOf(obo:SO_0001483 obo:SO_1000002) + +# Class: obo:SO_0001500 (heritable_phenotypic_marker) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001500 "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.") +AnnotationAssertion(rdfs:label obo:SO_0001500 "heritable_phenotypic_marker"@en) +SubClassOf(obo:SO_0001500 obo:GENO_0000481) + +# Class: obo:SO_0001505 (reference genome sequence) + +AnnotationAssertion(obo:IAO_0000112 obo:SO_0001505 "'GRCh37.p10' (a human reference genome build)") +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001505 "A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced.") +AnnotationAssertion(rdfs:label obo:SO_0001505 "reference genome sequence") +SubClassOf(obo:SO_0001505 obo:GENO_0000017) +SubClassOf(obo:SO_0001505 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000152)) + +# Class: obo:SO_0001742 (copy_number_gain) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001742 "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001742 "copy number gain"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001742 "gain"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001742 obo:so.owl) +AnnotationAssertion(obo:IAO_created_by obo:SO_0001742 "kareneilbeck"^^xsd:string) +AnnotationAssertion(obo:IAO_creation_date obo:SO_0001742 "Mon Feb 28 01:54:09 PST 2011"^^xsd:string) +AnnotationAssertion(obo:IAO_id obo:SO_0001742 "SO:0001742"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0001742 "DBVAR"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0001742 "copy_number_gain"^^xsd:string) +SubClassOf(obo:SO_0001742 obo:SO_0001019) + +# Class: obo:SO_0001743 (copy_number_loss) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001743 "A sequence alteration whereby the copy number of a given region is less than the reference sequence."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001743 "copy number loss"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001743 "loss"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001743 obo:so.owl) +AnnotationAssertion(obo:IAO_created_by obo:SO_0001743 "kareneilbeck"^^xsd:string) +AnnotationAssertion(obo:IAO_creation_date obo:SO_0001743 "Mon Feb 28 01:55:02 PST 2011"^^xsd:string) +AnnotationAssertion(obo:IAO_id obo:SO_0001743 "SO:0001743"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0001743 "DBVAR"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0001743 "copy_number_loss"^^xsd:string) +SubClassOf(obo:SO_0001743 obo:SO_0001019) + +# Class: obo:SO_0001744 (UPD) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001744 "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001744 "UPD"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001744 "uniparental disomy"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001744 obo:so.owl) +AnnotationAssertion(obo:IAO_created_by obo:SO_0001744 "kareneilbeck"^^xsd:string) +AnnotationAssertion(obo:IAO_creation_date obo:SO_0001744 "Mon Feb 28 02:01:05 PST 2011"^^xsd:string) +AnnotationAssertion(obo:IAO_id obo:SO_0001744 "SO:0001744"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0001744 "DBVAR"^^xsd:string) +AnnotationAssertion(obo:IAO_xref obo:SO_0001744 "http:http\\://en.wikipedia.org/wiki/Uniparental_disomy"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0001744 "UPD"^^xsd:string) +SubClassOf(obo:SO_0001744 obo:SO_0001059) + +# Class: obo:SO_0001745 (maternal_uniparental_disomy) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001745 "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001745 "maternal uniparental disomy"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001745 obo:so.owl) +AnnotationAssertion(obo:IAO_created_by obo:SO_0001745 "kareneilbeck"^^xsd:string) +AnnotationAssertion(obo:IAO_creation_date obo:SO_0001745 "Mon Feb 28 02:03:01 PST 2011"^^xsd:string) +AnnotationAssertion(obo:IAO_id obo:SO_0001745 "SO:0001745"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0001745 "maternal_uniparental_disomy"^^xsd:string) +SubClassOf(obo:SO_0001745 obo:SO_0001744) + +# Class: obo:SO_0001746 (paternal_uniparental_disomy) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001746 "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001746 "paternal uniparental disomy"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001746 obo:so.owl) +AnnotationAssertion(obo:IAO_created_by obo:SO_0001746 "kareneilbeck"^^xsd:string) +AnnotationAssertion(obo:IAO_creation_date obo:SO_0001746 "Mon Feb 28 02:03:30 PST 2011"^^xsd:string) +AnnotationAssertion(obo:IAO_id obo:SO_0001746 "SO:0001746"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0001746 "paternal_uniparental_disomy"^^xsd:string) +SubClassOf(obo:SO_0001746 obo:SO_0001744) + +# Class: obo:SO_0001784 (complex_structural_alteration) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_0001784 "A structural sequence alteration where there are multiple equally plausible explanations for the change."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_0001784 "complex"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001784 obo:so.owl) +AnnotationAssertion(obo:IAO_created_by obo:SO_0001784 "kareneilbeck"^^xsd:string) +AnnotationAssertion(obo:IAO_creation_date obo:SO_0001784 "Wed Mar 23 03:21:19 PDT 2011"^^xsd:string) +AnnotationAssertion(obo:IAO_id obo:SO_0001784 "SO:0001784"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0001784 "DBVAR"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0001784 "complex_structural_alteration"^^xsd:string) +SubClassOf(obo:SO_0001784 obo:SO_0001785) + +# Class: obo:SO_0001785 (structural_alteration) + +AnnotationAssertion(obo:IAO_0000412 obo:SO_0001785 obo:so.owl) +AnnotationAssertion(obo:IAO_created_by obo:SO_0001785 "kareneilbeck"^^xsd:string) +AnnotationAssertion(obo:IAO_creation_date obo:SO_0001785 "Fri Mar 25 02:27:41 PDT 2011"^^xsd:string) +AnnotationAssertion(obo:IAO_id obo:SO_0001785 "SO:0001785"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_0001785 "DBVAR"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_0001785 "structural_alteration"^^xsd:string) +SubClassOf(obo:SO_0001785 obo:SO_0001059) + +# Class: obo:SO_0005836 (regulatory_region) + +AnnotationAssertion(obo:IAO_0000116 obo:SO_0005836 "Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term.") +AnnotationAssertion(obo:IAO_0000118 obo:SO_0005836 "regulatory element") +AnnotationAssertion(obo:IAO_0000118 obo:SO_0005836 "regulatory gene region") +AnnotationAssertion(rdfs:label obo:SO_0005836 "regulatory_region") +SubClassOf(obo:SO_0005836 obo:GENO_0000666) + +# Class: obo:SO_1000002 (substitution) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000002 "Any change in genomic DNA caused by a single event."^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000002 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000002 "SO:1000002"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_1000002 "SOFA"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000002 "substitution"^^xsd:string) +SubClassOf(obo:SO_1000002 obo:SO_0001059) + +# Class: obo:SO_1000005 (complex_substitution) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000005 "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\\"complex\\\" should be used. Usually there are multiple equally plausible explanations for the change."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000005 "complex substitution"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000005 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000005 "SO:1000005"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_1000005 "SOFA"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000005 "complex_substitution"^^xsd:string) +SubClassOf(obo:SO_1000005 obo:SO_1000002) + +# Class: obo:SO_1000008 (point_mutation) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000008 "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000008 "point mutation"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000008 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000008 "SO:1000008"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_1000008 "SOFA"^^xsd:string) +AnnotationAssertion(obo:IAO_xref obo:SO_1000008 "http://en.wikipedia.org/wiki/Point_mutation"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000008 "point_mutation"^^xsd:string) +SubClassOf(obo:SO_1000008 obo:SO_0001483) + +# Class: obo:SO_1000009 (transition) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000009 "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide."^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000009 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000009 "SO:1000009"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000009 "transition"^^xsd:string) +SubClassOf(obo:SO_1000009 obo:SO_0001483) + +# Class: obo:SO_1000010 (pyrimidine_transition) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000010 "A substitution of a pyrimidine, C or T, for another pyrimidine."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000010 "pyrimidine transition"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000010 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000010 "SO:1000010"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000010 "pyrimidine_transition"^^xsd:string) +SubClassOf(obo:SO_1000010 obo:SO_1000009) + +# Class: obo:SO_1000011 (C_to_T_transition) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000011 "A transition of a cytidine to a thymine."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000011 "C to T transition"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000011 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000011 "SO:1000011"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000011 "C_to_T_transition"^^xsd:string) +SubClassOf(obo:SO_1000011 obo:SO_1000010) + +# Class: obo:SO_1000012 (C_to_T_transition_at_pCpG_site) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000012 "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000012 "C to T transition at pCpG site"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000012 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000012 "SO:1000012"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000012 "C_to_T_transition_at_pCpG_site"^^xsd:string) +SubClassOf(obo:SO_1000012 obo:SO_1000011) + +# Class: obo:SO_1000013 (T_to_C_transition) + +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000013 "T to C transition"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000013 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000013 "SO:1000013"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000013 "T_to_C_transition"^^xsd:string) +SubClassOf(obo:SO_1000013 obo:SO_1000010) + +# Class: obo:SO_1000014 (purine_transition) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000014 "A substitution of a purine, A or G, for another purine."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000014 "purine transition"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000014 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000014 "SO:1000014"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000014 "purine_transition"^^xsd:string) +SubClassOf(obo:SO_1000014 obo:SO_1000009) + +# Class: obo:SO_1000015 (A_to_G_transition) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000015 "A transition of an adenine to a guanine."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000015 "A to G transition"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000015 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000015 "SO:1000015"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000015 "A_to_G_transition"^^xsd:string) +SubClassOf(obo:SO_1000015 obo:SO_1000014) + +# Class: obo:SO_1000016 (G_to_A_transition) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000016 "A transition of a guanine to an adenine."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000016 "G to A transition"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000016 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000016 "SO:1000016"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000016 "G_to_A_transition"^^xsd:string) +SubClassOf(obo:SO_1000016 obo:SO_1000014) + +# Class: obo:SO_1000017 (transversion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000017 "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa."^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000017 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000017 "SO:1000017"^^xsd:string) +AnnotationAssertion(obo:IAO_xref obo:SO_1000017 "http://en.wikipedia.org/wiki/Transversion"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000017 "transversion"^^xsd:string) +SubClassOf(obo:SO_1000017 obo:SO_0001483) + +# Class: obo:SO_1000018 (pyrimidine_to_purine_transversion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000018 "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000018 "pyrimidine to purine transversion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000018 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000018 "SO:1000018"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000018 "pyrimidine_to_purine_transversion"^^xsd:string) +SubClassOf(obo:SO_1000018 obo:SO_1000017) + +# Class: obo:SO_1000019 (C_to_A_transversion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000019 "A transversion from cytidine to adenine."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000019 "C to A transversion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000019 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000019 "SO:1000019"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000019 "C_to_A_transversion"^^xsd:string) +SubClassOf(obo:SO_1000019 obo:SO_1000018) + +# Class: obo:SO_1000020 (C_to_G_transversion) + +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000020 "C to G transversion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000020 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000020 "SO:1000020"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000020 "C_to_G_transversion"^^xsd:string) +SubClassOf(obo:SO_1000020 obo:SO_1000018) + +# Class: obo:SO_1000021 (T_to_A_transversion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000021 "A transversion from T to A."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000021 "T to A transversion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000021 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000021 "SO:1000021"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000021 "T_to_A_transversion"^^xsd:string) +SubClassOf(obo:SO_1000021 obo:SO_1000018) + +# Class: obo:SO_1000022 (T_to_G_transversion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000022 "A transversion from T to G."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000022 "T to G transversion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000022 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000022 "SO:1000022"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000022 "T_to_G_transversion"^^xsd:string) +SubClassOf(obo:SO_1000022 obo:SO_1000018) + +# Class: obo:SO_1000023 (purine_to_pyrimidine_transversion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000023 "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000023 "purine to pyrimidine transversion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000023 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000023 "SO:1000023"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000023 "purine_to_pyrimidine_transversion"^^xsd:string) +SubClassOf(obo:SO_1000023 obo:SO_1000017) + +# Class: obo:SO_1000024 (A_to_C_transversion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000024 "A transversion from adenine to cytidine."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000024 "A to C transversion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000024 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000024 "SO:1000024"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000024 "A_to_C_transversion"^^xsd:string) +SubClassOf(obo:SO_1000024 obo:SO_1000023) + +# Class: obo:SO_1000025 (A_to_T_transversion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000025 "A transversion from adenine to thymine."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000025 "A to T transversion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000025 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000025 "SO:1000025"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000025 "A_to_T_transversion"^^xsd:string) +SubClassOf(obo:SO_1000025 obo:SO_1000023) + +# Class: obo:SO_1000026 (G_to_C_transversion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000026 "A transversion from guanine to cytidine."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000026 "G to C transversion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000026 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000026 "SO:1000026"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000026 "G_to_C_transversion"^^xsd:string) +SubClassOf(obo:SO_1000026 obo:SO_1000023) + +# Class: obo:SO_1000027 (G_to_T_transversion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000027 "A transversion from guanine to thymine."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000027 "G to T transversion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000027 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000027 "SO:1000027"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000027 "G_to_T_transversion"^^xsd:string) +SubClassOf(obo:SO_1000027 obo:SO_1000023) + +# Class: obo:SO_1000032 (indel) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000032 "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases."^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000032 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000032 "SO:1000032"^^xsd:string) +AnnotationAssertion(obo:IAO_xref obo:SO_1000032 "http://en.wikipedia.org/wiki/Indel"^^xsd:string) +AnnotationAssertion(rdfs:comment obo:SO_1000032 "Indels can have a different number of bases than the corresponding reference sequence."^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000032 "indel"^^xsd:string) +SubClassOf(obo:SO_1000032 obo:SO_0001059) + +# Class: obo:SO_1000035 (duplication) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000035 "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000035 "nucleotide duplication"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000035 "nucleotide_duplication"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000035 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000035 "SO:1000035"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000035 "duplication"^^xsd:string) +SubClassOf(obo:SO_1000035 obo:SO_0000667) + +# Class: obo:SO_1000036 (inversion) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000036 "A continuous nucleotide sequence is inverted in the same position."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000036 "inversion"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000036 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000036 "SO:1000036"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_1000036 "DBVAR"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_1000036 "SOFA"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000036 "inversion"^^xsd:string) +SubClassOf(obo:SO_1000036 obo:SO_0001059) + +# Class: obo:SO_1000039 (direct_tandem_duplication) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000039 "A tandem duplication where the individual regions are in the same orientation."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000039 "direct tandem duplication"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000039 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000039 "SO:1000039"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000039 "direct_tandem_duplication"^^xsd:string) +SubClassOf(obo:SO_1000039 obo:SO_1000173) + +# Class: obo:SO_1000040 (inverted_tandem_duplication) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000040 "A tandem duplication where the individual regions are not in the same orientation."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000040 "inverted tandem duplication"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000040 "mirror duplication"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000040 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000040 "SO:1000040"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000040 "inverted_tandem_duplication"^^xsd:string) +SubClassOf(obo:SO_1000040 obo:SO_1000173) + +# Class: obo:SO_1000173 (tandem_duplication) + +AnnotationAssertion(obo:IAO_0000115 obo:SO_1000173 "A duplication consisting of 2 identical adjacent regions."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000173 "erverted"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:SO_1000173 "tandem duplication"^^xsd:string) +AnnotationAssertion(obo:IAO_0000412 obo:SO_1000173 obo:so.owl) +AnnotationAssertion(obo:IAO_id obo:SO_1000173 "SO:1000173"^^xsd:string) +AnnotationAssertion(obo:IAO_subset obo:SO_1000173 "DBVAR"^^xsd:string) +AnnotationAssertion(rdfs:label obo:SO_1000173 "tandem_duplication"^^xsd:string) +SubClassOf(obo:SO_1000173 obo:SO_1000035) + +# Class: obo:UBERON_0000105 (life cycle stage) + +AnnotationAssertion(obo:IAO_0000116 obo:UBERON_0000105 "Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms)") +AnnotationAssertion(rdfs:label obo:UBERON_0000105 "life cycle stage") +SubClassOf(obo:UBERON_0000105 obo:GENO_0000351) + +# Class: obo:UBERON_0001062 (anatomical entity) + +AnnotationAssertion(obo:IAO_0000116 obo:UBERON_0001062 "Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies.") +AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_0001062 "http://purl.obolibrary.org/obo/CARO_0000000") +AnnotationAssertion(rdfs:label obo:UBERON_0001062 "anatomical entity"^^xsd:string) +SubClassOf(obo:UBERON_0001062 obo:BFO_0000040) +SubClassOf(obo:UBERON_0001062 ObjectSomeValuesFrom(obo:RO_0001000 obo:OBI_0100026)) + +# Class: obo:UPHENO_0001001 (Phenotype) + +AnnotationAssertion(obo:IAO_0000116 obo:UPHENO_0001001 "Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework.") +AnnotationAssertion(rdfs:comment obo:UPHENO_0001001 "1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition) + +2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment") +AnnotationAssertion(rdfs:label obo:UPHENO_0001001 "Phenotype") +SubClassOf(obo:UPHENO_0001001 obo:BFO_0000020) + +# Class: obo:WBPhenotype_0000886 (worm phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:WBPhenotype_0000886 "Animals exhibit variations compared to a given control.") +AnnotationAssertion(obo:IAO_0000116 obo:WBPhenotype_0000886 "'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes.") +AnnotationAssertion(obo:IAO_0000118 obo:WBPhenotype_0000886 "Variant") +AnnotationAssertion(obo:IAO_0000118 obo:WBPhenotype_0000886 "c. elegans phenotype") +AnnotationAssertion(rdfs:label obo:WBPhenotype_0000886 "worm phenotype"@en) +SubClassOf(obo:WBPhenotype_0000886 obo:UPHENO_0001001) + +# Class: obo:ZP_0000199 (abnormal(ly) malformed endocardium cell) + +AnnotationAssertion(rdfs:label obo:ZP_0000199 "abnormal(ly) malformed endocardium cell"@en) +SubClassOf(obo:ZP_0000199 obo:GENO_0000575) + +# Class: obo:ZP_0000386 (abnormal(ly) absent dorso-rostral cluster) + +AnnotationAssertion(rdfs:label obo:ZP_0000386 "abnormal(ly) absent dorso-rostral cluster"@en) +SubClassOf(obo:ZP_0000386 obo:GENO_0000575) + +# Class: obo:ZP_0000755 (abnormal(ly) disrupted diencephalon development) + +AnnotationAssertion(rdfs:label obo:ZP_0000755 "abnormal(ly) disrupted diencephalon development"@en) +SubClassOf(obo:ZP_0000755 obo:GENO_0000575) + +# Class: obo:ZP_0005531 (abnormal(ly) disrupted neutrophil aggregation) + +AnnotationAssertion(rdfs:label obo:ZP_0005531 "abnormal(ly) disrupted neutrophil aggregation"@en) +SubClassOf(obo:ZP_0005531 obo:GENO_0000575) + +# Class: obo:ZP_0005692 (abnormal(ly) absent adaxial cell) + +AnnotationAssertion(rdfs:label obo:ZP_0005692 "abnormal(ly) absent adaxial cell") +SubClassOf(obo:ZP_0005692 obo:GENO_0000575) + +# Class: (association) + +AnnotationAssertion(rdfs:label "association"@en) +SubClassOf( obo:IAO_0000030) + +# Class: (mus musculus shh gene) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000514) +AnnotationAssertion(rdfs:comment "Equivalent to: http://www.informatics.jax.org/marker/MGI:98297") +AnnotationAssertion(rdfs:label "mus musculus shh gene") +SubClassOf( obo:GENO_0000057) + +# Class: (danio rerio shha gene) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000514) +AnnotationAssertion(oboInOwl:hasDbXref "http://zfin.org/ZDB-GENE-980526-166") +AnnotationAssertion(rdfs:label "danio rerio shha gene") +SubClassOf( obo:GENO_0000047) + +# Class: (danio rerio cdkn1ca gene) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000514) +AnnotationAssertion(oboInOwl:hasDbXref "http://zfin.org/ZDB-GENE-040123-1") +AnnotationAssertion(rdfs:label "danio rerio cdkn1ca gene") +SubClassOf( obo:GENO_0000047) + +# Class: (homo sapiens SHH gene) + +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000514) +AnnotationAssertion(rdfs:comment "Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690 + +Codes for: http://www.uniprot.org/uniprot/Q15465") +AnnotationAssertion(rdfs:label "homo sapiens SHH gene"@en) +SubClassOf( obo:GENO_0000054) + + +############################ +# Named Individuals +############################ + +# Individual: obo:GENO_0000484 (exploratory term) + +AnnotationAssertion(rdfs:label obo:GENO_0000484 "exploratory term"@en) +ClassAssertion(obo:IAO_0000102 obo:GENO_0000484) + +# Individual: obo:GENO_0000514 (exemplar term) + +AnnotationAssertion(rdfs:label obo:GENO_0000514 "exemplar term"@en) +ClassAssertion(obo:IAO_0000102 obo:GENO_0000514) + + +SubClassOf(Annotation(rdfs:comment "Initially created such that integrated transgene infers as child of sequence_alteration.") ObjectSomeValuesFrom(obo:BFO_0000050 obo:SO_0001059) obo:SO_0001059) +SubObjectPropertyOf(ObjectPropertyChain(obo:BFO_0000051 obo:GENO_0000639) obo:GENO_0000639) +SubObjectPropertyOf(ObjectPropertyChain(obo:GENO_0000382 obo:GENO_0000418) obo:GENO_0000418) +SubObjectPropertyOf(Annotation(rdfs:comment "This is a case of inter-gneotype phenotype propagation, requiring propagation down oen genotype and then up another. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to have this chain. + +This property chain propagates a phenotype asserted on a sex-qualified intrinsic genotype, down to its sex-agnostic genotype part, and then up to a parent effective genotype that has it as a variant part. I think this is OK in all cases, so we can implement this as the one case where we can have inter-genotype pheno propagation. But as noted, there will likely be no data that actually meets criteria to use this chain, so we can probably leave it out.") ObjectPropertyChain(obo:GENO_0000382 obo:GENO_0000661 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype.") ObjectPropertyChain(obo:GENO_0000382 obo:GENO_0000743) obo:GENO_0000740) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype.") ObjectPropertyChain(obo:GENO_0000382 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(ObjectPropertyChain(obo:GENO_0000383 obo:GENO_0000408) obo:GENO_0000742) +SubObjectPropertyOf(ObjectPropertyChain(obo:GENO_0000383 obo:GENO_0000418) obo:GENO_0000418) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, to the coompnent variant parts of this sex-agnostic genotype.") ObjectPropertyChain(obo:GENO_0000383 obo:GENO_0000661 obo:GENO_0000383 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred phenotype associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype.") ObjectPropertyChain(obo:GENO_0000383 obo:GENO_0000661 obo:GENO_0000743) obo:GENO_0000740) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to move past the sex-agnostic genotype and down to its parts. + +The following shorter chain would also suffice here: +is_variant_part_of o inferred_to_cause_condition") ObjectPropertyChain(obo:GENO_0000383 obo:GENO_0000661 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration.") ObjectPropertyChain(obo:GENO_0000383 obo:GENO_0000743) obo:GENO_0000740) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration.") ObjectPropertyChain(obo:GENO_0000383 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, through the coompnent variant parts of this sex-agnostic genotype, and to the affected gene.") ObjectPropertyChain(obo:GENO_0000413 obo:GENO_0000383 obo:GENO_0000661 obo:GENO_0000383 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to propagate to genes. + +The shorter chain below would also suffice for this propagation: +has_allele o inferred_to_cause_condition") ObjectPropertyChain(obo:GENO_0000413 obo:GENO_0000383 obo:GENO_0000661 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred phenotype associations from an intrinsic genotype component (e.g. a (sequence-)variant locus instance) to a gene class.") ObjectPropertyChain(obo:GENO_0000413 obo:GENO_0000383 obo:GENO_0000743) obo:GENO_0000740) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred phenotype associations from a (sequence-)variant locus instance to a gene class (to support cases where the phenotype association is made at the level of the variant gene locus).") ObjectPropertyChain(obo:GENO_0000413 obo:GENO_0000743) obo:GENO_0000740) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred condition associations from an sequence alteration through the variant locus to a gene class. (separate chains are needed to propagate from the variant locus to the gene class, and another to propagate from a genotype, GVC, or VSLC to the gene class). + + +NOTE that i dont need this property chain if I have a property chain to infer a has_affected_locus link from a sequence alteration to a gene when the link is asserted from the variant locus to the gene: -AnnotationAssertion(rdfs:label "root node"@en) +is_variant_part_of o has_affected_locus --> has_affected_locus") ObjectPropertyChain(obo:GENO_0000445 obo:GENO_0000382 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(Annotation(rdfs:comment "Obsolete comment: Property chain to propagate inferred condition associations from an intrinsic genotype, GC, or VLSC to a gene class. (a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class). +The following, shorter chain, would also suffice here: +has_allele o inferred_to_cause_condition -> inferred_to_cause_condition") Annotation(rdfs:comment "Property chain to propagate inferred condition associations from an intrinsic genotype, GVC, or VLSC to an affected gene class, or from an extrinsic gneotype or component to an affected gene class. -) +The following, shorter chain, would also suffice here: +has_affected_locus o inferred_to_cause_condition -> inferred_to_cause_condition +Note that a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class in cases where the link to gene is through the variant locus rather than the seq alteration).") ObjectPropertyChain(obo:GENO_0000445 obo:GENO_0000383 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred condition associations from a variant locus instance to a gene class (to support cases where the phenotype association is made directly at the level of the variant locus/allele).") ObjectPropertyChain(obo:GENO_0000445 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred phenotype associations from an extrinnsic genotype component (e.g. a expression-variant gene instance) to a gene class.") ObjectPropertyChain(obo:GENO_0000449 obo:GENO_0000383 obo:GENO_0000743) obo:GENO_0000740) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred phenotype associations from an expression-variant gene instance to a gene class (to support cases where the phenotype association is made at the level of the expression-variant gene).") ObjectPropertyChain(obo:GENO_0000449 obo:GENO_0000743) obo:GENO_0000740) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype to a sex-agnostic intrinsic genotype.") ObjectPropertyChain(obo:GENO_0000661 obo:GENO_0000383 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred phenotype associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)") ObjectPropertyChain(obo:GENO_0000661 obo:GENO_0000743) obo:GENO_0000740) +SubObjectPropertyOf(Annotation(rdfs:comment "Property chain to propagate inferred condition associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)") ObjectPropertyChain(obo:GENO_0000661 obo:RO_0003303) obo:GENO_0000791) +SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0000053 obo:RO_0000059) obo:GENO_0000211) +) \ No newline at end of file From 06acbb50d2f737ed0baf0ffcc87c37552315f44c Mon Sep 17 00:00:00 2001 From: matentzn Date: Mon, 9 Sep 2019 17:24:37 +0100 Subject: [PATCH 05/11] First release (no OBO in OWL) --- geno-base.json | 9881 +++++++++++++ geno-base.obo | 3922 ++++++ geno-base.owl | 8289 +++++++++++ geno-full.json | 11682 ++++++++++++++++ geno-full.obo | 4218 ++++++ geno-full.owl | 9511 +++++++++++++ geno.json | 11682 ++++++++++++++++ geno.obo | 4218 ++++++ geno.owl | 9511 +++++++++++++ imports/iao_import.json | 3550 +++++ imports/iao_import.obo | 940 ++ imports/iao_import.owl | 2638 ++++ imports/ro_import.json | 4812 +++++++ imports/ro_import.obo | 1804 +++ imports/ro_import.owl | 4539 ++++++ reports/geno-edit.owl-obo-report.tsv | 330 + src/ontology/catalog-v001.xml | 4 +- src/ontology/geno-edit.owl | 1 - src/ontology/geno.Makefile | 2 + src/ontology/imports/oboInOwl.owl | 39 - src/ontology/json.json | 26 + src/ontology/oboInOwl.owl | 700 + .../reports/geno-edit.owl-obo-report.tsv | 330 + 23 files changed, 92586 insertions(+), 43 deletions(-) create mode 100644 geno-base.json create mode 100644 geno-base.obo create mode 100644 geno-base.owl create mode 100644 geno-full.json create mode 100644 geno-full.obo create mode 100644 geno-full.owl create mode 100644 geno.json create mode 100644 geno.obo create mode 100644 geno.owl create mode 100644 imports/iao_import.json create mode 100644 imports/iao_import.obo create mode 100644 imports/iao_import.owl create mode 100644 imports/ro_import.json create mode 100644 imports/ro_import.obo create mode 100644 imports/ro_import.owl create mode 100644 reports/geno-edit.owl-obo-report.tsv create mode 100644 src/ontology/json.json create mode 100644 src/ontology/oboInOwl.owl create mode 100644 src/ontology/reports/geno-edit.owl-obo-report.tsv diff --git a/geno-base.json b/geno-base.json new file mode 100644 index 0000000..1fe9c25 --- /dev/null +++ b/geno-base.json @@ -0,0 +1,9881 @@ +{ + "graphs" : [ { + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/SO_0000165", + "type" : "CLASS", + "lbl" : "enhancer" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000167", + "meta" : { + "definition" : { + "val" : "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "promoter" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001013", + "meta" : { + "definition" : { + "val" : "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multiple nucleotide polymorphism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001013" + } ] + }, + "type" : "CLASS", + "lbl" : "MNP" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000281", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25.\n\nIncludes things like loxP sites, inducible promoters, ires elements, etc." + } ] + }, + "type" : "CLASS", + "lbl" : "engineered_foreign_gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000060", + "meta" : { + "definition" : { + "val" : "A version/allele of a gene that serves as a standard against which variant genes are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development.\nhttp://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690\n\nNote that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference gene" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reference gene allele" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10090", + "type" : "CLASS", + "lbl" : "Mus musculus" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000057", + "meta" : { + "definition" : { + "val" : "A gene that originates from the genome of a mus musculus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "mus musculus gene" + }, { + "id" : "http://purl.obolibrary.org/obo/ERO_0000007", + "meta" : { + "definition" : { + "val" : "A technique is a planned process used to accomplish a specific activity or task.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "technique" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000159", + "meta" : { + "definition" : { + "val" : "The point at which one or more contiguous nucleotides were excised.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide_deletion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Nucleotide_deletion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000033" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000159" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide deletion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "deleted_sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "deletion" + }, { + "id" : "http://purl.obolibrary.org/obo/PCO_0000020", + "meta" : { + "definition" : { + "val" : "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "family" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000034", + "meta" : { + "definition" : { + "val" : "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "morpholino_oligo" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001483", + "meta" : { + "definition" : { + "val" : "SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single nucleotide variant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Thu Oct 08 11:37:49 PDT 2009" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001483" + } ] + }, + "type" : "CLASS", + "lbl" : "SNV" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000173", + "type" : "CLASS", + "lbl" : "promoter trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000172", + "type" : "CLASS", + "lbl" : "gene trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000175", + "type" : "CLASS", + "lbl" : "random transgene insertion technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000054", + "meta" : { + "definition" : { + "val" : "A gene that originates from the genome of a homo sapiens.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "homo sapiens gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000174", + "type" : "CLASS", + "lbl" : "targeted knock-in technique" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "color value" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_color brightness" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000435", + "meta" : { + "definition" : { + "val" : "An assay which generates data about a genotype from a specimen of genomic DNA. 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The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion.\n\nAn 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome." + } ] + }, + "type" : "CLASS", + "lbl" : "integrated transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_000244", + "meta" : { + "definition" : { + "val" : "Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "molecularly controls" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "meta" : { + "definition" : { + "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + } ] + }, + "type" : "PROPERTY", + "lbl" : "concretizes" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has participant" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "type" : "PROPERTY", + "lbl" : "input of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "inheres_in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "type" : "PROPERTY", + "lbl" : "output of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has input" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "type" : "PROPERTY", + "lbl" : "obsolete_formed as result of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has output" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "participates in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "type" : "PROPERTY", + "lbl" : "is member of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "meta" : { + "definition" : { + "val" : "has member is a mereological relation between a collection and an item.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes\n\nExample 2: a collection of information entities such as a genotype being comprised of a background component and a variant component" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has member" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "bearer of" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000105", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms)" + } ] + }, + "type" : "CLASS", + "lbl" : "life cycle stage" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "type" : "PROPERTY", + "lbl" : "temporally related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003307", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is preventative for condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003306", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to penetrance of condition" + } ] + }, + "type" : "PROPERTY", + "lbl" : "contributes to frequency of condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003308", + "meta" : { + "definition" : { + "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "correlated with condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003303", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "causes condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003302", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions." + } ] + }, + "type" : "PROPERTY", + "lbl" : "causes or contributes to condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to expressivity of condition" + } ] + }, + "type" : "PROPERTY", + "lbl" : "contributes to severity of condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003304", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "contributes to condition" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_8090", + "type" : "CLASS", + "lbl" : "Oryzias latipes" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001059", + "meta" : { + "definition" : { + "val" : "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. \n\nAlleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part.\n\n2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. \n\nFor a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference.\n\n3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001059" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': \n\n1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871.\n\n2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112.\n\n3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000007" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence variation" + } ] + }, + "type" : "CLASS", + "lbl" : "sequence_alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "type" : "PROPERTY", + "lbl" : "derives from" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "meta" : { + "definition" : { + "val" : "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Brush" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is model of" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0005531", + "type" : "CLASS", + "lbl" : "abnormal(ly) disrupted neutrophil aggregation" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "type" : "PROPERTY", + "lbl" : "phenotype of" + }, { + "id" : "http://biohackathon.org/resource/faldo#end", + "type" : "PROPERTY", + "lbl" : "end" + }, { + "id" : "http://www.ncbi.nlm.nih.gov/gene/20423", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Equivalent to: http://www.informatics.jax.org/marker/MGI:98297" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000514" + } ] + }, + "type" : "CLASS", + "lbl" : "mus musculus shh gene" + }, { + "id" : "http://www.ncbi.nlm.nih.gov/gene/30269", + "meta" : { + "xrefs" : [ { + "val" : "http://zfin.org/ZDB-GENE-980526-166" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000514" + } ] + }, + "type" : "CLASS", + "lbl" : "danio rerio shha gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000919", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000918", + "meta" : { + "definition" : { + "val" : "An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene." + } ] + }, + "type" : "CLASS", + "lbl" : "organellar plasmy" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000915", + "meta" : { + "definition" : { + "val" : "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_haplotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000914", + "meta" : { + "definition" : { + "val" : "A genome whose sequence is identical to that of a genome sequence considered to be the reference.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "reference genome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000917", + "meta" : { + "definition" : { + "val" : "Describes the number of members in some set.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_count" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_member_count" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000136", + "meta" : { + "definition" : { + "val" : "is_about is a (currently) primitive relation that relates an information artifact to an entity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is about" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000916", + "meta" : { + "definition" : { + "val" : "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.\n\nThe boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.\n\n-----------------------\n\n* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_haplotype block" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000911", + "type" : "CLASS", + "lbl" : "selectable marker role" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000910", + "type" : "CLASS", + "lbl" : "reporter role" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000912", + "type" : "CLASS", + "lbl" : "selectable marker region" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000293", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_specified_input" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000907", + "meta" : { + "definition" : { + "val" : "The molecular product resulting from transcription of a single gene (either a protein or RNA molecule)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "gene product" + }, { + "id" : "http://biohackathon.org/resource/faldo#reference", + "meta" : { + "definition" : { + "val" : "The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "reference" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000909", + "type" : "PROPERTY", + "lbl" : "gene symbol" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000299", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_specified_output" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0001148", + "meta" : { + "definition" : { + "val" : "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a \"targeted\" insertion." + } ] + }, + "type" : "CLASS", + "lbl" : "targeted gene knock-out technique" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0001149", + "type" : "CLASS", + "lbl" : "targeted gene knock-in technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000904", + "meta" : { + "definition" : { + "val" : "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "useful organizational term to collect entities that have genomes/genotypes." + }, { + "pred" : "http://purl.obolibrary.org/obo/GENO_0000905", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "organismal entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000903", + "meta" : { + "definition" : { + "val" : "A relation linking a sequence feature to the location it occupies on some reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occupies" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000906", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from." + } ] + }, + "type" : "PROPERTY", + "lbl" : "on strand" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000905", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models." + } ] + }, + "type" : "PROPERTY", + "lbl" : "mixin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000902", + "meta" : { + "definition" : { + "val" : "The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "VMC:Location" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed.\n\nFor example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. \n\t\n2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus.\n\n3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future.\n\nWe don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic locus" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic location" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic feature location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000901", + "meta" : { + "definition" : { + "val" : "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_allele cellular context" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "type" : "PROPERTY", + "lbl" : "is subsequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "meta" : { + "definition" : { + "val" : "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + }, + "type" : "PROPERTY", + "lbl" : "overlaps sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000931", + "meta" : { + "definition" : { + "val" : "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010983" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform." + } ] + }, + "type" : "CLASS", + "lbl" : "oligogenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "meta" : { + "definition" : { + "val" : "inverse of downstream of sequence of", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is upstream of sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000930", + "meta" : { + "definition" : { + "val" : "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010984" + } ] + }, + "type" : "CLASS", + "lbl" : "digenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "meta" : { + "definition" : { + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "bounds sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "meta" : { + "definition" : { + "val" : "x has subsequence y iff all of the sequence parts of x are sequence parts of y", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has subsequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000937", + "meta" : { + "definition" : { + "val" : "An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "complete X-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000936", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001417" + } ] + }, + "type" : "CLASS", + "lbl" : "X-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000815", + "meta" : { + "definition" : { + "val" : "The location of a sequence feature as defined by its start and end position on some reference coordinate system.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms).\n\n2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000818", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "modification-qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000939", + "meta" : { + "definition" : { + "val" : "An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "co-dominant X-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000938", + "meta" : { + "definition" : { + "val" : "An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "semi-dominant X-linked inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "incomplete X-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000933", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single-gene inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "monogenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "meta" : { + "definition" : { + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is downstream of sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000932", + "meta" : { + "definition" : { + "val" : "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010982" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Typically used for traits/conditions governed by more than three gene loci." + } ] + }, + "type" : "CLASS", + "lbl" : "polygenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000935", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010985" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gonosomal inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "allosomal inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000934", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "autosomal inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000929", + "meta" : { + "definition" : { + "val" : "An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001426" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multigenic inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-locus inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complex inherritance" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Diseases inherited in this manner are termed 'complex diseases'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-factorial inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-genic inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "multifactorial inheritance" + }, { + "id" : "http://biohackathon.org/resource/faldo#ReverseStrandPosition", + "type" : "CLASS", + "lbl" : "Negative strand" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000920", + "meta" : { + "definition" : { + "val" : "A set of qualified seqeunce features.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified sequence feature set" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000902", + "meta" : { + "definition" : { + "val" : "A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "On the relationship between 'transgenic insertions', 'transgenes', and 'alleles'\nTransgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete.\n\nIn addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. \n\nFor the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism).\n\nNote that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome." + } ] + }, + "type" : "CLASS", + "lbl" : "transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000926", + "meta" : { + "definition" : { + "val" : "A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "allelic cellular distribution" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000925", + "meta" : { + "definition" : { + "val" : "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_extrinsic sequence feature attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000928", + "meta" : { + "definition" : { + "val" : "A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "clonal" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000927", + "meta" : { + "definition" : { + "val" : "A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "constitutional" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000922", + "meta" : { + "definition" : { + "val" : "A set of biological sequences.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. \n\nA set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000921", + "meta" : { + "definition" : { + "val" : "A biolocical sequence, or set of such sequences.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "biological sequence or collection" + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence or set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000924", + "meta" : { + "definition" : { + "val" : "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_intrinsic sequence feature attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000923", + "meta" : { + "definition" : { + "val" : "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genetic dosage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "functional feature complement" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage)." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_functional copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000953", + "meta" : { + "definition" : { + "val" : "An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0031362" + } ] + }, + "type" : "CLASS", + "lbl" : "sex-limited autosomal recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000952", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001470" + } ] + }, + "type" : "CLASS", + "lbl" : "sex-limited autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/HsapDv_0000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A spatiotemporal region encompassing some part of the life cycle of an organism." + } ] + }, + "type" : "CLASS", + "lbl" : "human life cycle stage" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000959", + "meta" : { + "definition" : { + "val" : "Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference.\n\nFor copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_defining_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000958", + "meta" : { + "definition" : { + "val" : "Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_defining_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000719", + "meta" : { + "definition" : { + "val" : "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons." + } ] + }, + "type" : "CLASS", + "lbl" : "intrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000839", + "type" : "CLASS", + "lbl" : "knockdown reagent targeted gene complement" + }, { + "id" : "http://biohackathon.org/resource/faldo#ExactPosition", + "meta" : { + "definition" : { + "val" : "A position that is exactly known.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Exact position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000834", + "meta" : { + "definition" : { + "val" : "Used to annotation axioms that define identity criteria for instances of a class.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_identity_criteria" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000955", + "meta" : { + "definition" : { + "val" : "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number variation" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_variant copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000713", + "meta" : { + "definition" : { + "val" : "A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "qualified sequence feature or collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000712", + "type" : "PROPERTY", + "lbl" : "ObsoleteDataProperty" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000954", + "meta" : { + "definition" : { + "val" : "A set of discrete alleles within a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An \"Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'." + } ] + }, + "type" : "CLASS", + "lbl" : "allele set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000833", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each." + } ] + }, + "type" : "CLASS", + "lbl" : "genotype-phenotype association" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000715", + "meta" : { + "definition" : { + "val" : "A set of qualified sequence features that carry genomic sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele.\n\nA complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified genomic feature set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000957", + "meta" : { + "definition" : { + "val" : "Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location.\n\nFor copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_defining_location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000956", + "meta" : { + "definition" : { + "val" : "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000714", + "meta" : { + "definition" : { + "val" : "A qualified sequence feature that carries sequence derived from the genome of a cell or organism.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified genomic feature" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000219", + "meta" : { + "definition" : { + "val" : "Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of." + } ] + }, + "type" : "PROPERTY", + "lbl" : "denotes" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7955", + "type" : "CLASS", + "lbl" : "Danio rerio" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000011", + "meta" : { + "definition" : { + "val" : "A processual entity that realizes a plan which is the concretization of a plan specification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO." + } ] + }, + "type" : "CLASS", + "lbl" : "planned process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000942", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Z-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000941", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001450" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "holandric inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "Y-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000804", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "construct" + } ] + }, + "type" : "CLASS", + "lbl" : "engineered_region" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000948", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "W-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000947", + "meta" : { + "definition" : { + "val" : "A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Z-linked reccessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000708", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "organizational property to hold imports from faldo." + } ] + }, + "type" : "PROPERTY", + "lbl" : "faldo properties" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0000199", + "type" : "CLASS", + "lbl" : "abnormal(ly) malformed endocardium cell" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000949", + "meta" : { + "definition" : { + "val" : "An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy)." + } ] + }, + "type" : "CLASS", + "lbl" : "mitochondrial inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000944", + "meta" : { + "definition" : { + "val" : "A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "complete Z-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000823", + "meta" : { + "definition" : { + "val" : "A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "1. 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Some allelic genotype formats encode the genotype as a single string - e.g. \"GRCh38 Chr12:258635(A;T)\" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location.\n\nThis contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single locus genotype" + } ] + }, + "type" : "CLASS", + "lbl" : "allelic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000702", + "meta" : { + "definition" : { + "val" : "A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "VMC:State" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "biomacromolecular sequence" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "state" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000102", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology metadata" + } ] + }, + "type" : "CLASS", + "lbl" : "data about an ontology part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000701", + "meta" : { + "definition" : { + "val" : "A sequence feature or a set of such features.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence feature or collection" + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature or set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000943", + "meta" : { + "definition" : { + "val" : "A Z-linked inheritance pattern wherein the trait manifests in heterozygotes.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Z-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000946", + "meta" : { + "definition" : { + "val" : "An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "co-dominant Z-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000945", + "meta" : { + "definition" : { + "val" : "A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "semi-dominant Z-linked inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "incomplete Z-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000703", + "meta" : { + "definition" : { + "val" : "Shortcut relation linking a sequence feature directly to a string representing the 'state' of its sequence - i.e. the ordering of units that comprise it (e.g. 'atgcagctagctaccgtcgatcg').", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_string" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000016", + "meta" : { + "definition" : { + "val" : "A transition of a guanine to an adenine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000016" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "G to A transition" + } ] + }, + "type" : "CLASS", + "lbl" : "G_to_A_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000015", + "meta" : { + "definition" : { + "val" : "A transition of an adenine to a guanine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "A to G 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+ "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000018" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "pyrimidine to purine transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "pyrimidine_to_purine_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000017", + "meta" : { + "definition" : { + "val" : "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000017" + } ] + }, + "type" : "CLASS", + "lbl" : "transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000610", + "meta" : { + "definition" : { + "val" : "A relationship between a reference locus/allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_reference_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies." + } ] + }, + "type" : "CLASS", + "lbl" : "cell" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000611", + "meta" : { + "definition" : { + "val" : "A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "background genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic background" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000850", + "meta" : { + "definition" : { + "val" : "A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "P-element construct" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000618", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "chromosomal band brightness" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal band intensity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000619", + "type" : "CLASS", + "lbl" : "gpos" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000614", + "meta" : { + "definition" : { + "val" : "An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "New term request for SO." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal region" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000856", + "meta" : { + "definition" : { + "val" : "An engineered region that is used to transfer foreign genetic material into a host cell.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. \n\nConstructs are typically packaged as part of delivery systems such as plasmids or viral vectors." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "engineered_genetic_vector" + } ] + }, + "type" : "CLASS", + "lbl" : "engineered genetic construct" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000023", + "meta" : { + "definition" : { + "val" : "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000023" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "purine to pyrimidine transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "purine_to_pyrimidine_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000022", + "meta" : { + "definition" : { + "val" : "A transversion from T to G.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "T to G transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000022" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "T_to_G_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000616", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome sub-band" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000021", + "meta" : { + "definition" : { + "val" : "A transversion from T to A.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "T to A transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000021" + } ] + }, + "type" : "CLASS", + "lbl" : "T_to_A_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000737", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "expression-qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000830", + "meta" : { + "definition" : { + "val" : "An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "chromosomal feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gross chromosomal part" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome part" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000020", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "C to G transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "C_to_G_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000736", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell)." + } ] + }, + "type" : "CLASS", + "lbl" : "location-qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000005", + "meta" : { + "definition" : { + "val" : "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\\"complex\\\" should be used. Usually there are multiple equally plausible explanations for the change.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000005" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complex substitution" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + } ] + }, + "type" : "CLASS", + "lbl" : "complex_substitution" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000002", + "meta" : { + "definition" : { + "val" : "Any change in genomic DNA caused by a single event.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000002" + } ] + }, + "type" : "CLASS", + "lbl" : "substitution" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000009", + "meta" : { + "definition" : { + "val" : "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000009" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "transition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000008", + "meta" : { + "definition" : { + "val" : "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Point_mutation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "point mutation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000008" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + } ] + }, + "type" : "CLASS", + "lbl" : "point_mutation" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000841", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA26332-9" + } ] + }, + "type" : "PROPERTY", + "lbl" : "likely_pathogenic_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000962", + "meta" : { + "definition" : { + "val" : "A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a \"sequence feature level\" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred).\n\nFor example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome." + } ] + }, + "type" : "CLASS", + "lbl" : "variant copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000720", + "type" : "CLASS", + "lbl" : "DNA sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000840", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA6668-3" + } ] + }, + "type" : "PROPERTY", + "lbl" : "pathogenic_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000961", + "meta" : { + "definition" : { + "val" : "A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result.\n\nA 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. \n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome.\n\nWe represent the notion of copy number at the \"sequence level\" (as opposed to the \"sequence feature level\") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The \"sequence level\" representation here supports this use case. By contrast, a \"feature level\" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000964", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type." + } ] + }, + "type" : "CLASS", + "lbl" : "mosaic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000843", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA6675-8" + } ] + }, + "type" : "PROPERTY", + "lbl" : "benign_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000722", + "type" : "CLASS", + "lbl" : "amino acid sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000963", + "meta" : { + "definition" : { + "val" : "A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "functional genetic dosage" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence.\n\n'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nAs we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele." + } ] + }, + "type" : "CLASS", + "lbl" : "functional copy complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000842", + "meta" : { + "definition" : { + "val" : "Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "non-causal_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000721", + "type" : "CLASS", + "lbl" : "RNA sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000704", + "meta" : { + "definition" : { + "val" : "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Regarding the distinction between a 'gene' and a 'gene allele': \nEvery zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment)." + } ] + }, + "type" : "CLASS", + "lbl" : "gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000960", + "meta" : { + "definition" : { + "val" : "A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000849", + "type" : "PROPERTY", + "lbl" : "is_candidate_variant_for" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000848", + "meta" : { + "definition" : { + "val" : "A sequence alteration within the coding sequence of a gene.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_coding sequence alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000606", + "type" : "CLASS", + "lbl" : "hemizygous insertion-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000608", + "meta" : { + "definition" : { + "val" : "a relation to link a single locus complement to its zygosity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000845", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA26333-7" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_uncertain_significance_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000012", + "meta" : { + "definition" : { + "val" : "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "C to T transition at pCpG site" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000012" + } ] + }, + "type" : "CLASS", + "lbl" : "C_to_T_transition_at_pCpG_site" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000603", + "meta" : { + "definition" : { + "val" : "an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "heteroplasmic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000966", + "meta" : { + "definition" : { + "val" : "Relates a sequence feature location to an interval that defines its start and end position.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_interval" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000724", + "type" : "CLASS", + "lbl" : "obsolete_biological sequence or collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000965", + "meta" : { + "definition" : { + "val" : "A pair of integers representing start and end position of a location on a sequence coordinate system.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "sequence interval" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000602", + "meta" : { + "definition" : { + "val" : "an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "homoplasmic" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000011", + "meta" : { + "definition" : { + "val" : "A transition of a cytidine to a thymine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "C to T transition" + } ] + }, + "type" : "CLASS", + "lbl" : "C_to_T_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000844", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA26334-5" + } ] + }, + "type" : "PROPERTY", + "lbl" : "likely_benign_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000010", + "meta" : { + "definition" : { + "val" : "A substitution of a pyrimidine, C or T, for another pyrimidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "pyrimidine transition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000010" + } ] + }, + "type" : "CLASS", + "lbl" : "pyrimidine_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000726", + "meta" : { + "definition" : { + "val" : "A relation linking a qualified sequence feature to its component sequence feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_sequence_feature_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000847", + "meta" : { + "definition" : { + "val" : "A relation used to describe an environment contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_qualifying_environment" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000605", + "type" : "CLASS", + "lbl" : "hemizygous Y-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000604", + "type" : "CLASS", + "lbl" : "hemizygous X-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000846", + "meta" : { + "definition" : { + "val" : "A relation used to describe a process contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_qualifying_process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000967", + "meta" : { + "definition" : { + "val" : "Relates a 'sequence feature location' to a sequence that it is anchored to.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_reference_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000725", + "type" : "CLASS", + "lbl" : "obsolete_biological sequence collection" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000036", + "meta" : { + "definition" : { + "val" : "A continuous nucleotide sequence is inverted in the same position.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000036" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inversion" + } ] + }, + "type" : "CLASS", + "lbl" : "inversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000035", + "meta" : { + "definition" : { + "val" : "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide_duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000035" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide duplication" + } ] + }, + "type" : "CLASS", + "lbl" : "duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000039", + "meta" : { + "definition" : { + "val" : "A tandem duplication where the individual regions are in the same orientation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "direct tandem duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000039" + } ] + }, + "type" : "CLASS", + "lbl" : "direct_tandem_duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000874", + "meta" : { + "definition" : { + "val" : "A relation used to describe a process contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "repeat region alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000511", + "meta" : { + "definition" : { + "val" : "An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "wild-type" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000632", + "type" : "CLASS", + "lbl" : "gpos66" + }, { + "id" : "http://biohackathon.org/resource/faldo#ForwardStrandPosition", + "type" : "CLASS", + "lbl" : "Positive strand" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000873", + "meta" : { + "definition" : { + "val" : "A relation used to describe an environment contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "microsatellite alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000634", + "meta" : { + "definition" : { + "val" : "relation between an molecular agent and its molecular target", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_targeted_by" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000876", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allelic dosage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gene dosage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_genetic dosage" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000513", + "meta" : { + "definition" : { + "val" : "a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "aneusomic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000512", + "meta" : { + "definition" : { + "val" : "One of a set of sequence features known to exist at a particular genomic location.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations).\n\nAlleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variable feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene.\n\nTo be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene.\n\t\n[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17)\n[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17)\n[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17)\n[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17)\n[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17)\n[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17)\n[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483\n[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17)\n[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17)\n[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17)\n[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17)\n[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)" + } ] + }, + "type" : "CLASS", + "lbl" : "allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000875", + "meta" : { + "definition" : { + "val" : "A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "allelic state" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000633", + "type" : "CLASS", + "lbl" : "gpos33" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000870", + "meta" : { + "definition" : { + "val" : "A collection of more than one sequence feature.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence feature collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000872", + "meta" : { + "definition" : { + "val" : "A set of genomic sequences (a biological sequence that is of genomic origin).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number complement" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic sequence set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000871", + "meta" : { + "definition" : { + "val" : "A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/source", + "val" : "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. \n\nAs highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\n1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \n\n2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). \"Star alleles\" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/).\n\n3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. \n\nEach of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block.\n\nInstead, we can create an 'allele set' class as the haplotype parent?" + } ] + }, + "type" : "CLASS", + "lbl" : "haplotype" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000040", + "meta" : { + "definition" : { + "val" : "A tandem duplication where the individual regions are not in the same orientation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inverted tandem duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "mirror duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000040" + } ] + }, + "type" : "CLASS", + "lbl" : "inverted_tandem_duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000639", + "meta" : { + "definition" : { + "val" : "Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. \n\n2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds.\n\n3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "sequence_derives_from" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000878", + "meta" : { + "definition" : { + "val" : "Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "maternally inherited" + } ] + }, + "type" : "CLASS", + "lbl" : "maternal allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000515", + "meta" : { + "definition" : { + "val" : "An allele of a gene that contains some sequence alteration.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset." + } ] + }, + "type" : "CLASS", + "lbl" : "variant gene allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000877", + "meta" : { + "definition" : { + "val" : "A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variant origin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genetic origin" + } ] + }, + "type" : "CLASS", + "lbl" : "allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000514", + "type" : "INDIVIDUAL", + "lbl" : "exemplar term" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000638", + "meta" : { + "definition" : { + "val" : "A transgene part whose sequence is expressed in a gene product through transcription and/or translation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "coding transgene feature" + } ] + }, + "type" : "CLASS", + "lbl" : "expressed transgene region" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000516", + "meta" : { + "definition" : { + "val" : "A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allelic complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "homologous allele complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single locus feature complement" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes.\n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a.\n\nThe collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome." + } ] + }, + "type" : "CLASS", + "lbl" : "single locus complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000879", + "meta" : { + "definition" : { + "val" : "Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "paternally inherited" + } ] + }, + "type" : "CLASS", + "lbl" : "paternal allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000637", + "meta" : { + "definition" : { + "val" : "A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "regulatory transgene region" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000027", + "meta" : { + "definition" : { + "val" : "A transversion from guanine to thymine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000027" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "G to T transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "G_to_T_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000026", + "meta" : { + "definition" : { + "val" : "A transversion from guanine to cytidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000026" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "G to C transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "G_to_C_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000025", + "meta" : { + "definition" : { + "val" : "A transversion from adenine to thymine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "A to T transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000025" + } ] + }, + "type" : "CLASS", + "lbl" : "A_to_T_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000024", + "meta" : { + "definition" : { + "val" : "A transversion from adenine to cytidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000024" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "A to C transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "A_to_C_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000742", + "meta" : { + "definition" : { + "val" : "A relation linking a sequence_alteration to the gene it alters.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_within_allele_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_alteration_within" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000500", + "meta" : { + "definition" : { + "val" : "A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral allele" + } ] + }, + "type" : "CLASS", + "lbl" : "ancestral polymorphic allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000621", + "type" : "CLASS", + "lbl" : "gvar" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000741", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_has_regulatory_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000620", + "type" : "CLASS", + "lbl" : "gneg" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000502", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "wild-type gene allele" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation." + } ] + }, + "type" : "CLASS", + "lbl" : "wild-type gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000623", + "type" : "CLASS", + "lbl" : "gpos75" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000501", + "meta" : { + "definition" : { + "val" : "An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "wild-type allele" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain.\n\nThe notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis." + } ] + }, + "type" : "CLASS", + "lbl" : "wild-type allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000743", + "type" : "PROPERTY", + "lbl" : "has_asserted_phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000622", + "type" : "CLASS", + "lbl" : "gpos100" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000861", + "meta" : { + "definition" : { + "val" : "A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "non-integrated transgene" + } ] + }, + "type" : "CLASS", + "lbl" : "extra-chromosomal transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000740", + "type" : "PROPERTY", + "lbl" : "has_inferred_phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000629", + "meta" : { + "definition" : { + "val" : "A chromosome arm that is the longer of the two arms of a given chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "q-arm" + } ] + }, + "type" : "CLASS", + "lbl" : "long chromosome arm" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000628", + "meta" : { + "definition" : { + "val" : "A chromosome arm that is the shorter of the two arms of a given chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "stalk" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "p-arm" + } ] + }, + "type" : "CLASS", + "lbl" : "short chromosome arm" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000504", + "meta" : { + "definition" : { + "val" : "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position." + } ] + }, + "type" : "CLASS", + "lbl" : "reagent targeted gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000625", + "type" : "CLASS", + "lbl" : "gpos25" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000867", + "type" : "PROPERTY", + "lbl" : "proabalistic_quantifier" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000624", + "type" : "CLASS", + "lbl" : "gpos50" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000866", + "meta" : { + "definition" : { + "val" : "Property to link an assertion or association with some value quantifying its relevance or ranking.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The 'rank' quantifier in Bgee gene-anatomy associations, that indicates the imporatnace/specificity of a gene expression in a given anatommy relative to expressionin other anatomies for the same gene." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_quantifier" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000506", + "meta" : { + "definition" : { + "val" : "A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "extrinsic transgene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "experimentally-expressed transgene" + } ] + }, + "type" : "CLASS", + "lbl" : "transiently-expressed transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000032", + "meta" : { + "definition" : { + "val" : "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Indels can have a different number of bases than the corresponding reference sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Indel" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000032" + } ] + }, + "type" : "CLASS", + "lbl" : "indel" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000626", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_color_value" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_staining_intensity" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000181", + "meta" : { + "definition" : { + "val" : "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "population" + }, { + "id" : "http://biohackathon.org/resource/faldo#Region", + "meta" : { + "definition" : { + "val" : "A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "Region" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000780", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "deoxyribonucleic acid residue" + } ] + }, + "type" : "CLASS", + "lbl" : "DNA residue" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000533", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gene targeting reagent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence targeting reagent" + } ] + }, + "type" : "CLASS", + "lbl" : "gene knockdown reagent" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000654", + "meta" : { + "definition" : { + "val" : "An organizational class to hold relations of parthood between sequences/features.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000896", + "meta" : { + "definition" : { + "val" : "Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg').", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_string" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000411", + "meta" : { + "definition" : { + "val" : "A relation linking a gene class to a sequence-varaint or expression-variant of the gene.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_variant_instance" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Domain = punned gene class\nRange = genomic feature" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_has_genetic_variant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000653", + "meta" : { + "definition" : { + "val" : "A relationship between a wild-type allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_wild_type_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000895", + "meta" : { + "definition" : { + "val" : "The ending position of a sequence feature or interval.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "end_position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000414", + "meta" : { + "definition" : { + "val" : "A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets." + } ] + }, + "type" : "PROPERTY", + "lbl" : "targets_gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000898", + "meta" : { + "definition" : { + "val" : "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as \n\"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.\" Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location.\n\nCurrent definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424." + } ] + }, + "type" : "CLASS", + "lbl" : "haplotype block" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000777", + "meta" : { + "definition" : { + "val" : "An intrinsic genotype that specifies variation from a defined reference genome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "variant genomic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000897", + "meta" : { + "definition" : { + "val" : "An generically dependent continuant that carries biological sequence that is part of or derived from a genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/GENO_0000905", + "val" : "true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic entity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000030", + "meta" : { + "definition" : { + "val" : "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000142" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "information content entity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples of information content entites include journal articles, data, graphical layouts, and graphs." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Chris Stoeckert" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." + } ] + }, + "type" : "CLASS", + "lbl" : "information content entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000534", + "meta" : { + "definition" : { + "val" : "A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "targeted gene segment" + } ] + }, + "type" : "CLASS", + "lbl" : "reagent-targeted gene subregion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000413", + "meta" : { + "definition" : { + "val" : "A relation linking a gene class to one of its sequence-variant alleles.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = punned gene class\nRange = allele" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_sequence_variant" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000655", + "type" : "PROPERTY", + "lbl" : "is_sequence_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000892", + "meta" : { + "definition" : { + "val" : "A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "heteroplasmic mitochondrial inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000650", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sex_agnostic_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000770", + "type" : "CLASS", + "lbl" : "phenotypic inheritance process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000891", + "meta" : { + "definition" : { + "val" : "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/source", + "val" : "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.\n\nFormer axiom: denotes some 'obsolete_canonical allele'" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_contextual allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000894", + "meta" : { + "definition" : { + "val" : "The starting position of a sequence feature or interval.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "start_position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000410", + "meta" : { + "definition" : { + "val" : "A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_variant_instance_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Domain = genomic feature instance\nRange = punned gene class IRI" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_genetic_variant_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000652", + "meta" : { + "definition" : { + "val" : "A relationship between a polymorphic allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_polymorphic_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000773", + "meta" : { + "definition" : { + "val" : "An attribute describing a type of variation inhering in a sequence feature or collection.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allele attribute" + } ] + }, + "type" : "CLASS", + "lbl" : "variation attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000893", + "meta" : { + "definition" : { + "val" : "A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "homoplasmic mitochondrial inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0005692", + "type" : "CLASS", + "lbl" : "abnormal(ly) absent adaxial cell" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000651", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_mutant_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000772", + "meta" : { + "definition" : { + "val" : "A sequence attribute inhering in a feature whose identity is not specified.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_unspecified" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000637", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_engineered_plasmid" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000779", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "monomeric residue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "biological sequence residue" + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence unit" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000536", + "meta" : { + "definition" : { + "val" : "A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Scope of 'Genetic State': \n'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs.\n\n2. Genotype Subtypes:\nIn GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. \n\nTwo more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features.\n\n3. The Genotype Partonomy: \n'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype \"fgf8a; fgf3[AB]\", described at zfin.org/ZDB-FISH-150901-9362, include the following elements:\n\n - GVC: fgf8a; fgf3 (total intrinsic variation in the genome)\n - Genomic Background: AB (the reference against which the GVC is variant)\n - VSLC1: fgf8a (homozygous complement of gene alleles at one known variant locus)\n - VSLC2: fgf3 (heterozygous complement of gene alleles at another known variant locus)\n - Allele 1: fgf8a (variant version of the fgf8a gene, present in two copies)\n - Allele 2: fgf3 (variant version of the fgf3 gene, present in one copy)\n - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy)\n - Sequence Alteration1: (the specific mutation within the fgf8a gene that makes it variant)\n - Sequence Alteration2: (the specific mutation within the fgf3 gene that makes it variant)\n\nA graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md\n\nOne reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to \"propagate phenotypes\" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). \nNote however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above." + } ] + }, + "type" : "CLASS", + "lbl" : "genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000415", + "meta" : { + "definition" : { + "val" : "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "replaced with SO:engineered_region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "extra-genomic sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reagent sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000778", + "meta" : { + "definition" : { + "val" : "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "eliminating classes that are not necessary or add uneeded complexity." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence information entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000899", + "meta" : { + "definition" : { + "val" : "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "'Genomic Genotype' vs 'Genome' in GENO: \nA genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complete genotype" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000418", + "meta" : { + "definition" : { + "val" : "A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_affected_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000659", + "meta" : { + "definition" : { + "val" : "A set of sequence features.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus\n\n2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele.\n\n3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature).\n\nThe notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3].\n\n[1] https://www.snpedia.com/index.php/APOE-%CE%B54\n[2] https://www.snpedia.com/index.php/APOE-%CE%B52\n[3] https://www.snpedia.com/index.php/Gs270" + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature set" + }, { + "id" : "http://biohackathon.org/resource/faldo#StrandedPosition", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'." + } ] + }, + "type" : "CLASS", + "lbl" : "Stranded position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000890", + "meta" : { + "definition" : { + "val" : "One of a set of sequence features or haplotypes that exist at a particular genetic locus. ", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand.\n\nIn the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references)" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_canonical allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000885", + "meta" : { + "definition" : { + "val" : "An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement')\n\nAlt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "\"Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes.\"\nFrom https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/" + } ] + }, + "type" : "CLASS", + "lbl" : "diplotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000642", + "meta" : { + "definition" : { + "val" : "A transgene whose product is used as a selectable marker.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "selectable marker transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000524", + "meta" : { + "definition" : { + "val" : "A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment.\n\nThe 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "expression genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. \n\nOur rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. \n\nFinally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "experimental genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as:\n\n shha; shhb\n\nThis notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct." + } ] + }, + "type" : "CLASS", + "lbl" : "extrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000645", + "meta" : { + "definition" : { + "val" : "A genomic genotype where the genomic background specifies a male or female sex chromosome complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "intrinsic genotype (sex-specific)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances.\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nIn the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sex-qualified intrinsic genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sex-qualified genotype" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic genotype (sex-qualified)" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000887", + "type" : "CLASS", + "lbl" : "oryzias latipes strain" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000402", + "meta" : { + "definition" : { + "val" : "A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a/fgf8a)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "trans-heterozygous" + } ] + }, + "type" : "CLASS", + "lbl" : "compound heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000644", + "meta" : { + "definition" : { + "val" : "A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). \n\nA base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation)." + } ] + }, + "type" : "CLASS", + "lbl" : "karyotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000886", + "meta" : { + "definition" : { + "val" : "A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "allelic phase" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000881", + "meta" : { + "definition" : { + "val" : "Describes an allele whose origin is not known.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "unknown allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000880", + "meta" : { + "definition" : { + "val" : "Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. \n\t\t\nDe novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder." + } ] + }, + "type" : "CLASS", + "lbl" : "de novo allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000641", + "meta" : { + "definition" : { + "val" : "A relationship between a variant allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_variant_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000883", + "meta" : { + "definition" : { + "val" : "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "replaced by GENO:0000900 ! 'germline'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "germ-line" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_gametic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000882", + "meta" : { + "definition" : { + "val" : "Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells.\n\t\t\nThese acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "acquired" + } ] + }, + "type" : "CLASS", + "lbl" : "somatic allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000761", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Proposal for a property linking regulatory elements to larger features of which they are a part." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_regulatory_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000640", + "type" : "CLASS", + "lbl" : "reporter region" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000173", + "meta" : { + "definition" : { + "val" : "A duplication consisting of 2 identical adjacent regions.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "erverted" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tandem duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000173" + } ] + }, + "type" : "CLASS", + "lbl" : "tandem_duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000408", + "meta" : { + "definition" : { + "val" : "A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size).\n\nWhile conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like \"fgf8a is an allele of the Danio rerio fgf8a gene\", and we may create data where fgf8a is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene).\n\nIt is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. \n\nThis departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\\GAL4 gene.\n\nAt the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = allele \nRange = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that the allele is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " is_allele_of the 'danio rerio fgf8a' gene locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_sequence_variant_of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000529", + "meta" : { + "definition" : { + "val" : "A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism).\n\nThe identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "expression allele" + } ] + }, + "type" : "CLASS", + "lbl" : "expression-variant gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000889", + "meta" : { + "definition" : { + "val" : "An inheritance pattern that is not determined or not known.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unknown inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "undetermined inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000768", + "meta" : { + "definition" : { + "val" : "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic coordinates" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "remodeling notion of sequence feature position around the idea of a 'genomic locus'" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_genomic position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000647", + "meta" : { + "definition" : { + "val" : "A genomic genotype here the genomic background specifies a female sex chromosome complement.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "female intrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000888", + "meta" : { + "definition" : { + "val" : "Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parentally inherited" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parental origin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "hereditary" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells." + } ] + }, + "type" : "CLASS", + "lbl" : "germline allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000646", + "meta" : { + "definition" : { + "val" : "A genomic genotype here the genomic background specifies a male sex chromosome complement.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "male intrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000767", + "meta" : { + "definition" : { + "val" : "A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_has_position_component" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000525", + "meta" : { + "definition" : { + "val" : "A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" + } ] + }, + "type" : "CLASS", + "lbl" : "effective genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000649", + "meta" : { + "definition" : { + "val" : "A background genotype whose sequence or identity is not known or specified.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unspecified background genotype" + } ] + }, + "type" : "CLASS", + "lbl" : "unspecified genomic background" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000528", + "meta" : { + "definition" : { + "val" : "The set of all transgenes trransiently expressed in a biological system in the context of a given experiment.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "experimental transgene complement" + } ] + }, + "type" : "CLASS", + "lbl" : "transiently-expressed transgene complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000527", + "meta" : { + "definition" : { + "val" : "A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment." + } ] + }, + "type" : "CLASS", + "lbl" : "reagent-targeted gene complement" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000783", + "meta" : { + "definition" : { + "val" : "An attribute to describe a region that was modified in vitro.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "engineered" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000086", + "type" : "CLASS", + "lbl" : "reagent role" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000681", + "meta" : { + "definition" : { + "val" : "An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "transgenic extrachromosomal replicon" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "exogenous extrachromosomal replicon" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "aberrant extrachromosomal replicon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'." + } ] + }, + "type" : "CLASS", + "lbl" : "novel extrachromosomal replicon" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000680", + "meta" : { + "definition" : { + "val" : "A genomic feature that has an extent of zero.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Former logical def: \n'genomic feature'\n and (has_extent value 0)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A junction between bases, a deletion variant, a terminus at the end of a chromosome." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_null feature" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", + "type" : "CLASS", + "lbl" : "Homo sapiens" + }, { + "id" : "http://purl.obolibrary.org/obo/MP_0000001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "where to place this depends on if we take the organismal view or the quality centric view." + } ] + }, + "type" : "CLASS", + "lbl" : "mammalian phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000678", + "meta" : { + "definition" : { + "val" : "Property linking a sequence or sequence feature to an integer representing its length in terms of the number of units in the sequence.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_extent" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000793", + "type" : "PROPERTY", + "lbl" : "inferred_to_contribute_to_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000794", + "type" : "PROPERTY", + "lbl" : "inferred_to_correlate_with_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001746", + "meta" : { + "definition" : { + "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001746" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 02:03:30 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "paternal uniparental disomy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + } ] + }, + "type" : "CLASS", + "lbl" : "paternal_uniparental_disomy" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001745", + "meta" : { + "definition" : { + "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 02:03:01 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001745" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "maternal uniparental disomy" + } ] + }, + "type" : "CLASS", + "lbl" : "maternal_uniparental_disomy" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001505", + "meta" : { + "definition" : { + "val" : "A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'GRCh37.p10' (a human reference genome build)" + } ] + }, + "type" : "CLASS", + "lbl" : "reference genome sequence" + }, { + "id" : "http://www.ncbi.nlm.nih.gov/gene/399483", + "meta" : { + "xrefs" : [ { + "val" : "http://zfin.org/ZDB-GENE-040123-1" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000514" + } ] + }, + "type" : "CLASS", + "lbl" : "danio rerio cdkn1ca gene" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001742", + "meta" : { + "definition" : { + "val" : "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number gain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001742" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 01:54:09 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + } ] + }, + "type" : "CLASS", + "lbl" : "copy_number_gain" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001500", + "meta" : { + "definition" : { + "val" : "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "heritable_phenotypic_marker" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001744", + "meta" : { + "definition" : { + "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "uniparental disomy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 02:01:05 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "UPD" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001744" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http:http\\://en.wikipedia.org/wiki/Uniparental_disomy" + } ] + }, + "type" : "CLASS", + "lbl" : "UPD" + }, { + "id" : "http://purl.obolibrary.org/obo/WBPhenotype_0000886", + "meta" : { + "definition" : { + "val" : "Animals exhibit variations compared to a given control.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "c. elegans phenotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "Variant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes." + } ] + }, + "type" : "CLASS", + "lbl" : "worm phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001743", + "meta" : { + "definition" : { + "val" : "A sequence alteration whereby the copy number of a given region is less than the reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "loss" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001743" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 01:55:02 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number loss" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + } ] + }, + "type" : "CLASS", + "lbl" : "copy_number_loss" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000771", + "meta" : { + "definition" : { + "val" : "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quantitative trait locus" + } ] + }, + "type" : "CLASS", + "lbl" : "QTL" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000791", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains.\n\nBelow are the different kinds/paths of propagation we desire:\n1. Propagation 'down' a genotype (from larger components to smaller ones)\n2. Propagation 'up' a genotype (from smaller components to larger ones)\n3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype).\n4. From an effective genotype to its intrinsic and extrinsic components.\n5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele).\n6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this.\n\nNote that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha/shha [AB] to shha/shha [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition')" + } ] + }, + "type" : "PROPERTY", + "lbl" : "inferred_to_cause_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000790", + "type" : "PROPERTY", + "lbl" : "related_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000788", + "meta" : { + "definition" : { + "val" : "An attribute, quality, or state of a sequence feature or collection.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0000400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000667", + "meta" : { + "definition" : { + "val" : "A transgene that codes for a product used as a reporter of gene expression or activity.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "reporter transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000666", + "meta" : { + "definition" : { + "val" : "A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "SO:0000831 (gene member region)" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "defined gene part" + } ] + }, + "type" : "CLASS", + "lbl" : "gene part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000661", + "meta" : { + "definition" : { + "val" : "Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_sex_agnostic_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000782", + "type" : "CLASS", + "lbl" : "amino acid residue" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000781", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ribonucleic acid residue" + } ] + }, + "type" : "CLASS", + "lbl" : "RNA residue" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000660", + "meta" : { + "definition" : { + "val" : "A set of genomic features (i.e. sequence features that are of genomic origin).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature.\n\nThe notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic locus complement" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic feature set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000784", + "meta" : { + "definition" : { + "val" : "A relation between two seqeunces or features that are considered variant with each other along their entire extents.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "completely_varies_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000783", + "meta" : { + "definition" : { + "val" : "A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues)", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_unit" + }, { + "id" : "http://biohackathon.org/resource/faldo#location", + "type" : "PROPERTY", + "lbl" : "location" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001410", + "meta" : { + "definition" : { + "val" : "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "not currently needed to support modeling use cases. can re-introduce if becomes necessary." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_experimental_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000580", + "meta" : { + "definition" : { + "val" : "A relation used to describe a context or conditions that define and/or identify an entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_qualifying_context" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association.\n\nUsed in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_qualifier" + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000118", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "pulling in HP 'phenotypic abnormality' root here" + } ] + }, + "type" : "CLASS", + "lbl" : "human phenotypic abnormality" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000460", + "meta" : { + "definition" : { + "val" : "A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "transgene part" + }, { + "id" : "http://purl.org/oban/association_has_subject", + "type" : "PROPERTY", + "lbl" : "association has subject" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000458", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a)" + } ] + }, + "type" : "CLASS", + "lbl" : "simple heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "type" : "PROPERTY", + "lbl" : "is part of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000575", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl\nThis ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes." + } ] + }, + "type" : "CLASS", + "lbl" : "zebrafish phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000211", + "meta" : { + "definition" : { + "val" : "A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "materializes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence." + } ] + }, + "type" : "PROPERTY", + "lbl" : "bears_concretization_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000339", + "meta" : { + "definition" : { + "val" : "A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as \"the point at which one or more contiguous nucleotides were excised\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "absent aneusomic chromosome" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "lost aneusomic chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "type" : "PROPERTY", + "lbl" : "has part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000338", + "meta" : { + "definition" : { + "val" : "A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "duplicate chromosome" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome." + } ] + }, + "type" : "CLASS", + "lbl" : "gained aneusomic chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000445", + "meta" : { + "definition" : { + "val" : "A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "class_to_feature_relation" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_feature_affected_by" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000324", + "meta" : { + "definition" : { + "val" : "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_chromosome complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000447", + "meta" : { + "definition" : { + "val" : "A relation between a gene class and a gene targeting reagent that targets it.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_target_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Domain = punned gene class\nRange = gene knockdown reagent" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_gene_target_of" + }, { + "id" : "http://biohackathon.org/resource/faldo#position", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is." + } ] + }, + "type" : "PROPERTY", + "lbl" : "position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000688", + "meta" : { + "definition" : { + "val" : "A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "terminus" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000683", + "meta" : { + "definition" : { + "val" : "A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "varies_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000443", + "meta" : { + "definition" : { + "val" : "A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = expression variant feature.\nRange = punned gene class" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_expression_variant_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000685", + "meta" : { + "definition" : { + "val" : "An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "novel" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000684", + "meta" : { + "definition" : { + "val" : "A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles." + } ] + }, + "type" : "CLASS", + "lbl" : "novel replicon" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000667", + "meta" : { + "definition" : { + "val" : "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000034" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000667" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide_insertion" + } ] + }, + "type" : "CLASS", + "lbl" : "insertion" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the undetached arm of a human being" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an epidemic" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a forest fire" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an energy wave" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a human being" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a puff of smoke" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a hurricane" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a flame" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a sea wave" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a tornado" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an aggregate of human beings." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a photon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "material entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000207", + "meta" : { + "definition" : { + "val" : "A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/so_has_quality" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000449", + "meta" : { + "definition" : { + "val" : "A relation linking a gene class to one of an expression-variant of that gene..", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = punned gene class\nRange = expression variant feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_expression_variant_instance" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_expression_variant" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000341", + "meta" : { + "definition" : { + "val" : "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "\"Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band\n" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome band" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000340", + "meta" : { + "definition" : { + "val" : "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A complete chromosome sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000481", + "meta" : { + "definition" : { + "val" : "A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. \n\n2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). \n\n3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic feature" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10239", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies." + } ] + }, + "type" : "CLASS", + "lbl" : "Viruses" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000480", + "meta" : { + "definition" : { + "val" : "An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "mutant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000482", + "meta" : { + "definition" : { + "val" : "A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "genetic material" + }, { + "id" : "http://purl.obolibrary.org/obo/ERO_0002003", + "meta" : { + "definition" : { + "val" : "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "stem cell line" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000477", + "meta" : { + "definition" : { + "val" : "An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "polymorphic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000359", + "meta" : { + "definition" : { + "val" : "shortcut relation used to link a phenotype directly to a genotype of an organism", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_phenotype_of_organism_with_genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "phenotype_has_genotype" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Might expand to something like:\n\nphenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype)))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_phenotype_with_genotype" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_phenotype_of_genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/CHEBI_33696", + "type" : "CLASS", + "lbl" : "nucleic acid" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000111", + "meta" : { + "definition" : { + "val" : "a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider http://semanticscience.org/resource/SIO_001062 ! human population (\"A human population refers to a collection of human beings\")." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "homo sapiens population" + } ] + }, + "type" : "CLASS", + "lbl" : "human population" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000231", + "meta" : { + "definition" : { + "val" : "An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO)", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://semanticscience.org/resource/SIO_000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "No proper part relation anymore in RO/BFO?" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_proper_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000113", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon)" + } ] + }, + "type" : "CLASS", + "lbl" : "taxonomic group" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000476", + "meta" : { + "definition" : { + "val" : "An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "variant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000112", + "meta" : { + "definition" : { + "val" : "A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "organism strain or breed" + } ] + }, + "type" : "CLASS", + "lbl" : "strain or breed" + }, { + "id" : "http://purl.obolibrary.org/obo/ERO_0002002", + "meta" : { + "definition" : { + "val" : "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "embryonic stem cell line" + }, { + "id" : "http://purl.obolibrary.org/obo/UPHENO_0001001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition)\n\n2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework." + } ] + }, + "type" : "CLASS", + "lbl" : "Phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000337", + "type" : "CLASS", + "lbl" : "RNAi_reagent" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000119", + "type" : "CLASS", + "lbl" : "danio rerio strain" + }, { + "id" : "http://biohackathon.org/resource/faldo#begin", + "type" : "PROPERTY", + "lbl" : "begin" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001785", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001785" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Fri Mar 25 02:27:41 PDT 2011" + } ] + }, + "type" : "CLASS", + "lbl" : "structural_alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000239", + "meta" : { + "definition" : { + "val" : "A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "VMC:state" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_sequence_component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_state" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000118", + "type" : "CLASS", + "lbl" : "mus musculus strain" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000699", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A junction is a boundary between regions. A boundary has an extent of zero." + } ] + }, + "type" : "CLASS", + "lbl" : "junction" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0600043", + "meta" : { + "definition" : { + "val" : "the introduction. alteration or integration of genetic material into a cell or organism", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "genetic modification technique" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000577", + "type" : "CLASS", + "lbl" : "centromere" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001784", + "meta" : { + "definition" : { + "val" : "A structural sequence alteration where there are multiple equally plausible explanations for the change.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Wed Mar 23 03:21:19 PDT 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001784" + } ] + }, + "type" : "CLASS", + "lbl" : "complex_structural_alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000694", + "meta" : { + "definition" : { + "val" : "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single nucleotide polymorphism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000694" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + } ] + }, + "type" : "CLASS", + "lbl" : "SNP" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000351", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of biological processes from GO-BP." + } ] + }, + "type" : "CLASS", + "lbl" : "biological process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000346", + "meta" : { + "definition" : { + "val" : "A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complete aneusomic chromosome" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism.\n\nSimilarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication." + } ] + }, + "type" : "CLASS", + "lbl" : "aneusomic chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000345", + "meta" : { + "definition" : { + "val" : "A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome.\n\nLoss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "truncated chromosome terminus" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "dropped partial anneuploid chromosomal element" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "translocated absent chromosomal segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement" + } ] + }, + "type" : "CLASS", + "lbl" : "lost aneusomic chromosomal segment" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000106", + "meta" : { + "definition" : { + "val" : "A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic material" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000220", + "type" : "PROPERTY", + "lbl" : "is_genotype_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000344", + "meta" : { + "definition" : { + "val" : "A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "translocated duplicate chromosomal segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "translocated duplicate chromosomal element" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "duplicate partial aneuploid chromosomal element" + } ] + }, + "type" : "CLASS", + "lbl" : "gained aneusomic chromosomal segment" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000222", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and some level of genetic variation present in its genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000343", + "meta" : { + "definition" : { + "val" : "A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "aneusomic chromosomal subregion/segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Aneusomic chromosomal parts are examples of \"partial aneuploidy\" as described in http://en.wikipedia.org/wiki/Aneuploidy: \"The terms \"partial monosomy\" and \"partial trisomy\" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "partial aneusomic chromosomal element" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "aneuploid chromosomal segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism." + } ] + }, + "type" : "CLASS", + "lbl" : "aneusomic chromosomal part" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000207", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "simple sequence length polymorphism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "SSLP" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "simple sequence length variation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000207" + } ] + }, + "type" : "CLASS", + "lbl" : "simple_sequence_length_variation" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000108", + "meta" : { + "definition" : { + "val" : "A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "physical genome" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements.\n\nNote that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome." + } ] + }, + "type" : "CLASS", + "lbl" : "material genome" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mass of this piece of gold." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the length of the circumference of your waist" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of your nose" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the color of a tomato" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the ambient temperature of this portion of air" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of your nostril" + } ] + }, + "type" : "CLASS", + "lbl" : "quality" + }, { + "id" : "http://purl.org/oban/association_has_predicate", + "type" : "PROPERTY", + "lbl" : "association has predicate" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "type" : "PROPERTY", + "lbl" : "starts during" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "type" : "PROPERTY", + "lbl" : "ends during" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "meta" : { + "definition" : { + "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the life of an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the flight of a bird" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of cell-division, \\ a beating of the heart" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of sleeping" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of meiosis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "your process of aging." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the course of a disease" + } ] + }, + "type" : "CLASS", + "lbl" : "process" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the cell wall is disposed to filter chemicals in endocitosis and exocitosis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an atom of element X has the disposition to decay to an atom of element Y" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "children are innately disposed to categorize objects in certain ways." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "certain people have a predisposition to colon cancer" + } ] + }, + "type" : "CLASS", + "lbl" : "disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of your reproductive organs" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of your blood to coagulate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of this piece of metal to conduct electricity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of being a doctor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of this boundary to delineate where Utah and Colorado meet" + } ] + }, + "type" : "CLASS", + "lbl" : "realizable entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000382", + "meta" : { + "definition" : { + "val" : "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_variant_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000140", + "type" : "CLASS", + "lbl" : "non-heritable" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000142", + "meta" : { + "definition" : { + "val" : "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000141", + "meta" : { + "definition" : { + "val" : "The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/NCIT_C45827" + }, { + "val" : "http://purl.obolibrary.org/obo/HP_0000005" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, \"genetic context\" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. \n\nThese genetic and environmental \"interactions\" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "mode of inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "phenotypic inheritance pattern" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family." + } ] + }, + "type" : "CLASS", + "lbl" : "inheritance pattern" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000383", + "type" : "PROPERTY", + "lbl" : "is_variant_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000137", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "no-call zygosity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indeterminite zygosity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unknown zygosity" + } ] + }, + "type" : "CLASS", + "lbl" : "unspecified zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000499", + "meta" : { + "definition" : { + "val" : "A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "minor allele" + } ] + }, + "type" : "CLASS", + "lbl" : "minor polymorphic allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000136", + "type" : "CLASS", + "lbl" : "homozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000139", + "type" : "CLASS", + "lbl" : "heritable" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000017", + "meta" : { + "definition" : { + "val" : "A sequence that serves as a standard against which other sequences at the same location are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "reference sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000138", + "meta" : { + "definition" : { + "val" : "The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells).\n\nWe can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms." + } ] + }, + "type" : "CLASS", + "lbl" : "heritabililty" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000133", + "meta" : { + "definition" : { + "val" : "An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://semanticscience.org/resource/SIO_001263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "derived from https://en.wikipedia.org/wiki/Zygosity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allelic state" + } ] + }, + "type" : "CLASS", + "lbl" : "zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000495", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "expression construct feature" + } ] + }, + "type" : "CLASS", + "lbl" : "expression construct" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000132", + "meta" : { + "definition" : { + "val" : "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "in trans" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000253", + "type" : "PROPERTY", + "lbl" : "obsolete_is_specified_by" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000014", + "meta" : { + "definition" : { + "val" : "A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene)", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0001023 ! allele" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The \"mn004Gt\" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome.\n\nhttp://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722\n\nhttp://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion.\n\nA genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment).\n\nThis design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not." + } ] + }, + "type" : "CLASS", + "lbl" : "gene allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000498", + "meta" : { + "definition" : { + "val" : "A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "major allele" + } ] + }, + "type" : "CLASS", + "lbl" : "major polymorphic allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000135", + "type" : "CLASS", + "lbl" : "heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000134", + "type" : "CLASS", + "lbl" : "hemizygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000497", + "meta" : { + "definition" : { + "val" : "An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "PMID: 25741868 ACMG Guidelines" + } ] + }, + "type" : "CLASS", + "lbl" : "polymorphic allele" + }, { + "id" : "http://purl.org/oban/association_has_object", + "type" : "PROPERTY", + "lbl" : "association has object" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000019", + "meta" : { + "definition" : { + "val" : "a collection more than one sequence features (ie a collection of discontinuous sequence features)", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one)" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence feature collection" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000110", + "meta" : { + "definition" : { + "val" : "Any extent of continuous biological sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", + "meta" : { + "definition" : { + "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a spatial region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a leg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an orchestra." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an atom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a heart" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the bottom right portion of a human torso" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the interior of your mouth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a chair" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a molecule" + } ] + }, + "type" : "CLASS", + "lbl" : "independent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000492", + "meta" : { + "definition" : { + "val" : "A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "mutation" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000491", + "meta" : { + "definition" : { + "val" : "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required for any specific use case at this point so removed for simplicity. \nFormely asserted as allele and inferred as varaint allele. \nEq class definition:\nallele\n and (mutation or ('has subsequence' some mutation))" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_mutant allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000010", + "meta" : { + "definition" : { + "val" : "A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "OBI:genetic population background information" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic background" + } ] + }, + "type" : "CLASS", + "lbl" : "background genome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000494", + "meta" : { + "definition" : { + "val" : "A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "episomal replicon" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'." + } ] + }, + "type" : "CLASS", + "lbl" : "extrachromosomal replicon" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000252", + "type" : "PROPERTY", + "lbl" : "is_subject_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000131", + "meta" : { + "definition" : { + "val" : "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "in cis" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000251", + "type" : "PROPERTY", + "lbl" : "is_sequence_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000368", + "meta" : { + "definition" : { + "val" : "A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Exploratory/temporary property, as we formalize our phenotypic inheritance model." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_participates_in_inheritance_process" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "meta" : { + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/CARO_0000000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies." + } ] + }, + "type" : "CLASS", + "lbl" : "anatomical entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000125", + "meta" : { + "definition" : { + "val" : "sequence attribute that can inhere only in a collection of more than one sequence features", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence feature collection attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000488", + "meta" : { + "definition" : { + "val" : "A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways).", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_expression_variant_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000248", + "meta" : { + "definition" : { + "val" : "An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://semanticscience.org/resource/SIO_000093" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_proper_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/CLO_0000031", + "meta" : { + "definition" : { + "val" : "A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "cell line" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000243", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_approximates_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000484", + "type" : "INDIVIDUAL", + "lbl" : "exploratory term" + }, { + "id" : "http://biohackathon.org/resource/faldo#Position", + "meta" : { + "definition" : { + "val" : "Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "FALDO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region)." + } ] + }, + "type" : "CLASS", + "lbl" : "Position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000000", + "meta" : { + "definition" : { + "val" : "A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sex-agnostic intrinsic genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "organismal genotype" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Example zebrafish intrinsic genotype:\n\nGenotype = fgf8a; shha (AB)\nreference component (genomic background) = AB \nvariant component ('genomic variation complement') = fgf8a; shha\n\n. . . and within this variant component, there are two 'variant single locus complements' represented:\n\nallele complement 1 = fgf8a\nallele complement 2 = shha\n\nand within each of these 'variant single locus complements' there is one or more variant gene locus member:\n\nin complement 1: fgf8a\nin complement 2: shha" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genotype" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic genotype (sex-agnostic)" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000242", + "meta" : { + "definition" : { + "val" : "A relationship between an information content entity representing a specification, and the entity it specifies.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A geno:intrinnsic genotype 'specifies' a SO:genome.\nA geno:karyotype 'specifies' a geno:karyotype feature collection." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_specifies" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000002", + "meta" : { + "definition" : { + "val" : "An allele that varies in it sequence from what is considered the reference or canonical sequence at that location.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variant feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence-variant feature" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another.\n\nA variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "alternate allele" + } ] + }, + "type" : "CLASS", + "lbl" : "variant allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000486", + "meta" : { + "definition" : { + "val" : "A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_variant_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000244", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_resolves_to_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Julius Caesar" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Verdi’s Requiem" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the Second World War" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "your body mass index" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" + } ] + }, + "type" : "CLASS", + "lbl" : "entity" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000002", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" + } ] + }, + "type" : "CLASS", + "lbl" : "continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." + } ] + }, + "type" : "CLASS", + "lbl" : "occurrent" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000009", + "meta" : { + "definition" : { + "val" : "A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation.\n\nIn model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene))." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic variation complement" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000105", + "meta" : { + "definition" : { + "val" : "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome arm" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000143", + "meta" : { + "definition" : { + "val" : "A region of known length which may be used to manufacture a longer region.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_assembly_component" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000164", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "objective is to insert some specified sequence into the genome of a cell or virus" + } ] + }, + "type" : "CLASS", + "lbl" : "genetic insertion technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000042", + "meta" : { + "definition" : { + "val" : "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "hemizygous reference junction" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction.\n\nThe junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reference junction" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000160", + "type" : "CLASS", + "lbl" : "unspecified life cycle stage" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000037", + "meta" : { + "definition" : { + "val" : "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class def: 'genomic feature'\n and (has_sequence_attribute some unspecified)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_unspecified feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000033", + "meta" : { + "definition" : { + "val" : "A genome that varies at one or more loci from the sequence of some reference genome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here)" + } ] + }, + "type" : "CLASS", + "lbl" : "variant genome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000036", + "meta" : { + "definition" : { + "val" : "An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.\n\nIn model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared." + } ] + }, + "type" : "CLASS", + "lbl" : "reference allele" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of a hammer to drive in nails" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of amylase in saliva to break down starch into sugar" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" + } ] + }, + "type" : "CLASS", + "lbl" : "function" + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions.\n\n2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class \"system\". The relation \"environed_by\" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised." + } ] + }, + "type" : "CLASS", + "lbl" : "environmental system" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000031", + "meta" : { + "definition" : { + "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." + } ] + }, + "type" : "CLASS", + "lbl" : "generically dependent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000393", + "type" : "CLASS", + "lbl" : "trisomic homozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000030", + "meta" : { + "definition" : { + "val" : "A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variant allelic complement" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members.\n\nNote that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant." + } ] + }, + "type" : "CLASS", + "lbl" : "variant single locus complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000392", + "type" : "CLASS", + "lbl" : "aneusomic zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000150", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "duplicate term, use GENO:0000148" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_autosomal recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000394", + "type" : "CLASS", + "lbl" : "trisomic heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000152", + "meta" : { + "definition" : { + "val" : "An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another." + } ] + }, + "type" : "CLASS", + "lbl" : "reference" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000391", + "type" : "CLASS", + "lbl" : "disomic zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000148", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "autosomal recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000147", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0000006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "vertical inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000029", + "meta" : { + "definition" : { + "val" : "A single locus complement that serves as a standard against which 'variant' sequences are compared", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference allelic complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference single locus feature complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'single locus complement'\n and (has_sequence_attribute some reference)\n\nSC axioms:\n'has member' exactly 0 'variant allele'\n'has member' only 'reference genomic feature'\n'has member' some 'reference genomic feature'" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reference single locus complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000149", + "meta" : { + "definition" : { + "val" : "An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001419" + } ] + }, + "type" : "CLASS", + "lbl" : "X-linked recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000144", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "pure dominant inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "complete autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000022", + "meta" : { + "definition" : { + "val" : "A sequence feature collection comprised of discontiguous sequences from a single genome", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic feature collection" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_genomic feature collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000143", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "co-dominant autosomal inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000385", + "meta" : { + "definition" : { + "val" : "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_reference_sequence_part" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_reference_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000146", + "meta" : { + "definition" : { + "val" : "An X-linked inheritance pattern wherein the trait manifests in heterozygotes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001423" + } ] + }, + "type" : "CLASS", + "lbl" : "X-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000145", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "intermediate dominant autosomal inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "semi-dominant autosomal inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "incomplete autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000387", + "type" : "PROPERTY", + "lbl" : "is_reference_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001218", + "meta" : { + "definition" : { + "val" : "An insertion that derives from another organism, via the use of recombinant DNA technology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001218" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "transgenic insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "transgenic_insertion" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000023", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the priest role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a boundary to demarcate two neighboring administrative territories" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a stone in marking a property boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the student role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a building in serving as a military target" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of subject in a clinical trial" + } ] + }, + "type" : "CLASS", + "lbl" : "role" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0000755", + "type" : "CLASS", + "lbl" : "abnormal(ly) disrupted diencephalon development" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000020", + "meta" : { + "definition" : { + "val" : "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "of one-sided specifically dependent continuants: the mass of this tomato" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the pink color of a medium rare piece of grilled filet mignon at its center" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the smell of this portion of mozzarella" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of this heart: to pump blood" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of this hole." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of being a doctor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of this fish to decay" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mutual dependence of proton donors and acceptors in chemical reactions [79" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." + }, { + "pred" : 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"http://purl.obolibrary.org/obo/GENO_0000902" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000830", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000481" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000248", + "fillerId" : "http://purl.obolibrary.org/obo/SO_0000340" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000777", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000899" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000219", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000033" + } ] + } ], + "domainRangeAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002200", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002201", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000251", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" + } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000368", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000141" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000610", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000036" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000653", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000501" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000359", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000641", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000652", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000497" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000651", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000491" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000959", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000903", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000815" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000958", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000408", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000481" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000608", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000516" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000133" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000966", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000815" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000239", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000726", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000957", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000815" ] + } ], + "propertyChainAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000449", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000418", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000418" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000445", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000639", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/GENO_0000639" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000418", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/GENO_0000418" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000211", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000053", "http://purl.obolibrary.org/obo/RO_0000059" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000449", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000742", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000408" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000445", "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000445", "http://purl.obolibrary.org/obo/RO_0003303" ] + } ] + } ] +} \ No newline at end of file diff --git a/geno-base.obo b/geno-base.obo new file mode 100644 index 0000000..d56018f --- /dev/null +++ b/geno-base.obo @@ -0,0 +1,3922 @@ +format-version: 1.2 +data-version: geno/releases/2019-09-09/geno-base.owl +ontology: geno/geno-base +property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string +property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string +property_value: http://purl.org/dc/terms/license "Unspecified" xsd:string + +[Term] +id: BFO:0000001 +name: entity +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +is_a: BFO:0000001 ! entity +property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] +is_a: BFO:0000002 ! continuant +property_value: IAO:0000112 "a chair" xsd:string +property_value: IAO:0000112 "a heart" xsd:string +property_value: IAO:0000112 "a leg" xsd:string +property_value: IAO:0000112 "a molecule" xsd:string +property_value: IAO:0000112 "a spatial region" xsd:string +property_value: IAO:0000112 "an atom" xsd:string +property_value: IAO:0000112 "an orchestra." xsd:string +property_value: IAO:0000112 "an organism" xsd:string +property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string +property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] +is_a: BFO:0000003 ! occurrent +property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string +property_value: IAO:0000112 "a process of meiosis" xsd:string +property_value: IAO:0000112 "a process of sleeping" xsd:string +property_value: IAO:0000112 "the course of a disease" xsd:string +property_value: IAO:0000112 "the flight of a bird" xsd:string +property_value: IAO:0000112 "the life of an organism" xsd:string +property_value: IAO:0000112 "your process of aging." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role +property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string +property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string +property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string +property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocitosis and exocitosis" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89" xsd:string +property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000017 +name: realizable entity +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality +property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string +property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string +property_value: IAO:0000112 "the function of your reproductive organs" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string +property_value: IAO:0000112 "the color of a tomato" xsd:string +property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string +property_value: IAO:0000112 "the mass of this piece of gold." xsd:string +property_value: IAO:0000112 "the shape of your nose" xsd:string +property_value: IAO:0000112 "the shape of your nostril" xsd:string +property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] +is_a: BFO:0000002 ! continuant +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string +property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000023 +name: role +is_a: BFO:0000017 ! realizable entity +property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string +property_value: IAO:0000112 "the priest role" xsd:string +property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string +property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string +property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string +property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string +property_value: IAO:0000112 "the student role" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string +property_value: IAO:0000600 "b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] +is_a: BFO:0000002 ! continuant +property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition +property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string +property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string +property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string +property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +is_a: BFO:0000004 ! independent continuant +property_value: IAO:0000112 "a flame" xsd:string +property_value: IAO:0000112 "a forest fire" xsd:string +property_value: IAO:0000112 "a human being" xsd:string +property_value: IAO:0000112 "a hurricane" xsd:string +property_value: IAO:0000112 "a photon" xsd:string +property_value: IAO:0000112 "a puff of smoke" xsd:string +property_value: IAO:0000112 "a sea wave" xsd:string +property_value: IAO:0000112 "a tornado" xsd:string +property_value: IAO:0000112 "an aggregate of human beings." xsd:string +property_value: IAO:0000112 "an energy wave" xsd:string +property_value: IAO:0000112 "an epidemic" xsd:string +property_value: IAO:0000112 "the undetached arm of a human being" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BothStrandsPosition +name: Both strands +is_a: StrandedPosition ! Stranded position + +[Term] +id: CHEBI:23367 +name: molecular entity +is_a: BFO:0000040 ! material entity +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology." xsd:string + +[Term] +id: CHEBI:33696 +name: nucleic acid +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CL:0000000 +name: cell +comment: Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies. +is_a: UBERON:0001062 ! anatomical entity + +[Term] +id: CLO:0000031 +name: cell line +def: "A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture)." [] +is_a: BFO:0000040 ! material entity +relationship: RO:0001000 OBI:0100026 ! derives from organism + +[Term] +id: ENVO:01000254 +name: environmental system +comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. +is_a: BFO:0000040 ! material entity +property_value: IAO:0000116 "1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions.\n\n2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity)." xsd:string + +[Term] +id: ERO:0000007 +name: technique +def: "A technique is a planned process used to accomplish a specific activity or task." [] +is_a: OBI:0000011 ! planned process + +[Term] +id: ERO:0002002 +name: embryonic stem cell line +def: "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo." [] +is_a: ERO:0002003 ! stem cell line + +[Term] +id: ERO:0002003 +name: stem cell line +def: "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types." [] +is_a: CLO:0000031 ! cell line + +[Term] +id: ExactPosition +name: Exact position +def: "A position that is exactly known." [] +is_a: Position ! Position + +[Term] +id: ForwardStrandPosition +name: Positive strand +is_a: StrandedPosition ! Stranded position + +[Term] +id: GENO:0000000 +name: genomic genotype (sex-agnostic) +def: "A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement)" [] +comment: In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances). +is_a: GENO:0000899 ! genomic genotype +property_value: IAO:0000112 "Example zebrafish intrinsic genotype:\n\nGenotype = fgf8a; shha (AB)\nreference component (genomic background) = AB \nvariant component ('genomic variation complement') = fgf8a; shha\n\n. . . and within this variant component, there are two 'variant single locus complements' represented:\n\nallele complement 1 = fgf8a\nallele complement 2 = shha\n\nand within each of these 'variant single locus complements' there is one or more variant gene locus member:\n\nin complement 1: fgf8a\nin complement 2: shha" xsd:string +property_value: IAO:0000116 "This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype." xsd:string +property_value: IAO:0000118 "genotype" xsd:string +property_value: IAO:0000118 "organismal genotype" xsd:string +property_value: IAO:0000118 "sex-agnostic intrinsic genotype" xsd:string + +[Term] +id: GENO:0000002 +name: variant allele +def: "An allele that varies in it sequence from what is considered the reference or canonical sequence at that location." [] +comment: Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another.\n\nA variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence. +intersection_of: GENO:0000512 ! allele +intersection_of: GENO:0000683 GENO:0000036 ! varies_with reference allele +property_value: IAO:0000116 "The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles." xsd:string +property_value: IAO:0000118 "alternate allele" xsd:string +property_value: IAO:0000118 "sequence-variant feature" xsd:string +property_value: IAO:0000118 "variant feature" xsd:string + +[Term] +id: GENO:0000009 +name: genomic variation complement +def: "A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation.\n\nIn model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)). +intersection_of: GENO:0000660 ! genomic feature set +intersection_of: GENO:0000382 GENO:0000030 ! has_variant_part variant single locus complement +property_value: IAO:0000116 "Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases." xsd:string + +[Term] +id: GENO:0000010 +name: background genome +def: "A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations)." [] +xref: OBI:genetic population background information +is_a: GENO:0000914 ! reference genome +property_value: IAO:0000112 "The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB)" xsd:string +property_value: IAO:0000116 "Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it." xsd:string +property_value: IAO:0000118 "genomic background" xsd:string + +[Term] +id: GENO:0000014 +name: gene allele +def: "A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene)" [] +comment: In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion.\n\nA genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene. +xref: http://purl.obolibrary.org/obo/SO_0001023 ! allele +is_a: GENO:0000512 ! allele +relationship: GENO:0000408 SO:0000704 ! is_allele_of gene +property_value: IAO:0000112 "The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The \"mn004Gt\" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome.\n\nhttp://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722\n\nhttp://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8" xsd:string +property_value: IAO:0000116 "Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment).\n\nThis design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not." xsd:string + +[Term] +id: GENO:0000017 +name: reference sequence +def: "A sequence that serves as a standard against which other sequences at the same location are compared." [] +comment: A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence. +intersection_of: GENO:0000702 ! biological sequence +intersection_of: RO:0000087 GENO:0000152 ! has_role reference +property_value: IAO:0000116 "The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant." xsd:string +property_value: IAO:0000118 "reference sequence" xsd:string + +[Term] +id: GENO:0000019 +name: obsolete_sequence feature collection +def: "a collection more than one sequence features (ie a collection of discontinuous sequence features)" [] +comment: 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. +xref: perhaps not same as SO:sequence collection\, as here we explicitly include features that can have an extent of zero (and SO\:sequence collection is a collection of regions that have an extent of at least one) +is_a: ObsoleteClass + +[Term] +id: GENO:0000022 +name: obsolete_genomic feature collection +def: "A sequence feature collection comprised of discontiguous sequences from a single genome" [] +comment: Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. +is_a: ObsoleteClass +property_value: IAO:0000116 "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system." xsd:string +property_value: IAO:0000118 "genomic feature collection" xsd:string + +[Term] +id: GENO:0000029 +name: obsolete_reference single locus complement +def: "A single locus complement that serves as a standard against which 'variant' sequences are compared" [] +is_a: ObsoleteClass +property_value: IAO:0000118 "reference allelic complement" xsd:string +property_value: IAO:0000118 "reference single locus feature complement" xsd:string +property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'single locus complement'\n and (has_sequence_attribute some reference)\n\nSC axioms:\n'has member' exactly 0 'variant allele'\n'has member' only 'reference genomic feature'\n'has member' some 'reference genomic feature'" xsd:string + +[Term] +id: GENO:0000030 +name: variant single locus complement +def: "A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13)." [] +comment: Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members.\n\nNote that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant. +intersection_of: GENO:0000516 ! single locus complement +intersection_of: GENO:0000382 GENO:0000002 ! has_variant_part variant allele +property_value: IAO:0000118 "variant allelic complement" xsd:string + +[Term] +id: GENO:0000033 +name: variant genome +def: "A genome that varies at one or more loci from the sequence of some reference genome." [] +xref: http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here) +intersection_of: SO:0001026 ! genome +intersection_of: GENO:0000683 GENO:0000914 ! varies_with reference genome +relationship: GENO:0000382 SO:0001059 ! has_variant_part sequence_alteration + +[Term] +id: GENO:0000036 +name: reference allele +def: "An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome." [] +comment: Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.\n\nIn model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared. +intersection_of: GENO:0000512 ! allele +intersection_of: RO:0000087 GENO:0000152 ! has_role reference + +[Term] +id: GENO:0000037 +name: obsolete_unspecified feature +def: "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus)." [] +comment: An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). +is_a: ObsoleteClass +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '." xsd:string +property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class def: 'genomic feature'\n and (has_sequence_attribute some unspecified)" xsd:string + +[Term] +id: GENO:0000042 +name: obsolete_reference junction +def: "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature." [] +comment: In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction.\n\nThe junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. +is_a: ObsoleteClass +property_value: IAO:0000118 "hemizygous reference junction" xsd:string +property_value: IAO:0000231 "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" xsd:string + +[Term] +id: GENO:0000047 +name: danio rerio gene +def: "A gene that originates from the genome of a danio rerio." [] +intersection_of: SO:0000704 ! gene +intersection_of: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio + +[Term] +id: GENO:0000054 +name: homo sapiens gene +def: "A gene that originates from the genome of a homo sapiens." [] +intersection_of: SO:0000704 ! gene +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens + +[Term] +id: GENO:0000057 +name: mus musculus gene +def: "A gene that originates from the genome of a mus musculus." [] +intersection_of: SO:0000704 ! gene +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus + +[Term] +id: GENO:0000060 +name: obsolete_reference gene allele +def: "A version/allele of a gene that serves as a standard against which variant genes are compared." [] +comment: Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. +is_a: ObsoleteClass +property_value: IAO:0000112 "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development.\nhttp://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690\n\nNote that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469" xsd:string +property_value: IAO:0000118 "reference gene" xsd:string +property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" xsd:string + +[Term] +id: GENO:0000091 +name: obsolete_experimental insertion +is_a: ObsoleteClass + +[Term] +id: GENO:0000092 +name: gene trap insertion +is_a: SO:0000667 ! insertion +relationship: RO:0002353 GENO:0000172 ! output of gene trapping technique + +[Term] +id: GENO:0000093 +name: integrated transgene +def: "A transgene that has been integrated into a chrromosome in the host genome." [] +comment: An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion.\n\nAn 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome. +is_a: SO:0000902 ! transgene +relationship: BFO:0000050 SO:0001218 ! is part of transgenic_insertion + +[Term] +id: GENO:0000106 +name: genomic material +def: "A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny." [] +comment: 1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms. +is_a: GENO:0000482 ! genetic material +relationship: BFO:0000050 GENO:0000108 ! is part of material genome +relationship: RO:0000091 GENO:0000139 ! has disposition heritable +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way." xsd:string + +[Term] +id: GENO:0000108 +name: material genome +def: "A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion." [] +comment: A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements.\n\nNote that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome. +is_a: BFO:0000040 ! material entity +property_value: IAO:0000118 "physical genome" xsd:string + +[Term] +id: GENO:0000111 +name: human population +def: "a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)" [] +is_a: OBI:0000181 ! population +property_value: IAO:0000116 "Consider http://semanticscience.org/resource/SIO_001062 ! human population (\"A human population refers to a collection of human beings\")." xsd:string +property_value: IAO:0000118 "homo sapiens population" xsd:string + +[Term] +id: GENO:0000112 +name: strain or breed +def: "A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical." [] +comment: Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR) +is_a: GENO:0000113 ! taxonomic group +relationship: RO:0002162 OBI:0100026 ! in taxon organism +property_value: IAO:0000118 "organism strain or breed" xsd:string + +[Term] +id: GENO:0000113 +name: taxonomic group +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000116 "A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon)" xsd:string + +[Term] +id: GENO:0000118 +name: mus musculus strain +is_a: GENO:0000112 ! strain or breed + +[Term] +id: GENO:0000119 +name: danio rerio strain +is_a: GENO:0000112 ! strain or breed +relationship: RO:0002351 NCBITaxon:7955 ! has member Danio rerio +relationship: RO:0002351 NCBITaxon:7955 ! has member Danio rerio + +[Term] +id: GENO:0000125 +name: obsolete_sequence feature collection attribute +def: "sequence attribute that can inhere only in a collection of more than one sequence features" [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000131 +name: in cis +def: "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes)." [] +is_a: GENO:0000886 ! allelic phase + +[Term] +id: GENO:0000132 +name: in trans +def: "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes)." [] +is_a: GENO:0000886 ! allelic phase + +[Term] +id: GENO:0000133 +name: zygosity +def: "An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different)." [] +xref: http://semanticscience.org/resource/SIO_001263 +is_a: GENO:0000875 ! allelic state +relationship: RO:0000052 GENO:0000516 ! inheres_in single locus complement +property_value: IAO:0000118 "allelic state" xsd:string +property_value: IAO:0000119 "derived from https://en.wikipedia.org/wiki/Zygosity" xsd:string + +[Term] +id: GENO:0000134 +name: hemizygous +is_a: GENO:0000391 ! disomic zygosity + +[Term] +id: GENO:0000135 +name: heterozygous +is_a: GENO:0000391 ! disomic zygosity + +[Term] +id: GENO:0000136 +name: homozygous +is_a: GENO:0000391 ! disomic zygosity + +[Term] +id: GENO:0000137 +name: unspecified zygosity +is_a: GENO:0000133 ! zygosity +property_value: IAO:0000118 "indeterminite zygosity" xsd:string {comment="MGI uses this term when zygosity is not known."} +property_value: IAO:0000118 "no-call zygosity" xsd:string {comment="(this is how the GVF10 format/standard refers to loci without enough data to make an accurate call . . . see http://www.sequenceontology.org/resources/gvf.html#quick_gvf_examples)"} +property_value: IAO:0000118 "unknown zygosity" xsd:string + +[Term] +id: GENO:0000138 +name: heritabililty +def: "The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event." [] +comment: We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells).\n\nWe can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms. +is_a: BFO:0000016 ! disposition + +[Term] +id: GENO:0000139 +name: heritable +is_a: GENO:0000138 ! heritabililty + +[Term] +id: GENO:0000140 +name: non-heritable +is_a: GENO:0000138 ! heritabililty + +[Term] +id: GENO:0000141 +name: inheritance pattern +def: "The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment." [] +comment: An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, "genetic context" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. \n\nThese genetic and environmental "interactions" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y. +xref: http://purl.obolibrary.org/obo/HP_0000005 +xref: http://purl.obolibrary.org/obo/NCIT_C45827 +is_a: BFO:0000016 ! disposition +property_value: IAO:0000116 "The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family." xsd:string +property_value: IAO:0000118 "mode of inheritance" xsd:string +property_value: IAO:0000118 "phenotypic inheritance pattern" xsd:string + +[Term] +id: GENO:0000142 +name: obsolete_dominant inheritance +def: "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes" [] +is_a: ObsoleteClass +property_value: IAO:0000231 "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." xsd:string + +[Term] +id: GENO:0000143 +name: co-dominant autosomal inheritance +def: "An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." [] +is_a: GENO:0000147 ! autosomal dominant inheritance + +[Term] +id: GENO:0000144 +name: complete autosomal dominant inheritance +def: "An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." [] +is_a: GENO:0000147 ! autosomal dominant inheritance +property_value: IAO:0000118 "pure dominant inheritance" xsd:string + +[Term] +id: GENO:0000145 +name: incomplete autosomal dominant inheritance +def: "An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." [] +is_a: GENO:0000147 ! autosomal dominant inheritance +property_value: IAO:0000118 "intermediate dominant autosomal inheritance" xsd:string +property_value: IAO:0000118 "semi-dominant autosomal inheritance" xsd:string + +[Term] +id: GENO:0000146 +name: X-linked dominant inheritance +def: "An X-linked inheritance pattern wherein the trait manifests in heterozygotes." [] +xref: http://purl.obolibrary.org/obo/HP_0001423 +is_a: GENO:0000936 ! X-linked inheritance + +[Term] +id: GENO:0000147 +name: autosomal dominant inheritance +def: "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes." [] +xref: http://purl.obolibrary.org/obo/HP_0000006 +is_a: GENO:0000934 ! autosomal inheritance +property_value: IAO:0000118 "vertical inheritance" xsd:string + +[Term] +id: GENO:0000148 +name: autosomal recessive inheritance +def: "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals." [] +is_a: GENO:0000934 ! autosomal inheritance + +[Term] +id: GENO:0000149 +name: X-linked recessive inheritance +def: "An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals." [] +xref: http://purl.obolibrary.org/obo/HP_0001419 +is_a: GENO:0000936 ! X-linked inheritance + +[Term] +id: GENO:0000150 +name: obsolete_autosomal recessive inheritance +is_a: ObsoleteClass +property_value: IAO:0000231 "duplicate term, use GENO:0000148" xsd:string + +[Term] +id: GENO:0000152 +name: reference +def: "An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared." [] +comment: Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another. +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000160 +name: unspecified life cycle stage +is_a: UBERON:0000105 ! life cycle stage + +[Term] +id: GENO:0000164 +name: genetic insertion technique +comment: objective is to insert some specified sequence into the genome of a cell or virus +is_a: OBI:0600043 ! genetic modification technique + +[Term] +id: GENO:0000165 +name: mutagen treatment technique +is_a: OBI:0600043 ! genetic modification technique + +[Term] +id: GENO:0000166 +name: targeted gene mutation technique +def: "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping)." [] +comment: This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. +is_a: OBI:0600043 ! genetic modification technique +relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele + +[Term] +id: GENO:0000169 +name: random genetic insertion technique +comment: Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. +is_a: GENO:0000164 ! genetic insertion technique + +[Term] +id: GENO:0000170 +name: targeted genetic insertion technique +is_a: GENO:0000164 ! genetic insertion technique +relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele + +[Term] +id: GENO:0000171 +name: enhancer trapping technique +is_a: GENO:0000170 ! targeted genetic insertion technique +relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele + +[Term] +id: GENO:0000172 +name: gene trapping technique +is_a: GENO:0000170 ! targeted genetic insertion technique +relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele + +[Term] +id: GENO:0000173 +name: promoter trapping technique +is_a: GENO:0000170 ! targeted genetic insertion technique +relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele + +[Term] +id: GENO:0000174 +name: targeted knock-in technique +is_a: GENO:0000170 ! targeted genetic insertion technique +relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele + +[Term] +id: GENO:0000175 +name: random transgene insertion technique +is_a: GENO:0000169 ! random genetic insertion technique + +[Term] +id: GENO:0000324 +name: obsolete_chromosome complement +def: "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome" [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000338 +name: gained aneusomic chromosome +def: "A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation" [] +comment: This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome. +is_a: GENO:0000346 ! aneusomic chromosome +relationship: GENO:0000207 GENO:0000685 ! has_sequence_attribute novel +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "duplicate chromosome" xsd:string + +[Term] +id: GENO:0000339 +name: lost aneusomic chromosome +def: "A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation." [] +is_a: GENO:0000346 ! aneusomic chromosome +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as \"the point at which one or more contiguous nucleotides were excised\"." xsd:string +property_value: IAO:0000118 "absent aneusomic chromosome" xsd:string + +[Term] +id: GENO:0000343 +name: aneusomic chromosomal part +def: "A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation." [] +comment: Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome." +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000207 GENO:0000513 ! has_sequence_attribute aneusomic +relationship: GENO:0000248 SO:0000340 ! is_proper_part_of chromosome +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism." xsd:string +property_value: IAO:0000118 "aneuploid chromosomal segment" xsd:string +property_value: IAO:0000118 "aneusomic chromosomal subregion/segment" xsd:string +property_value: IAO:0000118 "partial aneusomic chromosomal element" xsd:string + +[Term] +id: GENO:0000344 +name: gained aneusomic chromosomal segment +def: "A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event." [] +comment: Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location. +is_a: GENO:0000343 ! aneusomic chromosomal part +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "duplicate partial aneuploid chromosomal element" xsd:string +property_value: IAO:0000118 "translocated duplicate chromosomal element" xsd:string +property_value: IAO:0000118 "translocated duplicate chromosomal segment" xsd:string + +[Term] +id: GENO:0000345 +name: lost aneusomic chromosomal segment +def: "A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome." [] +comment: This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome.\n\nLoss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus. +is_a: GENO:0000343 ! aneusomic chromosomal part +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement" xsd:string +property_value: IAO:0000118 "dropped partial anneuploid chromosomal element" xsd:string +property_value: IAO:0000118 "translocated absent chromosomal segment" xsd:string +property_value: IAO:0000118 "truncated chromosome terminus" xsd:string + +[Term] +id: GENO:0000346 +name: aneusomic chromosome +def: "A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation" [] +comment: Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism.\n\nSimilarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication. +is_a: SO:0000340 ! chromosome +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000207 GENO:0000513 ! has_sequence_attribute aneusomic +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "complete aneusomic chromosome" xsd:string + +[Term] +id: GENO:0000351 +name: biological process +is_a: BFO:0000015 ! process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of biological processes from GO-BP." xsd:string + +[Term] +id: GENO:0000391 +name: disomic zygosity +is_a: GENO:0000133 ! zygosity + +[Term] +id: GENO:0000392 +name: aneusomic zygosity +is_a: GENO:0000133 ! zygosity + +[Term] +id: GENO:0000393 +name: trisomic homozygous +is_a: GENO:0000392 ! aneusomic zygosity + +[Term] +id: GENO:0000394 +name: trisomic heterozygous +is_a: GENO:0000392 ! aneusomic zygosity + +[Term] +id: GENO:0000402 +name: compound heterozygous +def: "A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a/fgf8a)" [] +is_a: GENO:0000135 ! heterozygous +property_value: IAO:0000118 "trans-heterozygous" xsd:string + +[Term] +id: GENO:0000415 +name: obsolete_reagent sequence feature +def: "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)" [] +is_a: ObsoleteClass +property_value: IAO:0000116 "replaced with SO:engineered_region" xsd:string +property_value: IAO:0000118 "extra-genomic sequence" xsd:string + +[Term] +id: GENO:0000458 +name: simple heterozygous +comment: a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a) +is_a: GENO:0000135 ! heterozygous + +[Term] +id: GENO:0000460 +name: transgene part +def: "A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc)" [] +intersection_of: GENO:0000666 ! gene part +intersection_of: RO:0002525 SO:0000902 ! is subsequence of transgene + +[Term] +id: GENO:0000476 +name: variant +def: "An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level" [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000477 +name: polymorphic +def: "An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000480 +name: mutant +def: "An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000481 +name: genomic feature +def: "A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)" [] +comment: 1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. \n\n2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). \n\n3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome. +intersection_of: SO:0000110 ! sequence_feature +intersection_of: GENO:0000903 GENO:0000902 ! has_location genomic feature location +relationship: BFO:0000050 SO:0001026 ! is part of genome +relationship: GENO:0000239 GENO:0000960 ! has_sequence genomic sequence +relationship: RO:0002162 OBI:0100026 ! in taxon organism +property_value: IAO:0000116 "This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology." xsd:string + +[Term] +id: GENO:0000482 +name: genetic material +def: "A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion)." [] +comment: This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material. +is_a: CHEBI:33696 ! nucleic acid +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000491 +name: obsolete_mutant allele +def: "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain." [] +comment: 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. +is_a: ObsoleteClass +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000119 "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" xsd:string +property_value: IAO:0000231 "Not required for any specific use case at this point so removed for simplicity. \nFormely asserted as allele and inferred as varaint allele. \nEq class definition:\nallele\n and (mutation or ('has subsequence' some mutation))" xsd:string + +[Term] +id: GENO:0000492 +name: mutation +def: "A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain." [] +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000683 GENO:0000501 ! varies_with wild-type allele + +[Term] +id: GENO:0000494 +name: extrachromosomal replicon +def: "A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon)" [] +property_value: IAO:0000116 "Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element" xsd:string +property_value: IAO:0000118 "episomal replicon" xsd:string +property_value: IAO:0000231 "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'." xsd:string + +[Term] +id: GENO:0000495 +name: expression construct +is_a: GENO:0000856 ! engineered genetic construct +property_value: IAO:0000118 "expression construct feature" xsd:string + +[Term] +id: GENO:0000497 +name: polymorphic allele +def: "An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population." [] +comment: Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%). +is_a: GENO:0000512 ! allele +property_value: IAO:0000119 "PMID: 25741868 ACMG Guidelines" xsd:string + +[Term] +id: GENO:0000498 +name: major polymorphic allele +def: "A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location." [] +is_a: GENO:0000497 ! polymorphic allele +property_value: IAO:0000118 "major allele" xsd:string + +[Term] +id: GENO:0000499 +name: minor polymorphic allele +def: "A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location)." [] +is_a: GENO:0000497 ! polymorphic allele +property_value: IAO:0000118 "minor allele" xsd:string + +[Term] +id: GENO:0000500 +name: ancestral polymorphic allele +def: "A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree." [] +is_a: GENO:0000497 ! polymorphic allele +property_value: IAO:0000118 "ancestral allele" xsd:string + +[Term] +id: GENO:0000501 +name: wild-type allele +def: "An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared." [] +comment: 'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain.\n\nThe notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis. +is_a: GENO:0000512 ! allele +relationship: GENO:0000683 GENO:0000481 ! varies_with genomic feature +property_value: IAO:0000118 "wild-type allele" xsd:string + +[Term] +id: GENO:0000502 +name: wild-type gene +comment: A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation. +is_a: GENO:0000501 ! wild-type allele +is_a: SO:0000704 ! gene +property_value: IAO:0000118 "wild-type gene allele" xsd:string + +[Term] +id: GENO:0000504 +name: reagent targeted gene +def: "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." [] +comment: The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position. +is_a: GENO:0000529 ! expression-variant gene +relationship: GENO:0000231 GENO:0000534 ! has_proper_part reagent-targeted gene subregion +relationship: GENO:0000447 GENO:0000533 ! is_gene_target_of gene knockdown reagent + +[Term] +id: GENO:0000506 +name: transiently-expressed transgene +def: "A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome)." [] +is_a: GENO:0000529 ! expression-variant gene +property_value: IAO:0000118 "experimentally-expressed transgene" xsd:string +property_value: IAO:0000118 "extrinsic transgene" xsd:string + +[Term] +id: GENO:0000511 +name: wild-type +def: "An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000512 +name: allele +def: "One of a set of sequence features known to exist at a particular genomic location." [] +comment: An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations).\n\nAlleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence). +intersection_of: GENO:0000481 ! genomic feature +intersection_of: GENO:0000683 GENO:0000481 ! varies_with genomic feature +property_value: IAO:0000116 "A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene.\n\nTo be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene.\n \n[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17)\n[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17)\n[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17)\n[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17)\n[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17)\n[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17)\n[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483\n[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17)\n[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17)\n[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17)\n[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17)\n[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)" xsd:string +property_value: IAO:0000118 "variable feature" xsd:string + +[Term] +id: GENO:0000513 +name: aneusomic +def: "a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation." [] +is_a: GENO:0000773 ! variation attribute +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000515 +name: variant gene allele +def: "An allele of a gene that contains some sequence alteration." [] +comment: A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset. +intersection_of: GENO:0000014 ! gene allele +intersection_of: GENO:0000683 GENO:0000036 ! varies_with reference allele +relationship: GENO:0000382 SO:0001059 ! has_variant_part sequence_alteration +relationship: GENO:0000641 SO:0000704 ! is_variant_allele_of gene + +[Term] +id: GENO:0000516 +name: single locus complement +def: "A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes.\n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. +is_a: GENO:0000660 ! genomic feature set +property_value: IAO:0000112 "The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a.\n\nThe collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome." xsd:string +property_value: IAO:0000116 "TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label." xsd:string +property_value: IAO:0000118 "allelic complement" xsd:string +property_value: IAO:0000118 "homologous allele complement" xsd:string +property_value: IAO:0000118 "single locus feature complement" xsd:string + +[Term] +id: GENO:0000524 +name: extrinsic genotype +def: "A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state." [] +comment: An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment.\n\nThe 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations. +is_a: GENO:0000536 ! genotype +property_value: IAO:0000112 "In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as:\n\n shha; shhb\n\nThis notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct." xsd:string +property_value: IAO:0000116 "We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. \n\nOur rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. \n\nFinally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" xsd:string +property_value: IAO:0000118 "experimental genotype" xsd:string +property_value: IAO:0000118 "expression genotype" xsd:string + +[Term] +id: GENO:0000525 +name: effective genotype +def: "A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs)." [] +comment: An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment. +is_a: GENO:0000536 ! genotype +relationship: BFO:0000051 GENO:0000524 ! has part extrinsic genotype +relationship: BFO:0000051 GENO:0000719 ! has part intrinsic genotype +property_value: IAO:0000116 "Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" xsd:string + +[Term] +id: GENO:0000527 +name: reagent-targeted gene complement +def: "A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes)." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment. +is_a: GENO:0000715 ! qualified genomic feature set +relationship: RO:0002351 GENO:0000504 ! has member reagent targeted gene + +[Term] +id: GENO:0000528 +name: transiently-expressed transgene complement +def: "The set of all transgenes trransiently expressed in a biological system in the context of a given experiment." [] +is_a: GENO:0000715 ! qualified genomic feature set +relationship: GENO:0000382 GENO:0000506 ! has_variant_part transiently-expressed transgene +property_value: IAO:0000118 "experimental transgene complement" xsd:string + +[Term] +id: GENO:0000529 +name: expression-variant gene +def: "A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism)." [] +comment: Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism).\n\nThe identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system. +is_a: GENO:0000737 ! expression-qualified sequence feature +relationship: GENO:0000443 SO:0000704 ! is_expression_variant_of gene +property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes)." xsd:string +property_value: IAO:0000116 "See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself." xsd:string +property_value: IAO:0000118 "expression allele" xsd:string + +[Term] +id: GENO:0000533 +name: gene knockdown reagent +is_a: SO:0000804 ! engineered_region +property_value: IAO:0000118 "gene targeting reagent" xsd:string +property_value: IAO:0000118 "sequence targeting reagent" xsd:string + +[Term] +id: GENO:0000534 +name: reagent-targeted gene subregion +def: "A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent." [] +is_a: GENO:0000737 ! expression-qualified sequence feature +property_value: IAO:0000118 "targeted gene segment" xsd:string + +[Term] +id: GENO:0000536 +name: genotype +def: "A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference." [] +comment: 1. Scope of 'Genetic State': \n'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs.\n\n2. Genotype Subtypes:\nIn GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. \n\nTwo more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features.\n\n3. The Genotype Partonomy: \n'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a; fgf3[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements:\n\n - GVC: fgf8a; fgf3 (total intrinsic variation in the genome)\n - Genomic Background: AB (the reference against which the GVC is variant)\n - VSLC1: fgf8a (homozygous complement of gene alleles at one known variant locus)\n - VSLC2: fgf3 (heterozygous complement of gene alleles at another known variant locus)\n - Allele 1: fgf8a (variant version of the fgf8a gene, present in two copies)\n - Allele 2: fgf3 (variant version of the fgf3 gene, present in one copy)\n - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy)\n - Sequence Alteration1: (the specific mutation within the fgf8a gene that makes it variant)\n - Sequence Alteration2: (the specific mutation within the fgf3 gene that makes it variant)\n\nA graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md\n\nOne reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data. +is_a: IAO:0000030 ! information content entity +property_value: IAO:0000116 "As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above." xsd:string +property_value: IAO:0000119 "Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). \nNote however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO." xsd:string + +[Term] +id: GENO:0000575 +name: zebrafish phenotype +comment: ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl\nThis ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes. +is_a: UPHENO:0001001 ! Phenotype + +[Term] +id: GENO:0000602 +name: homoplasmic +def: "an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism." [] +is_a: GENO:0000918 ! organellar plasmy + +[Term] +id: GENO:0000603 +name: heteroplasmic +def: "an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism." [] +is_a: GENO:0000918 ! organellar plasmy + +[Term] +id: GENO:0000604 +name: hemizygous X-linked +is_a: GENO:0000134 ! hemizygous + +[Term] +id: GENO:0000605 +name: hemizygous Y-linked +is_a: GENO:0000134 ! hemizygous + +[Term] +id: GENO:0000606 +name: hemizygous insertion-linked +is_a: GENO:0000134 ! hemizygous + +[Term] +id: GENO:0000611 +name: genomic background +def: "A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations)." [] +intersection_of: GENO:0000899 ! genomic genotype +intersection_of: RO:0000087 GENO:0000152 ! has_role reference +relationship: IAO:0000219 GENO:0000010 ! denotes background genome +property_value: IAO:0000116 "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it." xsd:string +property_value: IAO:0000118 "background genotype" xsd:string + +[Term] +id: GENO:0000614 +name: chromosomal region +def: "An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band." [] +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 SO:0000105 ! is part of chromosome arm +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000116 "New term request for SO." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string + +[Term] +id: GENO:0000616 +name: chromosome sub-band +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 SO:0000341 ! is part of chromosome band +relationship: GENO:0000207 GENO:0000618 ! has_sequence_attribute chromosomal band intensity +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string + +[Term] +id: GENO:0000618 +name: chromosomal band intensity +is_a: GENO:0000788 ! sequence feature attribute +property_value: IAO:0000118 "chromosomal band brightness" xsd:string + +[Term] +id: GENO:0000619 +name: gpos +is_a: GENO:0000618 ! chromosomal band intensity + +[Term] +id: GENO:0000620 +name: gneg +is_a: GENO:0000618 ! chromosomal band intensity + +[Term] +id: GENO:0000621 +name: gvar +is_a: GENO:0000618 ! chromosomal band intensity + +[Term] +id: GENO:0000622 +name: gpos100 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000623 +name: gpos75 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000624 +name: gpos50 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000625 +name: gpos25 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000628 +name: short chromosome arm +def: "A chromosome arm that is the shorter of the two arms of a given chromosome." [] +is_a: SO:0000105 ! chromosome arm +property_value: IAO:0000118 "p-arm" xsd:string +property_value: IAO:0000118 "stalk" xsd:string + +[Term] +id: GENO:0000629 +name: long chromosome arm +def: "A chromosome arm that is the longer of the two arms of a given chromosome." [] +is_a: SO:0000105 ! chromosome arm +property_value: IAO:0000118 "q-arm" xsd:string + +[Term] +id: GENO:0000632 +name: gpos66 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000633 +name: gpos33 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000637 +name: regulatory transgene region +def: "A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed." [] +is_a: SO:0005836 ! regulatory_region +relationship: RO:0002525 SO:0000902 ! is subsequence of transgene + +[Term] +id: GENO:0000638 +name: expressed transgene region +def: "A transgene part whose sequence is expressed in a gene product through transcription and/or translation." [] +is_a: GENO:0000460 ! transgene part +relationship: RO:0002525 SO:0000902 ! is subsequence of transgene +property_value: IAO:0000118 "coding transgene feature" xsd:string + +[Term] +id: GENO:0000640 +name: reporter region +is_a: GENO:0000638 ! expressed transgene region + +[Term] +id: GENO:0000642 +name: selectable marker transgene +def: "A transgene whose product is used as a selectable marker." [] +intersection_of: SO:0000902 ! transgene +intersection_of: RO:0000087 GENO:0000911 ! has_role selectable marker role +relationship: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered + +[Term] +id: GENO:0000644 +name: karyotype +def: "A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell." [] +comment: Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). \n\nA base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation). +is_a: GENO:0000899 ! genomic genotype +relationship: IAO:0000219 SO:0001026 ! denotes genome +property_value: IAO:0000119 "Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28)" xsd:string + +[Term] +id: GENO:0000645 +name: genomic genotype (sex-qualified) +def: "A genomic genotype where the genomic background specifies a male or female sex chromosome complement." [] +comment: We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances.\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. +is_a: GENO:0000899 ! genomic genotype +relationship: GENO:0000650 GENO:0000000 ! has_sex_agnostic_part genomic genotype (sex-agnostic) +property_value: IAO:0000116 "This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nIn the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former." xsd:string +property_value: IAO:0000118 "intrinsic genotype (sex-specific)" xsd:string +property_value: IAO:0000118 "sex-qualified genotype" xsd:string +property_value: IAO:0000118 "sex-qualified intrinsic genotype" xsd:string + +[Term] +id: GENO:0000646 +name: male intrinsic genotype +def: "A genomic genotype here the genomic background specifies a male sex chromosome complement." [] +is_a: GENO:0000645 ! genomic genotype (sex-qualified) + +[Term] +id: GENO:0000647 +name: female intrinsic genotype +def: "A genomic genotype here the genomic background specifies a female sex chromosome complement." [] +is_a: GENO:0000645 ! genomic genotype (sex-qualified) + +[Term] +id: GENO:0000649 +name: unspecified genomic background +def: "A background genotype whose sequence or identity is not known or specified." [] +is_a: GENO:0000611 ! genomic background +property_value: IAO:0000118 "unspecified background genotype" xsd:string + +[Term] +id: GENO:0000659 +name: sequence feature set +def: "A set of sequence features." [] +comment: 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature).\n\nThe notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles \{rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3].\n\n[1] https://www.snpedia.com/index.php/APOE-%CE%B54\n[2] https://www.snpedia.com/index.php/APOE-%CE%B52\n[3] https://www.snpedia.com/index.php/Gs270 +is_a: GENO:0000701 ! sequence feature or set +relationship: RO:0002351 SO:0000110 ! has member sequence_feature +property_value: IAO:0000112 "1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus\n\n2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele.\n\n3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y}" xsd:string + +[Term] +id: GENO:0000660 +name: genomic feature set +def: "A set of genomic features (i.e. sequence features that are of genomic origin)." [] +comment: A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature.\n\nThe notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. +is_a: GENO:0000659 ! sequence feature set +relationship: RO:0002162 OBI:0100026 ! in taxon organism +relationship: RO:0002351 GENO:0000481 ! has member genomic feature +property_value: IAO:0000116 "In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member." xsd:string +property_value: IAO:0000118 "genomic locus complement" xsd:string + +[Term] +id: GENO:0000666 +name: gene part +def: "A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc)." [] +xref: SO:0000831 (gene member region) +intersection_of: GENO:0000481 ! genomic feature +intersection_of: RO:0002525 GENO:0000014 ! is subsequence of gene allele +property_value: IAO:0000118 "defined gene part" xsd:string + +[Term] +id: GENO:0000667 +name: reporter transgene +def: "A transgene that codes for a product used as a reporter of gene expression or activity." [] +intersection_of: SO:0000902 ! transgene +intersection_of: RO:0000087 GENO:0000910 ! has_role reporter role +relationship: BFO:0000051 GENO:0000640 ! has part reporter region +relationship: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered + +[Term] +id: GENO:0000680 +name: obsolete_null feature +def: "A genomic feature that has an extent of zero." [] +is_a: ObsoleteClass +property_value: IAO:0000112 "A junction between bases, a deletion variant, a terminus at the end of a chromosome." xsd:string +property_value: IAO:0000116 "Former logical def: \n'genomic feature'\n and (has_extent value 0)" xsd:string + +[Term] +id: GENO:0000681 +name: novel extrachromosomal replicon +def: "An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found." [] +comment: Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. +is_a: GENO:0000684 ! novel replicon +relationship: GENO:0000207 GENO:0000139 ! has_sequence_attribute heritable +relationship: GENO:0000207 GENO:0000685 ! has_sequence_attribute novel +property_value: IAO:0000118 "aberrant extrachromosomal replicon" xsd:string +property_value: IAO:0000118 "exogenous extrachromosomal replicon" xsd:string +property_value: IAO:0000118 "transgenic extrachromosomal replicon" xsd:string + +[Term] +id: GENO:0000684 +name: novel replicon +def: "A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome." [] +comment: Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles. +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000207 GENO:0000685 ! has_sequence_attribute novel +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature." xsd:string + +[Term] +id: GENO:0000685 +name: novel +def: "An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000688 +name: terminus +def: "A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide)." [] +is_a: SO:0000110 ! sequence_feature + +[Term] +id: GENO:0000701 +name: sequence feature or set +def: "A sequence feature or a set of such features." [] +comment: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location. +is_a: BFO:0000031 ! generically dependent continuant +union_of: GENO:0000701 ! sequence feature or set +union_of: SO:0000110 ! sequence_feature +property_value: IAO:0000118 "sequence feature or collection" xsd:string + +[Term] +id: GENO:0000702 +name: biological sequence +def: "A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides)." [] +comment: 'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome. +xref: VMC:State +is_a: GENO:0000921 ! biological sequence or set +disjoint_from: GENO:0000815 ! sequence feature location +disjoint_from: SO:0000110 ! sequence_feature +property_value: IAO:0000116 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." xsd:string +property_value: IAO:0000118 "biomacromolecular sequence" xsd:string +property_value: IAO:0000118 "state" xsd:string {http://purl.obolibrary.org/obo/IAO_0000116="In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele."} + +[Term] +id: GENO:0000713 +name: qualified sequence feature or collection +def: "A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification." [] +is_a: BFO:0000031 ! generically dependent continuant + +[Term] +id: GENO:0000714 +name: qualified genomic feature +def: "A qualified sequence feature that carries sequence derived from the genome of a cell or organism." [] +is_a: GENO:0000919 ! qualified sequence feature +relationship: GENO:0000726 GENO:0000481 {http://purl.obolibrary.org/obo/GENO_0000834="true", comment="Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position)."} ! has_sequence_feature genomic feature +relationship: RO:0002162 OBI:0100026 ! in taxon organism +property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." xsd:string + +[Term] +id: GENO:0000715 +name: qualified genomic feature set +def: "A set of qualified sequence features that carry genomic sequence." [] +comment: A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles \{rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele.\n\nA complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome. +is_a: GENO:0000920 ! qualified sequence feature set +relationship: GENO:0000726 GENO:0000660 ! has_sequence_feature genomic feature set +relationship: RO:0002162 OBI:0100026 ! in taxon organism +relationship: RO:0002351 GENO:0000714 ! has member qualified genomic feature +property_value: IAO:0000116 "Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member." xsd:string + +[Term] +id: GENO:0000719 +name: intrinsic genotype +def: "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype." [] +comment: 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. +is_a: GENO:0000536 ! genotype +property_value: IAO:0000116 "Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome." xsd:string + +[Term] +id: GENO:0000720 +name: DNA sequence +intersection_of: GENO:0000702 ! biological sequence +intersection_of: GENO:0000783 GENO:0000780 ! has_sequence_unit DNA residue +intersection_of: GENO:0000783 GENO:0000780 {all_only="true"} ! has_sequence_unit DNA residue + +[Term] +id: GENO:0000721 +name: RNA sequence +intersection_of: GENO:0000702 ! biological sequence +intersection_of: GENO:0000783 GENO:0000781 ! has_sequence_unit RNA residue +intersection_of: GENO:0000783 GENO:0000781 {all_only="true"} ! has_sequence_unit RNA residue + +[Term] +id: GENO:0000722 +name: amino acid sequence +intersection_of: GENO:0000702 ! biological sequence +intersection_of: GENO:0000783 GENO:0000782 ! has_sequence_unit amino acid residue +intersection_of: GENO:0000783 GENO:0000782 {all_only="true"} ! has_sequence_unit amino acid residue + +[Term] +id: GENO:0000724 +name: obsolete_biological sequence or collection +is_a: ObsoleteClass + +[Term] +id: GENO:0000725 +name: obsolete_biological sequence collection +is_a: GENO:0000724 ! obsolete_biological sequence or collection + +[Term] +id: GENO:0000736 +name: location-qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature." [] +comment: As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell). +is_a: GENO:0000714 ! qualified genomic feature +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000737 +name: expression-qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct)" [] +is_a: GENO:0000714 ! qualified genomic feature + +[Term] +id: GENO:0000768 +name: obsolete_genomic position +def: "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence." [] +is_a: ObsoleteClass +property_value: IAO:0000116 "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature." xsd:string +property_value: IAO:0000118 "genomic coordinates" xsd:string +property_value: IAO:0000231 "remodeling notion of sequence feature position around the idea of a 'genomic locus'" xsd:string + +[Term] +id: GENO:0000770 +name: phenotypic inheritance process +is_a: GENO:0000351 ! biological process + +[Term] +id: GENO:0000772 +name: obsolete_unspecified +def: "A sequence attribute inhering in a feature whose identity is not specified." [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000773 +name: variation attribute +def: "An attribute describing a type of variation inhering in a sequence feature or collection." [] +is_a: GENO:0000788 ! sequence feature attribute +property_value: IAO:0000118 "allele attribute" xsd:string + +[Term] +id: GENO:0000777 +name: variant genomic genotype +def: "An intrinsic genotype that specifies variation from a defined reference genome." [] +intersection_of: GENO:0000899 ! genomic genotype +intersection_of: IAO:0000219 GENO:0000033 ! denotes variant genome + +[Term] +id: GENO:0000778 +name: obsolete_sequence information entity +def: "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities." [] +is_a: ObsoleteClass +property_value: IAO:0000231 "eliminating classes that are not necessary or add uneeded complexity." xsd:string + +[Term] +id: GENO:0000779 +name: biological sequence unit +property_value: IAO:0000118 "biological sequence residue" xsd:string +property_value: IAO:0000118 "monomeric residue" xsd:string + +[Term] +id: GENO:0000780 +name: DNA residue +is_a: GENO:0000779 ! biological sequence unit +property_value: IAO:0000118 "deoxyribonucleic acid residue" xsd:string + +[Term] +id: GENO:0000781 +name: RNA residue +is_a: GENO:0000779 ! biological sequence unit +property_value: IAO:0000118 "ribonucleic acid residue" xsd:string + +[Term] +id: GENO:0000782 +name: amino acid residue +is_a: GENO:0000779 ! biological sequence unit + +[Term] +id: GENO:0000788 +name: sequence feature attribute +def: "An attribute, quality, or state of a sequence feature or collection." [] +comment: Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity. +xref: http://purl.obolibrary.org/obo/SO_0000400 +is_a: BFO:0000020 ! specifically dependent continuant + +[Term] +id: GENO:0000815 +name: sequence feature location +def: "The location of a sequence feature as defined by its start and end position on some reference coordinate system." [] +comment: 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms).\n\n2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there. +is_a: BFO:0000031 ! generically dependent continuant +disjoint_from: SO:0000110 ! sequence_feature + +[Term] +id: GENO:0000818 +name: modification-qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature)" [] +is_a: GENO:0000714 ! qualified genomic feature +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000823 +name: allelic genotype +def: "A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes." [] +comment: An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location.\n\nThis contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background. +intersection_of: GENO:0000719 ! intrinsic genotype +intersection_of: IAO:0000219 GENO:0000516 ! denotes single locus complement +property_value: IAO:0000112 "1. The zebrafish \"fgf8a/fgf8a<+>\" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state).\n\n2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308.\n\n ##fileformat=VCFv4.2\n ##FORMAT=\n #CHROM POS REF ALT FILTER FORMAT SAMP001\n 20 2300608 C T PASS GT 0/1 \n 20 2301308 T G PASS GT 1/1\n (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html)\n\n3. Some allelic genotype formats encode the genotype as a single string - e.g. \"GRCh38 Chr12:258635(A;T)\" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12." xsd:string +property_value: IAO:0000118 "single locus genotype" xsd:string + +[Term] +id: GENO:0000833 +name: genotype-phenotype association +is_a: http://purl.org/oban/association ! association +relationship: GENO:0000580 ENVO:01000254 {http://purl.obolibrary.org/obo/GENO_0000834="true"} ! has_qualifier environmental system +relationship: http://purl.org/oban/association_has_object UPHENO:0001001 {http://purl.obolibrary.org/obo/GENO_0000834="true"} ! Phenotype +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each." xsd:string + +[Term] +id: GENO:0000839 +name: knockdown reagent targeted gene complement +is_a: GENO:0000527 ! reagent-targeted gene complement +relationship: GENO:0000382 GENO:0000504 ! has_variant_part reagent targeted gene + +[Term] +id: GENO:0000848 +name: obsolete_coding sequence alteration +def: "A sequence alteration within the coding sequence of a gene." [] +is_a: ObsoleteClass +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000231 "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." xsd:string + +[Term] +id: GENO:0000850 +name: P-element construct +def: "A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: GENO:0000856 +name: engineered genetic construct +def: "An engineered region that is used to transfer foreign genetic material into a host cell." [] +comment: Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. \n\nConstructs are typically packaged as part of delivery systems such as plasmids or viral vectors. +is_a: SO:0000804 ! engineered_region +property_value: IAO:0000118 "engineered_genetic_vector" xsd:string + +[Term] +id: GENO:0000861 +name: extra-chromosomal transgene +def: "A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct." [] +is_a: SO:0000902 ! transgene +property_value: IAO:0000118 "non-integrated transgene" xsd:string + +[Term] +id: GENO:0000870 +name: obsolete_sequence feature collection +def: "A collection of more than one sequence feature." [] +xref: http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection +is_a: ObsoleteClass + +[Term] +id: GENO:0000871 +name: haplotype +def: "A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block." [] +comment: A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. \n\nAs highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\n1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \n\n2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). "Star alleles" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/).\n\n3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. \n\nEach of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. +is_a: GENO:0000660 ! genomic feature set +relationship: RO:0002351 GENO:0000512 ! has member allele +property_value: http://purl.org/dc/terms/source "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype." xsd:string +property_value: IAO:0000116 "Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block.\n\nInstead, we can create an 'allele set' class as the haplotype parent?" xsd:string + +[Term] +id: GENO:0000872 +name: genomic sequence set +def: "A set of genomic sequences (a biological sequence that is of genomic origin)." [] +comment: A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. +is_a: GENO:0000922 ! biological sequence set +property_value: IAO:0000118 "copy number complement" xsd:string + +[Term] +id: GENO:0000873 +name: microsatellite alteration +def: "A relation used to describe an environment contextualizing the identity of an entity." [] +is_a: GENO:0000874 ! repeat region alteration + +[Term] +id: GENO:0000874 +name: repeat region alteration +def: "A relation used to describe a process contextualizing the identity of an entity." [] +is_a: SO:0001059 ! sequence_alteration + +[Term] +id: GENO:0000875 +name: allelic state +def: "A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism" [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: GENO:0000876 +name: obsolete_genetic dosage +comment: Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. +is_a: ObsoleteClass +property_value: IAO:0000118 "allelic dosage" xsd:string +property_value: IAO:0000118 "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome." xsd:string +property_value: IAO:0000118 "gene dosage" xsd:string +property_value: IAO:0000231 "Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute." xsd:string + +[Term] +id: GENO:0000877 +name: allele origin +def: "A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent." [] +is_a: GENO:0000788 ! sequence feature attribute +property_value: IAO:0000118 "genetic origin" xsd:string +property_value: IAO:0000118 "variant origin" xsd:string + +[Term] +id: GENO:0000878 +name: maternal allele origin +def: "Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg." [] +is_a: GENO:0000888 ! germline allele origin +property_value: IAO:0000118 "maternally inherited" xsd:string + +[Term] +id: GENO:0000879 +name: paternal allele origin +def: "Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm." [] +is_a: GENO:0000888 ! germline allele origin +property_value: IAO:0000118 "paternally inherited" xsd:string + +[Term] +id: GENO:0000880 +name: de novo allele origin +def: "Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis." [] +comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. \n \nDe novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder. +is_a: GENO:0000877 ! allele origin +property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string + +[Term] +id: GENO:0000881 +name: unknown allele origin +def: "Describes an allele whose origin is not known." [] +is_a: GENO:0000877 ! allele origin + +[Term] +id: GENO:0000882 +name: somatic allele origin +def: "Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body." [] +comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells.\n \nThese acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations. +is_a: GENO:0000877 ! allele origin +property_value: IAO:0000118 "acquired" xsd:string +property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string + +[Term] +id: GENO:0000883 +name: obsolete_gametic +def: "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells)." [] +is_a: ObsoleteClass +property_value: IAO:0000118 "germ-line" xsd:string +property_value: IAO:0000231 "replaced by GENO:0000900 ! 'germline'" xsd:string + +[Term] +id: GENO:0000885 +name: diplotype +def: "An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement')\n\nAlt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome." [] +comment: "Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes."\nFrom https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/ + +[Term] +id: GENO:0000886 +name: allelic phase +def: "A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes." [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: GENO:0000887 +name: oryzias latipes strain +is_a: GENO:0000112 ! strain or breed +relationship: RO:0002351 NCBITaxon:8090 ! has member Oryzias latipes +relationship: RO:0002351 NCBITaxon:8090 ! has member Oryzias latipes + +[Term] +id: GENO:0000888 +name: germline allele origin +def: "Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg)." [] +comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells. +is_a: GENO:0000877 ! allele origin +property_value: IAO:0000118 "hereditary" xsd:string +property_value: IAO:0000118 "parental origin" xsd:string +property_value: IAO:0000118 "parentally inherited" xsd:string +property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string + +[Term] +id: GENO:0000889 +name: undetermined inheritance +def: "An inheritance pattern that is not determined or not known." [] +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000118 "unknown inheritance" xsd:string + +[Term] +id: GENO:0000890 +name: obsolete_canonical allele +def: "One of a set of sequence features or haplotypes that exist at a particular genetic locus. " [] +comment: As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand.\n\nIn the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) +is_a: ObsoleteClass +property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string +property_value: IAO:0000112 "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." xsd:string +property_value: IAO:0000116 "The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string +property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/ xsd:string +property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs." xsd:string + +[Term] +id: GENO:0000891 +name: obsolete_contextual allele +def: "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence." [] +comment: The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. +is_a: ObsoleteClass +property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string +property_value: IAO:0000116 "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string +property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ xsd:string +property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.\n\nFormer axiom: denotes some 'obsolete_canonical allele'" xsd:string + +[Term] +id: GENO:0000892 +name: heteroplasmic mitochondrial inheritance +def: "A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not." [] +is_a: GENO:0000949 ! mitochondrial inheritance + +[Term] +id: GENO:0000893 +name: homoplasmic mitochondrial inheritance +def: "A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited." [] +is_a: GENO:0000949 ! mitochondrial inheritance + +[Term] +id: GENO:0000897 +name: genomic entity +def: "An generically dependent continuant that carries biological sequence that is part of or derived from a genome." [] +is_a: BFO:0000031 ! generically dependent continuant +relationship: RO:0002162 OBI:0100026 ! in taxon organism +property_value: GENO:0000905 "true" xsd:boolean +property_value: IAO:0000116 "An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities." xsd:string + +[Term] +id: GENO:0000898 +name: haplotype block +def: "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations." [] +comment: A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000116 "Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as \n\"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.\" Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location.\n\nCurrent definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele." xsd:string +property_value: IAO:0000119 "Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424." xsd:string + +[Term] +id: GENO:0000899 +name: genomic genotype +def: "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype." [] +comment: 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. +intersection_of: GENO:0000719 ! intrinsic genotype +intersection_of: IAO:0000219 SO:0001026 ! denotes genome +relationship: GENO:0000385 GENO:0000611 ! has_reference_part genomic background +property_value: IAO:0000116 "'Genomic Genotype' vs 'Genome' in GENO: \nA genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome." xsd:string +property_value: IAO:0000118 "complete genotype" xsd:string + +[Term] +id: GENO:0000901 +name: obsolete_allele cellular context +def: "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)" [] +comment: Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. +is_a: ObsoleteClass +property_value: IAO:0000231 "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin" xsd:string + +[Term] +id: GENO:0000902 +name: genomic feature location +def: "The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system" [] +comment: 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. \n \n2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus.\n\n3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there. +xref: VMC:Location +is_a: GENO:0000815 ! sequence feature location +property_value: IAO:0000116 "In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future.\n\nWe don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences." xsd:string +property_value: IAO:0000116 "In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed.\n\nFor example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus)." xsd:string +property_value: IAO:0000118 "genomic location" xsd:string +property_value: IAO:0000118 "genomic locus" xsd:string + +[Term] +id: GENO:0000904 +name: organismal entity +def: "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc)." [] +is_a: BFO:0000040 ! material entity +property_value: GENO:0000905 "true" xsd:boolean +property_value: IAO:0000116 "useful organizational term to collect entities that have genomes/genotypes." xsd:string + +[Term] +id: GENO:0000907 +name: gene product +def: "The molecular product resulting from transcription of a single gene (either a protein or RNA molecule)" [] +is_a: SO:0000110 ! sequence_feature + +[Term] +id: GENO:0000910 +name: reporter role +is_a: OBI:0000086 ! reagent role + +[Term] +id: GENO:0000911 +name: selectable marker role +is_a: OBI:0000086 ! reagent role + +[Term] +id: GENO:0000912 +name: selectable marker region +is_a: GENO:0000638 ! expressed transgene region + +[Term] +id: GENO:0000914 +name: reference genome +def: "A genome whose sequence is identical to that of a genome sequence considered to be the reference." [] +is_a: SO:0001026 ! genome +relationship: GENO:0000239 SO:0001505 ! has_sequence reference genome sequence + +[Term] +id: GENO:0000915 +name: obsolete_haplotype +def: "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it." [] +comment: 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. +is_a: ObsoleteClass +property_value: IAO:0000116 "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"" xsd:string +property_value: IAO:0000119 "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype." xsd:string +property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" xsd:string + +[Term] +id: GENO:0000916 +name: obsolete_haplotype block +def: "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations." [] +comment: A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.\n\nThe boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.\n\n-----------------------\n\n* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. +is_a: ObsoleteClass +property_value: IAO:0000119 "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." xsd:string +property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets." xsd:string + +[Term] +id: GENO:0000918 +name: organellar plasmy +def: "An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell." [] +comment: Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene. +is_a: GENO:0000875 ! allelic state + +[Term] +id: GENO:0000919 +name: qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification." [] +comment: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). +comment: Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes. +is_a: GENO:0000713 ! qualified sequence feature or collection +property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." xsd:string + +[Term] +id: GENO:0000920 +name: qualified sequence feature set +def: "A set of qualified seqeunce features." [] +comment: 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'. +is_a: GENO:0000713 ! qualified sequence feature or collection +relationship: BFO:0000051 GENO:0000919 ! has part qualified sequence feature +relationship: GENO:0000726 GENO:0000659 ! has_sequence_feature sequence feature set + +[Term] +id: GENO:0000921 +name: biological sequence or set +def: "A biolocical sequence, or set of such sequences." [] +is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000118 "biological sequence or collection" xsd:string + +[Term] +id: GENO:0000922 +name: biological sequence set +def: "A set of biological sequences." [] +comment: 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. \n\nA set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence. +is_a: GENO:0000921 ! biological sequence or set + +[Term] +id: GENO:0000923 +name: obsolete_functional copy number complement +def: "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome." [] +comment: As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). +comment: The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. +is_a: ObsoleteClass +property_value: IAO:0000116 "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"" xsd:string +property_value: IAO:0000118 "functional feature complement" xsd:string +property_value: IAO:0000118 "genetic dosage" xsd:string +property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." xsd:string + +[Term] +id: GENO:0000924 +name: obsolete_intrinsic sequence feature attribute +def: "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form." [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000925 +name: obsolete_extrinsic sequence feature attribute +def: "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)" [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000926 +name: allelic cellular distribution +def: "A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism)." [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: GENO:0000927 +name: constitutional +def: "A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin." [] +is_a: GENO:0000926 ! allelic cellular distribution + +[Term] +id: GENO:0000928 +name: clonal +def: "A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin." [] +is_a: GENO:0000926 ! allelic cellular distribution + +[Term] +id: GENO:0000929 +name: multifactorial inheritance +def: "An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors." [] +comment: Diseases inherited in this manner are termed 'complex diseases'. +xref: http://purl.obolibrary.org/obo/HP_0001426 +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000118 "complex inherritance" xsd:string +property_value: IAO:0000118 "multi-factorial inheritance" xsd:string +property_value: IAO:0000118 "multi-genic inheritance" xsd:string +property_value: IAO:0000118 "multi-locus inheritance" xsd:string +property_value: IAO:0000118 "multigenic inheritance" xsd:string + +[Term] +id: GENO:0000930 +name: digenic inheritance +def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes." [] +xref: http://purl.obolibrary.org/obo/HP_0010984 +is_a: GENO:0000929 ! multifactorial inheritance + +[Term] +id: GENO:0000931 +name: oligogenic inheritance +def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes." [] +comment: It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform. +xref: http://purl.obolibrary.org/obo/HP_0010983 +is_a: GENO:0000929 ! multifactorial inheritance + +[Term] +id: GENO:0000932 +name: polygenic inheritance +def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes." [] +comment: Typically used for traits/conditions governed by more than three gene loci. +xref: http://purl.obolibrary.org/obo/HP_0010982 +is_a: GENO:0000929 ! multifactorial inheritance + +[Term] +id: GENO:0000933 +name: monogenic inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors." [] +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000118 "single-gene inheritance" xsd:string + +[Term] +id: GENO:0000934 +name: autosomal inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome." [] +is_a: GENO:0000933 ! monogenic inheritance + +[Term] +id: GENO:0000935 +name: allosomal inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome." [] +xref: http://purl.obolibrary.org/obo/HP_0010985 +is_a: GENO:0000933 ! monogenic inheritance +property_value: IAO:0000118 "gonosomal inheritance" xsd:string + +[Term] +id: GENO:0000936 +name: X-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome." [] +xref: http://purl.obolibrary.org/obo/HP_0001417 +is_a: GENO:0000935 ! allosomal inheritance + +[Term] +id: GENO:0000937 +name: complete X-linked dominant inheritance +def: "An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." [] +is_a: GENO:0000146 ! X-linked dominant inheritance + +[Term] +id: GENO:0000938 +name: incomplete X-linked dominant inheritance +def: "An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." [] +is_a: GENO:0000146 ! X-linked dominant inheritance +property_value: IAO:0000118 "semi-dominant X-linked inheritance" xsd:string + +[Term] +id: GENO:0000939 +name: co-dominant X-linked inheritance +def: "An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." [] +is_a: GENO:0000146 ! X-linked dominant inheritance + +[Term] +id: GENO:0000941 +name: Y-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome." [] +xref: http://purl.obolibrary.org/obo/HP_0001450 +is_a: GENO:0000935 ! allosomal inheritance +property_value: IAO:0000118 "holandric inheritance" xsd:string + +[Term] +id: GENO:0000942 +name: Z-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome." [] +is_a: GENO:0000935 ! allosomal inheritance + +[Term] +id: GENO:0000943 +name: Z-linked dominant inheritance +def: "A Z-linked inheritance pattern wherein the trait manifests in heterozygotes." [] +is_a: GENO:0000942 ! Z-linked inheritance + +[Term] +id: GENO:0000944 +name: complete Z-linked dominant inheritance +def: "A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." [] +is_a: GENO:0000943 ! Z-linked dominant inheritance + +[Term] +id: GENO:0000945 +name: incomplete Z-linked dominant inheritance +def: "A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." [] +is_a: GENO:0000943 ! Z-linked dominant inheritance +property_value: IAO:0000118 "semi-dominant Z-linked inheritance" xsd:string + +[Term] +id: GENO:0000946 +name: co-dominant Z-linked inheritance +def: "An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." [] +is_a: GENO:0000943 ! Z-linked dominant inheritance + +[Term] +id: GENO:0000947 +name: Z-linked reccessive inheritance +def: "A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals." [] +is_a: GENO:0000942 ! Z-linked inheritance + +[Term] +id: GENO:0000948 +name: W-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome." [] +is_a: GENO:0000935 ! allosomal inheritance + +[Term] +id: GENO:0000949 +name: mitochondrial inheritance +def: "An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome." [] +comment: Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy). +xref: http://purl.obolibrary.org/obo/HP_0001427 +is_a: GENO:0000141 ! inheritance pattern + +[Term] +id: GENO:0000952 +name: sex-limited autosomal dominant inheritance +def: "An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females)." [] +xref: http://purl.obolibrary.org/obo/HP_0001470 +is_a: GENO:0000147 ! autosomal dominant inheritance + +[Term] +id: GENO:0000953 +name: sex-limited autosomal recessive inheritance +def: "An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females)." [] +xref: http://purl.obolibrary.org/obo/HP_0031362 +is_a: GENO:0000148 ! autosomal recessive inheritance + +[Term] +id: GENO:0000954 +name: allele set +def: "A set of discrete alleles within a particular genome." [] +comment: 'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An "Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'. +is_a: GENO:0000660 ! genomic feature set + +[Term] +id: GENO:0000955 +name: obsolete_variant copy number complement +def: "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s)." [] +comment: In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. +is_a: GENO:0000956 ! obsolete_copy number complement +property_value: IAO:0000118 "copy number variation" xsd:string +property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level." xsd:string + +[Term] +id: GENO:0000956 +name: obsolete_copy number complement +def: "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger." [] +comment: 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. +is_a: ObsoleteClass +property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." xsd:string + +[Term] +id: GENO:0000960 +name: genomic sequence +def: "A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)." [] +comment: A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. +is_a: GENO:0000702 ! biological sequence + +[Term] +id: GENO:0000961 +name: copy number complement +def: "A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome." [] +comment: The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result.\n\nA 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. \n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. +comment: The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence. +is_a: GENO:0000872 ! genomic sequence set +property_value: IAO:0000116 "The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome.\n\nWe represent the notion of copy number at the \"sequence level\" (as opposed to the \"sequence feature level\") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The \"sequence level\" representation here supports this use case. By contrast, a \"feature level\" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity)." xsd:string + +[Term] +id: GENO:0000962 +name: variant copy number complement +def: "A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s)." [] +comment: 'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome. +is_a: GENO:0000961 ! copy number complement +property_value: IAO:0000116 "Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a \"sequence feature level\" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred).\n\nFor example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains." xsd:string + +[Term] +id: GENO:0000963 +name: functional copy complement +def: "A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence.\n\n'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nAs we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele. +is_a: GENO:0000872 ! genomic sequence set +property_value: IAO:0000118 "functional genetic dosage" xsd:string + +[Term] +id: GENO:0000964 +name: mosaic +comment: A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type. +is_a: GENO:0000928 ! clonal + +[Term] +id: GENO:0000965 +name: sequence interval +def: "A pair of integers representing start and end position of a location on a sequence coordinate system." [] +is_a: IAO:0000030 ! information content entity + +[Term] +id: GO:0003674 +name: molecular function +is_a: BFO:0000034 ! function + +[Term] +id: GO:0032502 +name: developmental process +def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete]" [] +is_a: GENO:0000351 ! biological process + +[Term] +id: HP:0000118 +name: human phenotypic abnormality +comment: pulling in HP 'phenotypic abnormality' root here +is_a: UPHENO:0001001 ! Phenotype + +[Term] +id: HsapDv:0000000 +name: human life cycle stage +is_a: GENO:0000351 ! biological process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology." xsd:string +property_value: IAO:0000119 "A spatiotemporal region encompassing some part of the life cycle of an organism." xsd:string + +[Term] +id: IAO:0000030 +name: information content entity +def: "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity" [] +is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000111 "information content entity" xsd:string +property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000119 "OBI_0000142" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +is_a: IAO:0000030 ! information content entity +property_value: IAO:0000118 "ontology metadata" xsd:string + +[Term] +id: MP:0000001 +name: mammalian phenotype +comment: where to place this depends on if we take the organismal view or the quality centric view. +is_a: UPHENO:0001001 ! Phenotype + +[Term] +id: NCBITaxon:10090 +name: Mus musculus +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:10239 +name: Viruses +comment: Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies. +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:7955 +name: Danio rerio +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:8090 +name: Oryzias latipes +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:9606 +name: Homo sapiens +is_a: OBI:0100026 ! organism + +[Term] +id: OBI:0000011 +name: planned process +def: "A processual entity that realizes a plan which is the concretization of a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO." xsd:string + +[Term] +id: OBI:0000086 +name: reagent role +is_a: BFO:0000023 ! role + +[Term] +id: OBI:0000181 +name: population +def: "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area" [] +is_a: GENO:0000113 ! taxonomic group + +[Term] +id: OBI:0000435 +name: genotyping assay +def: "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions." [] +is_a: ERO:0000007 ! technique + +[Term] +id: OBI:0001148 +name: targeted gene knock-out technique +def: "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods." [] +comment: A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. +is_a: GENO:0000166 ! targeted gene mutation technique + +[Term] +id: OBI:0001149 +name: targeted gene knock-in technique +is_a: GENO:0000166 ! targeted gene mutation technique + +[Term] +id: OBI:0100026 +name: organism +is_a: BFO:0000040 ! material entity +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy." xsd:string + +[Term] +id: OBI:0600043 +name: genetic modification technique +def: "the introduction. alteration or integration of genetic material into a cell or organism" [] +is_a: ERO:0000007 ! technique + +[Term] +id: PATO:0000016 +name: obsolete_color brightness +is_a: ObsoleteClass +property_value: IAO:0000116 "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html" xsd:string +property_value: IAO:0000116 "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." xsd:string +property_value: IAO:0000118 "color value" xsd:string + +[Term] +id: PATO:0000383 +name: female +is_a: PATO:0001894 ! phenotypic sex + +[Term] +id: PATO:0000384 +name: male +is_a: PATO:0001894 ! phenotypic sex + +[Term] +id: PATO:0001894 +name: phenotypic sex +is_a: BFO:0000019 ! quality + +[Term] +id: PCO:0000000 +name: collection of organisms +def: "A material entity that consists of two or more organisms, viruses, or viroids." [] +comment: A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role). +is_a: BFO:0000040 ! material entity +relationship: RO:0002351 OBI:0100026 ! has member organism + +[Term] +id: PCO:0000020 +name: family +def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] +is_a: PCO:0000000 ! collection of organisms + +[Term] +id: Position +name: Position +def: "Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate." [] +is_a: GENO:0000902 ! genomic feature location +property_value: IAO:0000116 "We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region)." xsd:string +property_value: IAO:0000412 "FALDO" xsd:string + +[Term] +id: Region +name: Region +def: "A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene." [] +is_a: SO:0000110 ! sequence_feature +relationship: begin Position {cardinality="1"} ! Position +relationship: end Position {cardinality="1"} ! Position +property_value: IAO:0000116 "From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence." xsd:string + +[Term] +id: ReverseStrandPosition +name: Negative strand +is_a: StrandedPosition ! Stranded position + +[Term] +id: SO:0000034 +name: morpholino_oligo +def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [] +is_a: GENO:0000533 ! gene knockdown reagent + +[Term] +id: SO:0000105 +name: chromosome arm +def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [] +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 SO:0000830 ! is part of chromosome part +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000116 "Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string + +[Term] +id: SO:0000110 +name: sequence_feature +def: "Any extent of continuous biological sequence." [] +comment: A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome. +is_a: GENO:0000701 ! sequence feature or set +relationship: GENO:0000239 GENO:0000702 {http://purl.obolibrary.org/obo/GENO_0000834="true", comment="Formalizes the first identity criteria for a sequence feature of its sequence."} ! has_sequence biological sequence +relationship: GENO:0000903 GENO:0000815 {http://purl.obolibrary.org/obo/GENO_0000834="true", comment="Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property)."} ! has_location sequence feature location +property_value: IAO:0000116 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." xsd:string + +[Term] +id: SO:0000143 +name: obsolete_assembly_component +def: "A region of known length which may be used to manufacture a longer region." [] +is_a: SO:0001410 ! obsolete_experimental_feature + +[Term] +id: SO:0000149 +name: obsolete_contig +def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [] +is_a: SO:0000143 ! obsolete_assembly_component + +[Term] +id: SO:0000159 +name: deletion +def: "The point at which one or more contiguous nucleotides were excised." [] +xref: http://en.wikipedia.org/wiki/Nucleotide_deletion +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000033 xsd:string +property_value: IAO:0000118 "deleted_sequence" xsd:string +property_value: IAO:0000118 "nucleotide deletion" xsd:string +property_value: IAO:0000118 "nucleotide_deletion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0000165 +name: enhancer +is_a: SO:0005836 ! regulatory_region + +[Term] +id: SO:0000167 +name: promoter +def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [] +is_a: SO:0005836 ! regulatory_region + +[Term] +id: SO:0000199 +name: translocation +def: "A region of nucleotide sequence that has translocated to a new position." [] +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000118 "transchr" xsd:string +property_value: IAO:0000118 "translocated sequence" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0000207 +name: simple_sequence_length_variation +is_a: SO:0000248 ! sequence_length_variation +property_value: IAO:0000118 "simple sequence length polymorphism" xsd:string +property_value: IAO:0000118 "simple sequence length variation" xsd:string +property_value: IAO:0000118 "SSLP" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0000248 +name: sequence_length_variation +is_a: SO:1000002 ! substitution +property_value: IAO:0000118 "sequence length variation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0000281 +name: engineered_foreign_gene +is_a: SO:0000704 ! gene +relationship: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered +property_value: IAO:0000116 "See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25.\n\nIncludes things like loxP sites, inducible promoters, ires elements, etc." xsd:string + +[Term] +id: SO:0000289 +name: microsatellite +def: "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [] +comment: A defined feature that includes any type of VNTR or SSLP locus. +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000119 http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29 xsd:string + +[Term] +id: SO:0000337 +name: RNAi_reagent +is_a: GENO:0000533 ! gene knockdown reagent + +[Term] +id: SO:0000340 +name: chromosome +def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [] +comment: A complete chromosome sequence. +is_a: GENO:0000481 ! genomic feature + +[Term] +id: SO:0000341 +name: chromosome band +def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [] +comment: "Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 GENO:0000614 ! is part of chromosomal region +relationship: GENO:0000207 GENO:0000618 ! has_sequence_attribute chromosomal band intensity +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band\n" xsd:string + +[Term] +id: SO:0000577 +name: centromere +is_a: SO:0000830 ! chromosome part + +[Term] +id: SO:0000637 +name: obsolete_engineered_plasmid +is_a: ObsoleteClass +property_value: IAO:0000116 "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." xsd:string + +[Term] +id: SO:0000667 +name: insertion +def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [] +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000034 xsd:string +property_value: IAO:0000118 "insertion" xsd:string +property_value: IAO:0000118 "nucleotide insertion" xsd:string +property_value: IAO:0000118 "nucleotide_insertion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0000694 +name: SNP +def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [] +is_a: SO:0001483 ! SNV +property_value: IAO:0000118 "single nucleotide polymorphism" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0000699 +name: junction +comment: A junction is a boundary between regions. A boundary has an extent of zero. +is_a: SO:0000110 ! sequence_feature + +[Term] +id: SO:0000704 +name: gene +def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [] +comment: A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion. +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000116 "Regarding the distinction between a 'gene' and a 'gene allele': \nEvery zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment)." xsd:string + +[Term] +id: SO:0000771 +name: QTL +def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [] +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000118 "quantitative trait locus" xsd:string + +[Term] +id: SO:0000783 +name: engineered +def: "An attribute to describe a region that was modified in vitro." [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: SO:0000804 +name: engineered_region +intersection_of: SO:0000110 ! sequence_feature +intersection_of: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered +property_value: IAO:0000118 "construct" xsd:string + +[Term] +id: SO:0000830 +name: chromosome part +def: "An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'." [] +intersection_of: GENO:0000481 ! genomic feature +intersection_of: GENO:0000248 SO:0000340 ! is_proper_part_of chromosome +property_value: IAO:0000118 "chromosomal feature" xsd:string +property_value: IAO:0000118 "gross chromosomal part" xsd:string + +[Term] +id: SO:0000902 +name: transgene +def: "A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome)." [] +comment: On the relationship between 'transgenic insertions', 'transgenes', and 'alleles'\nTransgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete.\n\nIn addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. \n\nFor the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach. +comment: Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism).\n\nNote that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome. +is_a: SO:0000704 ! gene + +[Term] +id: SO:0001013 +name: MNP +def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [] +is_a: SO:1000002 ! substitution +property_value: IAO:0000118 "multiple nucleotide polymorphism" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001019 +name: copy_number_variation +def: "A variation that increases or decreases the copy number of a given region." [] +xref: http://en.wikipedia.org/wiki/Copy_number_variation +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000118 "CNP" xsd:string +property_value: IAO:0000118 "CNV" xsd:string +property_value: IAO:0000118 "copy number polymorphism" xsd:string +property_value: IAO:0000118 "copy number variation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0001026 +name: genome +def: "A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny)" [] +comment: A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'. +is_a: GENO:0000660 ! genomic feature set +relationship: RO:0002162 OBI:0100026 ! in taxon organism +property_value: IAO:0000116 "Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence." xsd:string +property_value: IAO:0000118 "'genome sequence'" xsd:string + +[Term] +id: SO:0001059 +name: sequence_alteration +def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [] +comment: 1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. \n\nAlleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part.\n\n2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. \n\nFor a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference.\n\n3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism. +intersection_of: GENO:0000512 ! allele +intersection_of: GENO:0000784 GENO:0000481 ! completely_varies_with genomic feature +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000004 xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000007 xsd:string +property_value: IAO:0000112 "A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': \n\n1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871.\n\n2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112.\n\n3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112." xsd:string +property_value: IAO:0000118 "sequence variation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0001218 +name: transgenic_insertion +def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [] +is_a: SO:0000667 ! insertion +relationship: BFO:0000051 GENO:0000093 ! has part integrated transgene +property_value: IAO:0000118 "transgenic insertion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001410 +name: obsolete_experimental_feature +def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [] +is_a: ObsoleteClass +property_value: IAO:0000231 "not currently needed to support modeling use cases. can re-introduce if becomes necessary." xsd:string + +[Term] +id: SO:0001477 +name: gene_trap_construct +def: "A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: SO:0001478 +name: promoter_trap_construct +def: "A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: SO:0001479 +name: enhancer_trap_construct +def: "A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: SO:0001483 +name: SNV +def: "SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist." [] +is_a: SO:1000002 ! substitution +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Thu Oct 08 11:37:49 PDT 2009" xsd:string +property_value: IAO:0000118 "single nucleotide variant" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0001500 +name: heritable_phenotypic_marker +def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [] +is_a: GENO:0000481 ! genomic feature + +[Term] +id: SO:0001505 +name: reference genome sequence +def: "A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced." [] +is_a: GENO:0000017 ! reference sequence +relationship: RO:0000087 GENO:0000152 ! has_role reference +property_value: IAO:0000112 "'GRCh37.p10' (a human reference genome build)" xsd:string + +[Term] +id: SO:0001742 +name: copy_number_gain +def: "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [] +is_a: SO:0001019 ! copy_number_variation +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 01:54:09 PST 2011" xsd:string +property_value: IAO:0000118 "copy number gain" xsd:string +property_value: IAO:0000118 "gain" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001743 +name: copy_number_loss +def: "A sequence alteration whereby the copy number of a given region is less than the reference sequence." [] +is_a: SO:0001019 ! copy_number_variation +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 01:55:02 PST 2011" xsd:string +property_value: IAO:0000118 "copy number loss" xsd:string +property_value: IAO:0000118 "loss" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001744 +name: UPD +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [] +xref: http:http\\\://en.wikipedia.org/wiki/Uniparental_disomy +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:01:05 PST 2011" xsd:string +property_value: IAO:0000118 "uniparental disomy" xsd:string +property_value: IAO:0000118 "UPD" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001745 +name: maternal_uniparental_disomy +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [] +is_a: SO:0001744 ! UPD +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:03:01 PST 2011" xsd:string +property_value: IAO:0000118 "maternal uniparental disomy" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001746 +name: paternal_uniparental_disomy +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [] +is_a: SO:0001744 ! UPD +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:03:30 PST 2011" xsd:string +property_value: IAO:0000118 "paternal uniparental disomy" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001784 +name: complex_structural_alteration +def: "A structural sequence alteration where there are multiple equally plausible explanations for the change." [] +is_a: SO:0001785 ! structural_alteration +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Wed Mar 23 03:21:19 PDT 2011" xsd:string +property_value: IAO:0000118 "complex" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001785 +name: structural_alteration +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 25 02:27:41 PDT 2011" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0005836 +name: regulatory_region +is_a: GENO:0000666 ! gene part +property_value: IAO:0000116 "Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term." xsd:string +property_value: IAO:0000118 "regulatory element" xsd:string +property_value: IAO:0000118 "regulatory gene region" xsd:string + +[Term] +id: SO:1000002 +name: substitution +def: "Any change in genomic DNA caused by a single event." [] +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000005 +name: complex_substitution +def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\\"complex\\\" should be used. Usually there are multiple equally plausible explanations for the change." [] +is_a: SO:1000002 ! substitution +property_value: IAO:0000118 "complex substitution" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000008 +name: point_mutation +def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [] +xref: http://en.wikipedia.org/wiki/Point_mutation +is_a: SO:0001483 ! SNV +property_value: IAO:0000118 "point mutation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000009 +name: transition +def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [] +is_a: SO:0001483 ! SNV +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000010 +name: pyrimidine_transition +def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [] +is_a: SO:1000009 ! transition +property_value: IAO:0000118 "pyrimidine transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000011 +name: C_to_T_transition +def: "A transition of a cytidine to a thymine." [] +is_a: SO:1000010 ! pyrimidine_transition +property_value: IAO:0000118 "C to T transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000012 +name: C_to_T_transition_at_pCpG_site +def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [] +is_a: SO:1000011 ! C_to_T_transition +property_value: IAO:0000118 "C to T transition at pCpG site" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000013 +name: T_to_C_transition +is_a: SO:1000010 ! pyrimidine_transition +property_value: IAO:0000118 "T to C transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000014 +name: purine_transition +def: "A substitution of a purine, A or G, for another purine." [] +is_a: SO:1000009 ! transition +property_value: IAO:0000118 "purine transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000015 +name: A_to_G_transition +def: "A transition of an adenine to a guanine." [] +is_a: SO:1000014 ! purine_transition +property_value: IAO:0000118 "A to G transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000016 +name: G_to_A_transition +def: "A transition of a guanine to an adenine." [] +is_a: SO:1000014 ! purine_transition +property_value: IAO:0000118 "G to A transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000017 +name: transversion +def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [] +xref: http://en.wikipedia.org/wiki/Transversion +is_a: SO:0001483 ! SNV +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000018 +name: pyrimidine_to_purine_transversion +def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [] +is_a: SO:1000017 ! transversion +property_value: IAO:0000118 "pyrimidine to purine transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000019 +name: C_to_A_transversion +def: "A transversion from cytidine to adenine." [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "C to A transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000020 +name: C_to_G_transversion +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "C to G transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000021 +name: T_to_A_transversion +def: "A transversion from T to A." [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "T to A transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000022 +name: T_to_G_transversion +def: "A transversion from T to G." [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "T to G transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000023 +name: purine_to_pyrimidine_transversion +def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [] +is_a: SO:1000017 ! transversion +property_value: IAO:0000118 "purine to pyrimidine transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000024 +name: A_to_C_transversion +def: "A transversion from adenine to cytidine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "A to C transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000025 +name: A_to_T_transversion +def: "A transversion from adenine to thymine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "A to T transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000026 +name: G_to_C_transversion +def: "A transversion from guanine to cytidine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "G to C transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000027 +name: G_to_T_transversion +def: "A transversion from guanine to thymine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "G to T transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000032 +name: indel +def: "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [] +comment: Indels can have a different number of bases than the corresponding reference sequence. +xref: http://en.wikipedia.org/wiki/Indel +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000035 +name: duplication +def: "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point." [] +is_a: SO:0000667 ! insertion +property_value: IAO:0000118 "nucleotide duplication" xsd:string +property_value: IAO:0000118 "nucleotide_duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000036 +name: inversion +def: "A continuous nucleotide sequence is inverted in the same position." [] +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000118 "inversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000039 +name: direct_tandem_duplication +def: "A tandem duplication where the individual regions are in the same orientation." [] +is_a: SO:1000173 ! tandem_duplication +property_value: IAO:0000118 "direct tandem duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000040 +name: inverted_tandem_duplication +def: "A tandem duplication where the individual regions are not in the same orientation." [] +is_a: SO:1000173 ! tandem_duplication +property_value: IAO:0000118 "inverted tandem duplication" xsd:string +property_value: IAO:0000118 "mirror duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000173 +name: tandem_duplication +def: "A duplication consisting of 2 identical adjacent regions." [] +is_a: SO:1000035 ! duplication +property_value: IAO:0000118 "erverted" xsd:string +property_value: IAO:0000118 "tandem duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: StrandedPosition +name: Stranded position +comment: Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'. +is_a: Position ! Position + +[Term] +id: UBERON:0000105 +name: life cycle stage +is_a: GENO:0000351 ! biological process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms)" xsd:string + +[Term] +id: UBERON:0001062 +name: anatomical entity +xref: http://purl.obolibrary.org/obo/CARO_0000000 +is_a: BFO:0000040 ! material entity +relationship: RO:0001000 OBI:0100026 ! derives from organism +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies." xsd:string + +[Term] +id: UPHENO:0001001 +name: Phenotype +comment: 1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition)\n\n2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000116 "Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework." xsd:string + +[Term] +id: WBPhenotype:0000886 +name: worm phenotype +def: "Animals exhibit variations compared to a given control." [] +is_a: UPHENO:0001001 ! Phenotype +property_value: IAO:0000116 "'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes." xsd:string +property_value: IAO:0000118 "c. elegans phenotype" xsd:string +property_value: IAO:0000118 "Variant" xsd:string + +[Term] +id: ZP:0000199 +name: abnormal(ly) malformed endocardium cell +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0000386 +name: abnormal(ly) absent dorso-rostral cluster +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0000755 +name: abnormal(ly) disrupted diencephalon development +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0005531 +name: abnormal(ly) disrupted neutrophil aggregation +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0005692 +name: abnormal(ly) absent adaxial cell +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: http://purl.org/oban/association +name: association +is_a: IAO:0000030 ! information content entity + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/20423 +name: mus musculus shh gene +comment: Equivalent to: http://www.informatics.jax.org/marker/MGI:98297 +is_a: GENO:0000057 ! mus musculus gene +property_value: IAO:0000114 GENO:0000514 + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/30269 +name: danio rerio shha gene +xref: http://zfin.org/ZDB-GENE-980526-166 +is_a: GENO:0000047 ! danio rerio gene +property_value: IAO:0000114 GENO:0000514 + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/399483 +name: danio rerio cdkn1ca gene +xref: http://zfin.org/ZDB-GENE-040123-1 +is_a: GENO:0000047 ! danio rerio gene +property_value: IAO:0000114 GENO:0000514 + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/6469 +name: homo sapiens SHH gene +comment: Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690\n\nCodes for: http://www.uniprot.org/uniprot/Q15465 +is_a: GENO:0000054 ! homo sapiens gene +property_value: IAO:0000114 GENO:0000514 + +[Typedef] +id: BFO:0000050 +name: is part of +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: GENO:0000207 +name: has_sequence_attribute +def: "A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'." [] +xref: http://purl.obolibrary.org/obo/so_has_quality +property_value: IAO:0000116 "Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants." xsd:string + +[Typedef] +id: GENO:0000211 +name: bears_concretization_of +def: "A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes" [] +comment: Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence. +property_value: IAO:0000118 "materializes" xsd:string +holds_over_chain: RO:0000053 RO:0000059 + +[Typedef] +id: GENO:0000220 +name: is_genotype_of +inverse_of: GENO:0000222 ! has_genotype + +[Typedef] +id: GENO:0000222 +name: has_genotype +def: "A relationship that holds between a biological entity and some level of genetic variation present in its genome." [] +comment: The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations. +property_value: IAO:0000116 "This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype." xsd:string + +[Typedef] +id: GENO:0000231 +name: has_proper_part +def: "An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO)" [] +xref: http://semanticscience.org/resource/SIO_000053 +property_value: IAO:0000116 "No proper part relation anymore in RO/BFO?" xsd:string +is_transitive: true +is_a: BFO:0000051 ! has part +inverse_of: GENO:0000248 ! is_proper_part_of + +[Typedef] +id: GENO:0000239 +name: has_sequence +def: "A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears." [] +comment: 'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule. +xref: VMC:state +property_value: IAO:0000118 "has_sequence_component" xsd:string +property_value: IAO:0000118 "has_state" xsd:string +range: GENO:0000702 ! biological sequence +inverse_of: GENO:0000251 ! is_sequence_of + +[Typedef] +id: GENO:0000242 +name: obsolete_specifies +def: "A relationship between an information content entity representing a specification, and the entity it specifies." [] +property_value: IAO:0000112 "A geno:intrinnsic genotype 'specifies' a SO:genome.\nA geno:karyotype 'specifies' a geno:karyotype feature collection." xsd:string +is_a: ObsoleteProperty +inverse_of: GENO:0000253 ! obsolete_is_specified_by + +[Typedef] +id: GENO:0000243 +name: obsolete_approximates_sequence +property_value: IAO:0000116 "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000244 +name: obsolete_resolves_to_sequence +property_value: IAO:0000116 "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000248 +name: is_proper_part_of +def: "An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole." [] +xref: http://semanticscience.org/resource/SIO_000093 +is_a: BFO:0000050 ! is part of + +[Typedef] +id: GENO:0000251 +name: is_sequence_of +domain: GENO:0000702 ! biological sequence + +[Typedef] +id: GENO:0000252 +name: is_subject_of +inverse_of: IAO:0000136 ! is about + +[Typedef] +id: GENO:0000253 +name: obsolete_is_specified_by +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000359 +name: obsolete_is_phenotype_of_genotype +def: "shortcut relation used to link a phenotype directly to a genotype of an organism" [] +comment: Might expand to something like:\n\nphenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype))))))) +property_value: IAO:0000118 "is_phenotype_of_organism_with_genotype" xsd:string +property_value: IAO:0000118 "is_phenotype_with_genotype" xsd:string +property_value: IAO:0000118 "phenotype_has_genotype" xsd:string +domain: UPHENO:0001001 ! Phenotype +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000368 +name: obsolete_participates_in_inheritance_process +def: "A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next." [] +property_value: IAO:0000116 "Exploratory/temporary property, as we formalize our phenotypic inheritance model." xsd:string +range: GENO:0000141 ! inheritance pattern +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000382 +name: has_variant_part +def: "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression." [] +is_transitive: true +is_a: GENO:0000654 ! has_sequence_part +inverse_of: GENO:0000383 ! is_variant_part_of + +[Typedef] +id: GENO:0000383 +name: is_variant_part_of +is_transitive: true +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000385 +name: has_reference_part +def: "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant." [] +property_value: IAO:0000118 "has_reference_sequence_part" xsd:string +is_transitive: true +is_a: GENO:0000654 ! has_sequence_part +inverse_of: GENO:0000387 ! is_reference_part_of + +[Typedef] +id: GENO:0000387 +name: is_reference_part_of +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000408 +name: is_allele_of +def: "A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size." [] +comment: To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size).\n\nWhile conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like "fgf8a is an allele of the Danio rerio fgf8a gene", and we may create data where fgf8a is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene).\n\nIt is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. \n\nThis departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\\GAL4 gene.\n\nAt the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'. +property_value: IAO:0000112 " is_allele_of the 'danio rerio fgf8a' gene locus." xsd:string +property_value: IAO:0000116 "Domain = allele \nRange = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation)." xsd:string +property_value: IAO:0000116 "Note that the allele is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product." xsd:string +property_value: IAO:0000118 "is_sequence_variant_of" xsd:string +domain: GENO:0000481 ! genomic feature +is_a: GENO:0000418 ! has_affected_feature +inverse_of: GENO:0000413 ! has_allele + +[Typedef] +id: GENO:0000410 +name: obsolete_is_genetic_variant_of +def: "A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level)." [] +comment: Domain = genomic feature instance\nRange = punned gene class IRI +property_value: IAO:0000118 "is_variant_instance_of" xsd:string +property_value: IAO:0000231 "formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus)" xsd:string +is_a: ObsoleteProperty +inverse_of: GENO:0000411 ! obsolete_has_genetic_variant + +[Typedef] +id: GENO:0000411 +name: obsolete_has_genetic_variant +def: "A relation linking a gene class to a sequence-varaint or expression-variant of the gene." [] +comment: Domain = punned gene class\nRange = genomic feature +property_value: IAO:0000118 "has_variant_instance" xsd:string +property_value: IAO:0000231 "formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by)" xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000413 +name: has_allele +def: "A relation linking a gene class to one of its sequence-variant alleles." [] +property_value: IAO:0000116 "Domain = punned gene class\nRange = allele" xsd:string +property_value: IAO:0000118 "has_sequence_variant" xsd:string +is_a: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000414 +name: targets_gene +def: "A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets." [] +comment: This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets. +is_a: GENO:0000418 ! has_affected_feature +inverse_of: GENO:0000447 ! is_gene_target_of + +[Typedef] +id: GENO:0000418 +name: has_affected_feature +def: "A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression." [] +comment: This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset. +holds_over_chain: GENO:0000382 GENO:0000418 +holds_over_chain: GENO:0000383 GENO:0000418 +inverse_of: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000443 +name: is_expression_variant_of +def: "A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents." [] +comment: This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class. +property_value: IAO:0000116 "Domain = expression variant feature.\nRange = punned gene class" xsd:string +is_a: GENO:0000418 ! has_affected_feature +inverse_of: GENO:0000449 ! has_expression_variant + +[Typedef] +id: GENO:0000445 +name: is_feature_affected_by +def: "A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature." [] +comment: This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases) +property_value: IAO:0000118 "class_to_feature_relation" xsd:string + +[Typedef] +id: GENO:0000447 +name: is_gene_target_of +def: "A relation between a gene class and a gene targeting reagent that targets it." [] +comment: Domain = punned gene class\nRange = gene knockdown reagent +property_value: IAO:0000118 "is_target_of" xsd:string +is_a: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000449 +name: has_expression_variant +def: "A relation linking a gene class to one of an expression-variant of that gene.." [] +property_value: IAO:0000116 "Domain = punned gene class\nRange = expression variant feature" xsd:string +property_value: IAO:0000118 "has_expression_variant_instance" xsd:string +is_a: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000486 +name: obsolete_is_variant_with +def: "A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression." [] +comment: This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of. +property_value: IAO:0000231 "Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property." xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000488 +name: obsolete_is_expression_variant_with +def: "A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways)." [] +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000580 +name: has_qualifier +def: "A relation used to describe a context or conditions that define and/or identify an entity." [] +property_value: IAO:0000116 "Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association.\n\nUsed in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features." xsd:string +property_value: IAO:0000118 "has_qualifying_context" xsd:string + +[Typedef] +id: GENO:0000608 +name: has_zygosity +def: "a relation to link a single locus complement to its zygosity." [] +domain: GENO:0000516 ! single locus complement +range: GENO:0000133 ! zygosity +is_a: GENO:0000207 ! has_sequence_attribute + +[Typedef] +id: GENO:0000610 +name: is_reference_allele_of +def: "A relationship between a reference locus/allele and the gene class it is an allele of." [] +domain: GENO:0000036 ! reference allele +is_a: GENO:0000408 ! is_allele_of + +[Typedef] +id: GENO:0000626 +name: has_staining_intensity +comment: Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized. +property_value: IAO:0000116 "Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed." xsd:string +property_value: IAO:0000118 "has_color_value" xsd:string +is_a: GENO:0000207 ! has_sequence_attribute + +[Typedef] +id: GENO:0000634 +name: is_targeted_by +def: "relation between an molecular agent and its molecular target" [] +property_value: IAO:0000112 "Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant." xsd:string + +[Typedef] +id: GENO:0000639 +name: sequence_derives_from +def: "Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence." [] +property_value: IAO:0000112 "1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. \n\n2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds.\n\n3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC)" xsd:string +holds_over_chain: BFO:0000051 GENO:0000639 + +[Typedef] +id: GENO:0000641 +name: is_variant_allele_of +def: "A relationship between a variant allele and the gene class it is an allele of." [] +domain: GENO:0000002 ! variant allele +is_a: GENO:0000408 ! is_allele_of + +[Typedef] +id: GENO:0000650 +name: has_sex_agnostic_part +property_value: IAO:0000116 "Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases." xsd:string +is_a: GENO:0000654 ! has_sequence_part +inverse_of: GENO:0000661 ! is_sex_agnostic_part_of + +[Typedef] +id: GENO:0000651 +name: is_mutant_allele_of +comment: A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of. +domain: GENO:0000491 ! obsolete_mutant allele +is_a: GENO:0000641 ! is_variant_allele_of + +[Typedef] +id: GENO:0000652 +name: is_polymorphic_allele_of +def: "A relationship between a polymorphic allele and the gene class it is an allele of." [] +domain: GENO:0000497 ! polymorphic allele +is_a: GENO:0000641 ! is_variant_allele_of + +[Typedef] +id: GENO:0000653 +name: is_wild_type_allele_of +def: "A relationship between a wild-type allele and the gene class it is an allele of." [] +domain: GENO:0000501 ! wild-type allele +is_a: GENO:0000408 ! is_allele_of + +[Typedef] +id: GENO:0000654 +name: has_sequence_part +def: "An organizational class to hold relations of parthood between sequences/features." [] +is_a: BFO:0000051 ! has part +inverse_of: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000655 +name: is_sequence_part_of +is_a: BFO:0000050 ! is part of + +[Typedef] +id: GENO:0000661 +name: is_sex_agnostic_part_of +def: "Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases." [] +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000683 +name: varies_with +def: "A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part)." [] +comment: This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of) +is_symmetric: true + +[Typedef] +id: GENO:0000708 +name: faldo properties +comment: organizational property to hold imports from faldo. + +[Typedef] +id: GENO:0000726 +name: has_sequence_feature +def: "A relation linking a qualified sequence feature to its component sequence feature." [] +comment: In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism. +property_value: IAO:0000118 "has_sequence_feature_component" xsd:string +range: SO:0000110 ! sequence_feature + +[Typedef] +id: GENO:0000740 +name: has_inferred_phenotype +holds_over_chain: GENO:0000382 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype."} +holds_over_chain: GENO:0000383 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration."} +holds_over_chain: GENO:0000413 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations from a (sequence-)variant locus instance to a gene class (to support cases where the phenotype association is made at the level of the variant gene locus)."} +holds_over_chain: GENO:0000449 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations from an expression-variant gene instance to a gene class (to support cases where the phenotype association is made at the level of the expression-variant gene)."} +holds_over_chain: GENO:0000661 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)"} +is_a: RO:0002200 ! has phenotype + +[Typedef] +id: GENO:0000741 +name: obsolete_has_regulatory_part +comment: Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes. +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000742 +name: obsolete_is_alteration_within +def: "A relation linking a sequence_alteration to the gene it alters." [] +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "is_within_allele_of" xsd:string +holds_over_chain: GENO:0000383 GENO:0000408 +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000743 +name: has_asserted_phenotype +is_a: RO:0002200 ! has phenotype + +[Typedef] +id: GENO:0000761 +name: is_regulatory_part_of +property_value: IAO:0000116 "Proposal for a property linking regulatory elements to larger features of which they are a part." xsd:string +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000767 +name: obsolete_has_position_component +def: "A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances." [] +property_value: IAO:0000116 "For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them." xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000783 +name: has_sequence_unit +def: "A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues)" [] +is_a: GENO:0000654 ! has_sequence_part + +[Typedef] +id: GENO:0000784 +name: completely_varies_with +def: "A relation between two seqeunces or features that are considered variant with each other along their entire extents." [] +is_symmetric: true +is_a: GENO:0000683 ! varies_with + +[Typedef] +id: GENO:0000790 +name: related_condition + +[Typedef] +id: GENO:0000791 +name: inferred_to_cause_condition +property_value: IAO:0000116 "Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene)" xsd:string +property_value: IAO:0000116 "The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains.\n\nBelow are the different kinds/paths of propagation we desire:\n1. Propagation 'down' a genotype (from larger components to smaller ones)\n2. Propagation 'up' a genotype (from smaller components to larger ones)\n3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype).\n4. From an effective genotype to its intrinsic and extrinsic components.\n5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele).\n6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this.\n\nNote that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha/shha [AB] to shha/shha [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition')" xsd:string +holds_over_chain: GENO:0000382 RO:0003303 {comment="Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype."} +holds_over_chain: GENO:0000383 RO:0003303 {comment="Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration."} +holds_over_chain: GENO:0000445 RO:0003303 {comment="Property chain to propagate inferred condition associations from a variant locus instance to a gene class (to support cases where the phenotype association is made directly at the level of the variant locus/allele)."} +holds_over_chain: GENO:0000661 RO:0003303 {comment="Property chain to propagate inferred condition associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)"} +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000793 +name: inferred_to_contribute_to_condition +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000794 +name: inferred_to_correlate_with_condition +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000840 +name: pathogenic_for_condition +xref: LOINC:LA6668-3 +is_a: RO:0003303 ! causes condition + +[Typedef] +id: GENO:0000841 +name: likely_pathogenic_for_condition +xref: LOINC:LA26332-9 +is_a: RO:0003303 ! causes condition + +[Typedef] +id: GENO:0000842 +name: non-causal_for_condition +def: "Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to." [] +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000843 +name: benign_for_condition +xref: LOINC:LA6675-8 +is_a: GENO:0000842 ! non-causal_for_condition + +[Typedef] +id: GENO:0000844 +name: likely_benign_for_condition +xref: LOINC:LA26334-5 +is_a: GENO:0000842 ! non-causal_for_condition + +[Typedef] +id: GENO:0000845 +name: has_uncertain_significance_for_condition +xref: LOINC:LA26333-7 +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000846 +name: has_qualifying_process +def: "A relation used to describe a process contextualizing the identity of an entity." [] +is_a: GENO:0000580 ! has_qualifier + +[Typedef] +id: GENO:0000847 +name: has_qualifying_environment +def: "A relation used to describe an environment contextualizing the identity of an entity." [] +is_a: GENO:0000580 ! has_qualifier + +[Typedef] +id: GENO:0000849 +name: is_candidate_variant_for +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000903 +name: has_location +def: "A relation linking a sequence feature to the location it occupies on some reference sequence." [] +property_value: IAO:0000118 "occupies" xsd:string +domain: SO:0000110 ! sequence_feature +range: GENO:0000815 ! sequence feature location + +[Typedef] +id: GENO:0000906 +name: on strand +comment: Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from. + +[Typedef] +id: GENO:0000957 +name: has_defining_location +def: "Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement." [] +comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location.\n\nFor copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. +range: GENO:0000815 ! sequence feature location + +[Typedef] +id: GENO:0000958 +name: has_defining_sequence +def: "Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement." [] +comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement. +range: GENO:0000702 ! biological sequence + +[Typedef] +id: GENO:0000959 +name: has_defining_feature +def: "Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement." [] +comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference.\n\nFor copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. +range: SO:0000110 ! sequence_feature + +[Typedef] +id: GENO:0000966 +name: has_interval +def: "Relates a sequence feature location to an interval that defines its start and end position." [] +comment: Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects. +domain: GENO:0000815 ! sequence feature location + +[Typedef] +id: GENO:0000967 +name: has_reference_sequence +def: "Relates a 'sequence feature location' to a sequence that it is anchored to." [] + +[Typedef] +id: IAO:0000136 +name: is about +def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." [] + +[Typedef] +id: IAO:0000219 +name: denotes +def: "Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" [] +property_value: IAO:0000116 "Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of." xsd:string +is_a: IAO:0000136 ! is about + +[Typedef] +id: OBI:0000293 +name: has_specified_input +def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +is_a: RO:0002233 ! has input + +[Typedef] +id: OBI:0000299 +name: has_specified_output +def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +is_a: RO:0002234 ! has output + +[Typedef] +id: RO:0000052 +name: inheres_in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] + +[Typedef] +id: RO:0000059 +name: concretizes +def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000087 +name: has_role +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0001000 +name: derives from + +[Typedef] +id: RO:0002091 +name: starts during +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002093 +name: ends during +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +is_symmetric: true + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] + +[Typedef] +id: RO:0002200 +name: has phenotype +def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] +range: UPHENO:0001001 ! Phenotype +inverse_of: RO:0002201 ! phenotype of + +[Typedef] +id: RO:0002201 +name: phenotype of +domain: UPHENO:0001001 ! Phenotype + +[Typedef] +id: RO:0002222 +name: temporally related to + +[Typedef] +id: RO:0002233 +name: has input +def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +is_a: RO:0000057 ! has participant + +[Typedef] +id: RO:0002234 +name: has output +def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." [] +is_a: RO:0000057 ! has participant +inverse_of: RO:0002353 ! output of + +[Typedef] +id: RO:0002350 +name: is member of +is_a: BFO:0000050 ! is part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000112 "Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes\n\nExample 2: a collection of information entities such as a genotype being comprised of a background component and a variant component" xsd:string +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002352 +name: input of +is_a: RO:0000056 ! participates in + +[Typedef] +id: RO:0002353 +name: output of +is_a: RO:0000056 ! participates in + +[Typedef] +id: RO:0002354 +name: obsolete_formed as result of +is_a: ObsoleteProperty + +[Typedef] +id: RO:000244 +name: molecularly controls +def: "Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b" [] + +[Typedef] +id: RO:0002522 +name: bounds sequence of +def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: GENO:0000654 ! has_sequence_part + +[Typedef] +id: RO:0002524 +name: has subsequence +def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +is_a: GENO:0000654 ! has_sequence_part +inverse_of: RO:0002525 ! is subsequence of + +[Typedef] +id: RO:0002525 +name: is subsequence of +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: RO:0002526 +name: overlaps sequence of +def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +property_value: http://purl.org/dc/terms/source http://biorxiv.org/content/early/2014/06/27/006650.abstract xsd:string +is_a: RO:0002131 ! overlaps + +[Typedef] +id: RO:0002528 +name: is upstream of sequence of +def: "inverse of downstream of sequence of" [] + +[Typedef] +id: RO:0002529 +name: is downstream of sequence of +def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] + +[Typedef] +id: RO:0003301 +name: is model of +def: "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] +comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. +property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" xsd:string +property_value: IAO:0000117 "Matthew Brush" xsd:string + +[Typedef] +id: RO:0003302 +name: causes or contributes to condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions. +property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." xsd:string +property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: RO:0003303 +name: causes condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003304 +name: contributes to condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003305 +name: contributes to severity of condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual." [] +property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003306 +name: contributes to frequency of condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population." [] +property_value: IAO:0000118 "contributes to penetrance of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003307 +name: is preventative for condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions. +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: RO:0003308 +name: correlated with condition +def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: begin +name: begin +is_a: GENO:0000708 ! faldo properties + +[Typedef] +id: end +name: end +is_a: GENO:0000708 ! faldo properties + +[Typedef] +id: http://purl.org/oban/association_has_object +name: association has object + +[Typedef] +id: http://purl.org/oban/association_has_predicate +name: association has predicate + +[Typedef] +id: http://purl.org/oban/association_has_subject +name: association has subject + +[Typedef] +id: location +name: location +is_a: GENO:0000708 ! faldo properties + +[Typedef] +id: reference +name: reference +def: "The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly." [] +is_a: GENO:0000708 ! faldo properties + diff --git a/geno-base.owl b/geno-base.owl new file mode 100644 index 0000000..8750a6b --- /dev/null +++ b/geno-base.owl @@ -0,0 +1,8289 @@ + + + + + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. + +Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 + GENO ontology + Unspecified + + + + + + + + + + + + + Used to annotation axioms that define identity criteria for instances of a class. + is_identity_criteria + + + + + + + + + proabalistic_quantifier + + + + + + + + Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models. + mixin + + + + + + + + + gene symbol + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + begin + + + + + + + + + end + + + + + + + + + location + + + + + + + + + The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly. + reference + + + + + + + + + + + is part of + + + + + + + + + + has part + + + + + + + + + + + + + + + + + + A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'. + Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants. + http://purl.obolibrary.org/obo/so_has_quality + has_sequence_attribute + + + + + + + + + + + + A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes + materializes + Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence. + bears_concretization_of + + + + + + + + + is_genotype_of + + + + + + + + + + + + + + + + + + + A relationship that holds between a biological entity and some level of genetic variation present in its genome. + This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype. + The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations. + has_genotype + + + + + + + + + + + An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO) + No proper part relation anymore in RO/BFO? + http://semanticscience.org/resource/SIO_000053 + has_proper_part + + + + + + + + + + A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears. + has_sequence_component + has_state + VMC:state + 'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule. + has_sequence + + + + + + + + + + A geno:intrinnsic genotype 'specifies' a SO:genome. +A geno:karyotype 'specifies' a geno:karyotype feature collection. + A relationship between an information content entity representing a specification, and the entity it specifies. + obsolete_specifies + + + + + + + + + Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. + obsolete_approximates_sequence + + + + + + + + + Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. + obsolete_resolves_to_sequence + + + + + + + + + An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole. + http://semanticscience.org/resource/SIO_000093 + is_proper_part_of + + + + + + + + + is_sequence_of + + + + + + + + + is_subject_of + + + + + + + + + obsolete_is_specified_by + + + + + + + + + + shortcut relation used to link a phenotype directly to a genotype of an organism + is_phenotype_of_organism_with_genotype + is_phenotype_with_genotype + phenotype_has_genotype + Might expand to something like: + +phenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype))))))) + obsolete_is_phenotype_of_genotype + + + + + + + + + + A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next. + Exploratory/temporary property, as we formalize our phenotypic inheritance model. + obsolete_participates_in_inheritance_process + + + + + + + + + + + A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression. + has_variant_part + + + + + + + + + + is_variant_part_of + + + + + + + + + + + A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant. + has_reference_sequence_part + has_reference_part + + + + + + + + + is_reference_part_of + + + + + + + + + + + <fgf8a^ti282a> is_allele_of the 'danio rerio fgf8a' gene locus. + A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size. + Domain = allele +Range = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation). + Note that the allele <fgf8a^ti282a> is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the <fgf8a^ti282a> allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product. + is_sequence_variant_of + To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size). + +While conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like "fgf8a<ti282a> is an allele of the Danio rerio fgf8a gene", and we may create data where fgf8a<ti282a> is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene). + +It is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. + +This departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\GAL4 gene. + +At the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'. + is_allele_of + + + + + + + + + + A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level). + is_variant_instance_of + formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus) + Domain = genomic feature instance +Range = punned gene class IRI + obsolete_is_genetic_variant_of + + + + + + + + + A relation linking a gene class to a sequence-varaint or expression-variant of the gene. + has_variant_instance + formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by) + Domain = punned gene class +Range = genomic feature + obsolete_has_genetic_variant + + + + + + + + + A relation linking a gene class to one of its sequence-variant alleles. + Domain = punned gene class +Range = allele + has_sequence_variant + has_allele + + + + + + + + + + A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets. + This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets. + targets_gene + + + + + + + + + + + + + + + + + A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression. + This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset. + has_affected_feature + + + + + + + + + + A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents. + Domain = expression variant feature. +Range = punned gene class + This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class. + is_expression_variant_of + + + + + + + + A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature. + class_to_feature_relation + This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases) + is_feature_affected_by + + + + + + + + + A relation between a gene class and a gene targeting reagent that targets it. + is_target_of + Domain = punned gene class +Range = gene knockdown reagent + is_gene_target_of + + + + + + + + + A relation linking a gene class to one of an expression-variant of that gene.. + Domain = punned gene class +Range = expression variant feature + has_expression_variant_instance + has_expression_variant + + + + + + + + + A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression. + Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property. + This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of. + obsolete_is_variant_with + + + + + + + + + A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways). + obsolete_is_expression_variant_with + + + + + + + + A relation used to describe a context or conditions that define and/or identify an entity. + Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association. + +Used in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features. + has_qualifying_context + has_qualifier + + + + + + + + + + + a relation to link a single locus complement to its zygosity. + has_zygosity + + + + + + + + + + A relationship between a reference locus/allele and the gene class it is an allele of. + is_reference_allele_of + + + + + + + + + Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed. + has_color_value + Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized. + has_staining_intensity + + + + + + + + Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant. + relation between an molecular agent and its molecular target + is_targeted_by + + + + + + + + + + + + + 1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. + +2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds. + +3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC) + Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence. + sequence_derives_from + + + + + + + + + + A relationship between a variant allele and the gene class it is an allele of. + is_variant_allele_of + + + + + + + + + + Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases. + has_sex_agnostic_part + + + + + + + + + + A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of. + is_mutant_allele_of + + + + + + + + + + A relationship between a polymorphic allele and the gene class it is an allele of. + is_polymorphic_allele_of + + + + + + + + + + A relationship between a wild-type allele and the gene class it is an allele of. + is_wild_type_allele_of + + + + + + + + + + An organizational class to hold relations of parthood between sequences/features. + has_sequence_part + + + + + + + + + is_sequence_part_of + + + + + + + + + Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases. + is_sex_agnostic_part_of + + + + + + + + + A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part). + This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of) + varies_with + + + + + + + + organizational property to hold imports from faldo. + faldo properties + + + + + + + + + + + + + + + + + A relation linking a qualified sequence feature to its component sequence feature. + has_sequence_feature_component + In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism. + has_sequence_feature + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_inferred_phenotype + + + + + + + + + Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype. + + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration. + + + + + + + + + + Property chain to propagate inferred phenotype associations from an intrinsic genotype component (e.g. a (sequence-)variant locus instance) to a gene class. + + + + + + + + + Property chain to propagate inferred phenotype associations from a (sequence-)variant locus instance to a gene class (to support cases where the phenotype association is made at the level of the variant gene locus). + + + + + + + + + + Property chain to propagate inferred phenotype associations from an extrinnsic genotype component (e.g. a expression-variant gene instance) to a gene class. + + + + + + + + + Property chain to propagate inferred phenotype associations from an expression-variant gene instance to a gene class (to support cases where the phenotype association is made at the level of the expression-variant gene). + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components) + + + + + + + + + Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes. + obsolete_has_regulatory_part + + + + + + + + + + + + + + A relation linking a sequence_alteration to the gene it alters. + is_within_allele_of + obsolete_is_alteration_within + + + + + + + + + has_asserted_phenotype + + + + + + + + + Proposal for a property linking regulatory elements to larger features of which they are a part. + is_regulatory_part_of + + + + + + + + + A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances. + For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them. + obsolete_has_position_component + + + + + + + + + A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues) + has_sequence_unit + + + + + + + + + + A relation between two seqeunces or features that are considered variant with each other along their entire extents. + completely_varies_with + + + + + + + + related_condition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene) + The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains. + +Below are the different kinds/paths of propagation we desire: +1. Propagation 'down' a genotype (from larger components to smaller ones) +2. Propagation 'up' a genotype (from smaller components to larger ones) +3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype). +4. From an effective genotype to its intrinsic and extrinsic components. +5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele). +6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this. + +Note that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha<tbx392>/shha<tbx392> [AB] to shha<tbx392>/shha<tbx392> [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition') + inferred_to_cause_condition + + + + + + + + + + This is a case of inter-gneotype phenotype propagation, requiring propagation down oen genotype and then up another. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to have this chain. + +This property chain propagates a phenotype asserted on a sex-qualified intrinsic genotype, down to its sex-agnostic genotype part, and then up to a parent effective genotype that has it as a variant part. I think this is OK in all cases, so we can implement this as the one case where we can have inter-genotype pheno propagation. But as noted, there will likely be no data that actually meets criteria to use this chain, so we can probably leave it out. + + + + + + + + + Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype. + + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, to the coompnent variant parts of this sex-agnostic genotype. + + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to move past the sex-agnostic genotype and down to its parts. + +The following shorter chain would also suffice here: +is_variant_part_of o inferred_to_cause_condition + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration. + + + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, through the coompnent variant parts of this sex-agnostic genotype, and to the affected gene. + + + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to propagate to genes. + +The shorter chain below would also suffice for this propagation: +has_allele o inferred_to_cause_condition + + + + + + + + + + Property chain to propagate inferred condition associations from an sequence alteration through the variant locus to a gene class. (separate chains are needed to propagate from the variant locus to the gene class, and another to propagate from a genotype, GVC, or VSLC to the gene class). + + +NOTE that i dont need this property chain if I have a property chain to infer a has_affected_locus link from a sequence alteration to a gene when the link is asserted from the variant locus to the gene: + +is_variant_part_of o has_affected_locus --> has_affected_locus + + + + + + + + + + Obsolete comment: Property chain to propagate inferred condition associations from an intrinsic genotype, GC, or VLSC to a gene class. (a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class). + +The following, shorter chain, would also suffice here: +has_allele o inferred_to_cause_condition -> inferred_to_cause_condition + Property chain to propagate inferred condition associations from an intrinsic genotype, GVC, or VLSC to an affected gene class, or from an extrinsic gneotype or component to an affected gene class. + +The following, shorter chain, would also suffice here: +has_affected_locus o inferred_to_cause_condition -> inferred_to_cause_condition + +Note that a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class in cases where the link to gene is through the variant locus rather than the seq alteration). + + + + + + + + + Property chain to propagate inferred condition associations from a variant locus instance to a gene class (to support cases where the phenotype association is made directly at the level of the variant locus/allele). + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype to a sex-agnostic intrinsic genotype. + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components) + + + + + + + + + inferred_to_contribute_to_condition + + + + + + + + + inferred_to_correlate_with_condition + + + + + + + + + LOINC:LA6668-3 + pathogenic_for_condition + + + + + + + + + LOINC:LA26332-9 + likely_pathogenic_for_condition + + + + + + + + + Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to. + non-causal_for_condition + + + + + + + + + LOINC:LA6675-8 + benign_for_condition + + + + + + + + + LOINC:LA26334-5 + likely_benign_for_condition + + + + + + + + + LOINC:LA26333-7 + has_uncertain_significance_for_condition + + + + + + + + + A relation used to describe a process contextualizing the identity of an entity. + has_qualifying_process + + + + + + + + + A relation used to describe an environment contextualizing the identity of an entity. + has_qualifying_environment + + + + + + + + + is_candidate_variant_for + + + + + + + + + + A relation linking a sequence feature to the location it occupies on some reference sequence. + occupies + has_location + + + + + + + + Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from. + on strand + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location. + +For copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. + has_defining_location + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement. + has_defining_sequence + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference. + +For copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. + has_defining_feature + + + + + + + + + Relates a sequence feature location to an interval that defines its start and end position. + Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects. + has_interval + + + + + + + + Relates a 'sequence feature location' to a sequence that it is anchored to. + has_reference_sequence + + + + + + + + is_about is a (currently) primitive relation that relates an information artifact to an entity. + is about + + + + + + + + + Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically + Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of. + denotes + + + + + + + + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + has_specified_input + + + + + + + + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + has_specified_output + + + + + + + + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + inheres_in + + + + + + + + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + bearer of + + + + + + + + + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates in + + + + + + + + a relation between a process and a continuant, in which the continuant is somehow involved in the process + has participant + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + has quality + + + + + + + + + has_role + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + derives from + + + + + + + + + starts during + + + + + + + + + ends during + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + overlaps + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + in taxon + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + has phenotype + + + + + + + + + phenotype of + + + + + + + + temporally related to + + + + + + + + + p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + has input + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + has output + + + + + + + + + + is member of + + + + + + + + + Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes + +Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component + has member is a mereological relation between a collection and an item. + has member + + + + + + + + + input of + + + + + + + + + output of + + + + + + + + + obsolete_formed as result of + + + + + + + + Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b + molecularly controls + + + + + + + + + x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + Chris Mungall + bounds sequence of + + + + + + + + + + x has subsequence y iff all of the sequence parts of x are sequence parts of y + has subsequence + + + + + + + + + is subsequence of + + + + + + + + + x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. + http://biorxiv.org/content/early/2014/06/27/006650.abstract + overlaps sequence of + + + + + + + + inverse of downstream of sequence of + is upstream of sequence of + + + + + + + + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + is downstream of sequence of + + + + + + + + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + Matthew Brush + The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + is model of + + + + + + + + + The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. + +An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition. + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. + causes or contributes to condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition. + causes condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition. + contributes to condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual. + contributes to expressivity of condition + contributes to severity of condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population. + contributes to penetrance of condition + contributes to frequency of condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. + is preventative for condition + + + + + + + + + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + correlated with condition + + + + + + + + association has object + + + + + + + + association has predicate + + + + + + + + association has subject + + + + + + + + + + + + + + + + + + + The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is. + position + + + + + + + + + Property linking a sequence or sequence feature to an integer representing its length in terms of the number of units in the sequence. + has_extent + + + + + + + + + + Shortcut relation linking a sequence feature directly to a string representing the 'state' of its sequence - i.e. the ordering of units that comprise it (e.g. 'atgcagctagctaccgtcgatcg'). + has_sequence_string + + + + + + + + ObsoleteDataProperty + + + + + + + + The 'rank' quantifier in Bgee gene-anatomy associations, that indicates the imporatnace/specificity of a gene expression in a given anatommy relative to expressionin other anatomies for the same gene. + Property to link an assertion or association with some value quantifying its relevance or ranking. + has_quantifier + + + + + + + + The starting position of a sequence feature or interval. + start_position + + + + + + + + The ending position of a sequence feature or interval. + end_position + + + + + + + + + + Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg'). + has_string + + + + + + + + Describes the number of members in some set. + has_count + In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'. + has_member_count + + + + + + + + + + + + + + Both strands + + + + + + + + + A position that is exactly known. + Exact position + + + + + + + + + Positive strand + + + + + + + + + Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate. + We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region). + FALDO + Position + + + + + + + + + + + + + + 1 + + + + + 1 + + + + + + A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene. + From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence. + Region + + + + + + + + + Negative strand + + + + + + + + + Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'. + Stranded position + + + + + + + + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + + + + + + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + continuant + continuant + + + + + + + + + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + occurrent + occurrent + + + + + + + + + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + independent continuant + independent continuant + + + + + + + + + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + + process + process + + + + + + + + + + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocitosis and exocitosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89 + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + + disposition + disposition + + + + + + + + + + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + realizable entity + realizable entity + + + + + + + + + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + + quality + quality + + + + + + + + + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + specifically dependent continuant + specifically dependent continuant + + + + + + + + + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + role + role + + + + + + + + + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + generically dependent continuant + generically dependent continuant + + + + + + + + + the function of a hammer to drive in nails + the function of a heart pacemaker to regulate the beating of a heart through electricity + the function of amylase in saliva to break down starch into sugar + BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + + function + + + + + + + + + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + material entity + material entity + + + + + + + + + Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology. + molecular entity + + + + + + + + + nucleic acid + + + + + + + + + + + + + + + A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). + cell line + + + + + + + + + Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies. + cell + + + + + + + + + 1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions. + +2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity). + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system + + + + + + + + + A technique is a planned process used to accomplish a specific activity or task. + technique + + + + + + + + + A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo. + embryonic stem cell line + + + + + + + + + A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types. + stem cell line + + + + + + + + + Example zebrafish intrinsic genotype: + +Genotype = fgf8a<ti282a/+>; shha<tb392/tb392> (AB) +reference component (genomic background) = AB +variant component ('genomic variation complement') = fgf8a<ti282a/+>; shha<tb392/tb392> + +. . . and within this variant component, there are two 'variant single locus complements' represented: + +allele complement 1 = fgf8a<ti282a/+> +allele complement 2 = shha<tb392/tb392> + +and within each of these 'variant single locus complements' there is one or more variant gene locus member: + +in complement 1: fgf8a<ti282a> +in complement 2: shha<ttb392> + A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement) + This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). + +Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. + genotype + organismal genotype + sex-agnostic intrinsic genotype + In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances). + genomic genotype (sex-agnostic) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An allele that varies in it sequence from what is considered the reference or canonical sequence at that location. + The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles. + alternate allele + sequence-variant feature + variant feature + Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another. + +A variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence. + variant allele + + + + + + + + + + + + + + + + + + + A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype. + Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases. + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation. + +In model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a<t1282a/+>(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)). + genomic variation complement + + + + + + + + + The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB) + A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). + Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it. + genomic background + OBI:genetic population background information + background genome + + + + + + + + + + + + + + + The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The "mn004Gt" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome. + +http://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722 + +http://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8 + A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene) + Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment). + +This design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not. + http://purl.obolibrary.org/obo/SO_0001023 ! allele + In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion. + +A genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene. + gene allele + + + + + + + + + + + + + + + + + + + A sequence that serves as a standard against which other sequences at the same location are compared. + The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant. + reference sequence + A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence. + reference sequence + + + + + + + + + a collection more than one sequence features (ie a collection of discontinuous sequence features) + perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one) + 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. + obsolete_sequence feature collection + + + + + + + + + A sequence feature collection comprised of discontiguous sequences from a single genome + Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system. + genomic feature collection + Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. + obsolete_genomic feature collection + + + + + + + + + A single locus complement that serves as a standard against which 'variant' sequences are compared + reference allelic complement + reference single locus feature complement + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class axiom: +'single locus complement' + and (has_sequence_attribute some reference) + +SC axioms: +'has member' exactly 0 'variant allele' +'has member' only 'reference genomic feature' +'has member' some 'reference genomic feature' + obsolete_reference single locus complement + + + + + + + + + + + + + + + + + + + A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13). + variant allelic complement + Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members. + +Note that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant. + variant single locus complement + + + + + + + + + + + + + + + + + + + + + + + + + A genome that varies at one or more loci from the sequence of some reference genome. + http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here) + variant genome + + + + + + + + + + + + + + + + + + + An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome. + Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population. + +In model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared. + reference allele + + + + + + + + + + A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus). + Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '. + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class def: 'genomic feature' + and (has_sequence_attribute some unspecified) + An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). + obsolete_unspecified feature + + + + + + + + + A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature. + hemizygous reference junction + Eliminating unecessary defined/organizational classes. Former logical def: + +junction + and (has_sequence_attribute some reference) + +Subclass axiom: +is_variant_with some insertion + In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. + +The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. + obsolete_reference junction + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a danio rerio. + danio rerio gene + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a homo sapiens. + homo sapiens gene + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a mus musculus. + mus musculus gene + + + + + + + + + A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development. +http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690 + +Note that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469 + A version/allele of a gene that serves as a standard against which variant genes are compared. + reference gene + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class axiom: +'gene allele' + and (has_sequence_attribute some reference) + +SC axioms: +is_variant_with some 'gene allele' +is_reference_allele_of some gene + Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. + +In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. + obsolete_reference gene allele + + + + + + + + + obsolete_experimental insertion + + + + + + + + + + + + + + + gene trap insertion + + + + + + + + + + + + + + + A transgene that has been integrated into a chrromosome in the host genome. + An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion. + +An 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome. + integrated transgene + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny. + 1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. + +2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way. + 1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. + +2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms. + genomic material + + + + + + + + + A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion. + physical genome + A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements. + +Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome. + material genome + + + + + + + + + a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role) + Consider http://semanticscience.org/resource/SIO_001062 ! human population ("A human population refers to a collection of human beings"). + homo sapiens population + human population + + + + + + + + + + + + + + + A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical. + organism strain or breed + Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR) + strain or breed + + + + + + + + + A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon) + taxonomic group + + + + + + + + + mus musculus strain + + + + + + + + + + + + + + + + + + + + + danio rerio strain + + + + + + + + + sequence attribute that can inhere only in a collection of more than one sequence features + obsolete_sequence feature collection attribute + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes). + in cis + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes). + in trans + + + + + + + + + + + + + + + An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different). + allelic state + derived from https://en.wikipedia.org/wiki/Zygosity + http://semanticscience.org/resource/SIO_001263 + zygosity + + + + + + + + + hemizygous + + + + + + + + + heterozygous + + + + + + + + + homozygous + + + + + + + + + indeterminite zygosity + no-call zygosity + unknown zygosity + unspecified zygosity + + + + + indeterminite zygosity + MGI uses this term when zygosity is not known. + + + + + no-call zygosity + (this is how the GVF10 format/standard refers to loci without enough data to make an accurate call . . . see http://www.sequenceontology.org/resources/gvf.html#quick_gvf_examples) + + + + + + + + + The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event. + We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells). + +We can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms. + heritabililty + + + + + + + + + heritable + + + + + + + + + non-heritable + + + + + + + + + The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment. + The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family. + mode of inheritance + phenotypic inheritance pattern + http://purl.obolibrary.org/obo/HP_0000005 + http://purl.obolibrary.org/obo/NCIT_C45827 + An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, "genetic context" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. + +These genetic and environmental "interactions" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y. + inheritance pattern + + + + + + + + + disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes + Triage until decide if want to define this as grouping class that would result in multiple-inheritance. + obsolete_dominant inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant autosomal inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + pure dominant inheritance + complete autosomal dominant inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + intermediate dominant autosomal inheritance + semi-dominant autosomal inheritance + incomplete autosomal dominant inheritance + + + + + + + + + An X-linked inheritance pattern wherein the trait manifests in heterozygotes. + http://purl.obolibrary.org/obo/HP_0001423 + X-linked dominant inheritance + + + + + + + + + An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes. + vertical inheritance + http://purl.obolibrary.org/obo/HP_0000006 + autosomal dominant inheritance + + + + + + + + + An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals. + autosomal recessive inheritance + + + + + + + + + An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals. + http://purl.obolibrary.org/obo/HP_0001419 + X-linked recessive inheritance + + + + + + + + + duplicate term, use GENO:0000148 + obsolete_autosomal recessive inheritance + + + + + + + + + An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared. + Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another. + reference + + + + + + + + + unspecified life cycle stage + + + + + + + + + objective is to insert some specified sequence into the genome of a cell or virus + genetic insertion technique + + + + + + + + + mutagen treatment technique + + + + + + + + + + + + + + + a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). + This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. + targeted gene mutation technique + + + + + + + + + Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. + random genetic insertion technique + + + + + + + + + + + + + + + targeted genetic insertion technique + + + + + + + + + + + + + + + enhancer trapping technique + + + + + + + + + + + + + + + gene trapping technique + + + + + + + + + + + + + + + promoter trapping technique + + + + + + + + + + + + + + + targeted knock-in technique + + + + + + + + + random transgene insertion technique + + + + + + + + + A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome + obsolete_chromosome complement + + + + + + + + + + + + + + + + A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation + duplicate chromosome + This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome. + gained aneusomic chromosome + + + + + + + + + + + + 0 + + + + A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation. + This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as "the point at which one or more contiguous nucleotides were excised". + absent aneusomic chromosome + lost aneusomic chromosome + + + + + + + + + + + + + + + + + + + + + + A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation. + Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism. + aneuploid chromosomal segment + aneusomic chromosomal subregion/segment + partial aneusomic chromosomal element + Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome." + aneusomic chromosomal part + + + + + + + + + + A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event. + duplicate partial aneuploid chromosomal element + translocated duplicate chromosomal element + translocated duplicate chromosomal segment + Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location. + gained aneusomic chromosomal segment + + + + + + + + + + + + 0 + + + + A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome. + In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement + dropped partial anneuploid chromosomal element + translocated absent chromosomal segment + truncated chromosome terminus + This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome. + +Loss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus. + lost aneusomic chromosomal segment + + + + + + + + + + + + + + + + + A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation + complete aneusomic chromosome + Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism. + +Similarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication. + aneusomic chromosome + + + + + + + + + Stub class to serve as root of hierarchy for imports of biological processes from GO-BP. + biological process + + + + + + + + + disomic zygosity + + + + + + + + + aneusomic zygosity + + + + + + + + + trisomic homozygous + + + + + + + + + trisomic heterozygous + + + + + + + + + A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a<ti282a>/fgf8a<x15>) + trans-heterozygous + compound heterozygous + + + + + + + + + A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe) + replaced with SO:engineered_region + extra-genomic sequence + obsolete_reagent sequence feature + + + + + + + + + a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a<ti282a/+>) + simple heterozygous + + + + + + + + + + + + + + + + + + + A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc) + transgene part + + + + + + + + + An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level + variant + + + + + + + + + An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant. + polymorphic + + + + + + + + + An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence. + mutant + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism) + This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology. + 1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. + +2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). + +3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome. + genomic feature + + + + + + + + + + A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion). + This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material. + genetic material + + + + + + + + + + An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain. + Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines + Not required for any specific use case at this point so removed for simplicity. +Formely asserted as allele and inferred as varaint allele. +Eq class definition: +allele + and (mutation or ('has subsequence' some mutation)) + 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. + obsolete_mutant allele + + + + + + + + + + + + + + + A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain. + mutation + + + + + + + + + + + + + + + + + + + + + + + + + + + A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon) + Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element + episomal replicon + Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. + extrachromosomal replicon + + + + + + + + + expression construct feature + expression construct + + + + + + + + + An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population. + PMID: 25741868 ACMG Guidelines + Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%). + polymorphic allele + + + + + + + + + A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location. + major allele + major polymorphic allele + + + + + + + + + A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location). + minor allele + minor polymorphic allele + + + + + + + + + A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree. + ancestral allele + ancestral polymorphic allele + + + + + + + + + + + + + + + An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared. + wild-type allele + 'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain. + +The notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis. + wild-type allele + + + + + + + + + + wild-type gene allele + A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation. + wild-type gene + + + + + + + + + + + + + + + + + + + + + A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi. + The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position. + reagent targeted gene + + + + + + + + + A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome). + experimentally-expressed transgene + extrinsic transgene + transiently-expressed transgene + + + + + + + + + An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared. + wild-type + + + + + + + + + + + + + + + + + + + One of a set of sequence features known to exist at a particular genomic location. + A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene. + +To be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene. + +[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17) +[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17) +[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17) +[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17) +[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17) +[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17) +[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483 +[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17) +[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17) +[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17) +[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17) +[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17) + variable feature + An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). + +Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence). + allele + + + + + + + + + + a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation. + aneusomic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An allele of a gene that contains some sequence alteration. + A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset. + variant gene allele + + + + + + + + + The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a<ti282a/+>. + +The collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome. + A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism. + TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label. + allelic complement + homologous allele complement + single locus feature complement + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes. + +The fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. + single locus complement + + + + + + + + + In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as: + + shha<MO1-1ng/ul>; shhb<pFLAG-mmusShhb> + +This notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct. + A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state. + We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. + +Our rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. + +Finally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." + experimental genotype + expression genotype + An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment. + +The 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations. + extrinsic genotype + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs). + Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." + An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment. + effective genotype + + + + + + + + + + + + + + + A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes). + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment. + reagent-targeted gene complement + + + + + + + + + + + + + + + The set of all transgenes trransiently expressed in a biological system in the context of a given experiment. + experimental transgene complement + transiently-expressed transgene complement + + + + + + + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes). + A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism). + See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself. + expression allele + Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism). + +The identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system. + expression-variant gene + + + + + + + + + gene targeting reagent + sequence targeting reagent + gene knockdown reagent + + + + + + + + + A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent. + targeted gene segment + reagent-targeted gene subregion + + + + + + + + + + + + + + + + + + + + + + A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference. + As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh<tbx292>, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above. + Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). +Note however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO. + 1. Scope of 'Genetic State': +'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs. + +2. Genotype Subtypes: +In GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. + +Two more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features. + +3. The Genotype Partonomy: +'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a<ti282a/ti282a>; fgf3<t24149/+>[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements: + + - GVC: fgf8a<ti282a/ti282a>; fgf3<t24149/+> (total intrinsic variation in the genome) + - Genomic Background: AB (the reference against which the GVC is variant) + - VSLC1: fgf8a<ti282a/ti282a> (homozygous complement of gene alleles at one known variant locus) + - VSLC2: fgf3<t24149/+> (heterozygous complement of gene alleles at another known variant locus) + - Allele 1: fgf8a<ti282a> (variant version of the fgf8a gene, present in two copies) + - Allele 2: fgf3<t24149> (variant version of the fgf3 gene, present in one copy) + - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy) + - Sequence Alteration1: <ti282a> (the specific mutation within the fgf8a gene that makes it variant) + - Sequence Alteration2: <t24149> (the specific mutation within the fgf3 gene that makes it variant) + +A graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md + +One reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data. + genotype + + + + + + + + + ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl +This ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes. + zebrafish phenotype + + + + + + + + + an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. + homoplasmic + + + + + + + + + an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. + heteroplasmic + + + + + + + + + hemizygous X-linked + + + + + + + + + hemizygous Y-linked + + + + + + + + + hemizygous insertion-linked + + + + + + + + + + + + + + + + + + + + + + + + + A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). + Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it. + background genotype + genomic background + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. + New term request for SO. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosomal region + + + + + + + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosome sub-band + + + + + + + + + chromosomal band brightness + chromosomal band intensity + + + + + + + + + gpos + + + + + + + + + gneg + + + + + + + + + gvar + + + + + + + + + gpos100 + + + + + + + + + gpos75 + + + + + + + + + gpos50 + + + + + + + + + gpos25 + + + + + + + + + A chromosome arm that is the shorter of the two arms of a given chromosome. + p-arm + stalk + short chromosome arm + + + + + + + + + A chromosome arm that is the longer of the two arms of a given chromosome. + q-arm + long chromosome arm + + + + + + + + + gpos66 + + + + + + + + + gpos33 + + + + + + + + + + + + + + + A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed. + regulatory transgene region + + + + + + + + + + + + + + + A transgene part whose sequence is expressed in a gene product through transcription and/or translation. + coding transgene feature + expressed transgene region + + + + + + + + + reporter region + + + + + + + + + + + + + + + + + + + + + + + + + A transgene whose product is used as a selectable marker. + selectable marker transgene + + + + + + + + + + + + + + + A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell. + Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28) + Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). + +A base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation). + karyotype + + + + + + + + + + + + + + + A genomic genotype where the genomic background specifies a male or female sex chromosome complement. + This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). + +In the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former. + intrinsic genotype (sex-specific) + sex-qualified genotype + sex-qualified intrinsic genotype + We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances. + +Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. + genomic genotype (sex-qualified) + + + + + + + + + A genomic genotype here the genomic background specifies a male sex chromosome complement. + male intrinsic genotype + + + + + + + + + A genomic genotype here the genomic background specifies a female sex chromosome complement. + female intrinsic genotype + + + + + + + + + A background genotype whose sequence or identity is not known or specified. + unspecified background genotype + unspecified genomic background + + + + + + + + + + + + + + + + + + + + + 1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus + +2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele. + +3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y} + A set of sequence features. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature). + +The notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3]. + +[1] https://www.snpedia.com/index.php/APOE-%CE%B54 +[2] https://www.snpedia.com/index.php/APOE-%CE%B52 +[3] https://www.snpedia.com/index.php/Gs270 + sequence feature set + + + + + + + + + + + + + + + + + + + + + A set of genomic features (i.e. sequence features that are of genomic origin). + In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member. + genomic locus complement + A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature. + +The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. + genomic feature set + + + + + + + + + + + + + + + + + + + A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc). + defined gene part + SO:0000831 (gene member region) + gene part + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A transgene that codes for a product used as a reporter of gene expression or activity. + reporter transgene + + + + + + + + + A junction between bases, a deletion variant, a terminus at the end of a chromosome. + A genomic feature that has an extent of zero. + Former logical def: +'genomic feature' + and (has_extent value 0) + obsolete_null feature + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found. + aberrant extrachromosomal replicon + exogenous extrachromosomal replicon + transgenic extrachromosomal replicon + Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. + novel extrachromosomal replicon + + + + + + + + + + + + + + + + A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome. + This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature. + Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles. + novel replicon + + + + + + + + + An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome. + novel + + + + + + + + + A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide). + terminus + + + + + + + + + + + + + + + + + A sequence feature or a set of such features. + sequence feature or collection + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location. + sequence feature or set + + + + + + + + + + + + + + + + + A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides). + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + biomacromolecular sequence + state + VMC:State + 'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome. + biological sequence + + + + + + + + + + + true + + + + + state + In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele. + + + + + + + + + A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification. + qualified sequence feature or collection + + + + + + + + + + + + + + + + + + + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes). + A qualified sequence feature that carries sequence derived from the genome of a cell or organism. + qualified genomic feature + + + + + + + + + + + true + This axiom is an initial attempt to formalize the identity criteria of an extrinnsic context that separates qualified sequence features from sequence features (i.e. the context of its material bearer). As we further develop our efforts here this will get refined and more precise. + + + + + + + + + + + true + Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position). + + + + + + + + + + + + + + + + + + + + + + + + + + + A set of qualified sequence features that carry genomic sequence. + Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member. + A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele. + +A complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome. + qualified genomic feature set + + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. + Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome. + 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. + +2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. + intrinsic genotype + + + + + + + + + + + + + + + + + + + + + + + DNA sequence + + + + + + + + + + + + + + + + + + + + + + + RNA sequence + + + + + + + + + + + + + + + + + + + + + + + amino acid sequence + + + + + + + + + obsolete_biological sequence or collection + + + + + + + + + obsolete_biological sequence collection + + + + + + + + + + A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature. + As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell). + location-qualified sequence feature + + + + + + + + + A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct) + expression-qualified sequence feature + + + + + + + + + A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence. + This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature. + genomic coordinates + remodeling notion of sequence feature position around the idea of a 'genomic locus' + obsolete_genomic position + + + + + + + + + phenotypic inheritance process + + + + + + + + + A sequence attribute inhering in a feature whose identity is not specified. + obsolete_unspecified + + + + + + + + + An attribute describing a type of variation inhering in a sequence feature or collection. + allele attribute + variation attribute + + + + + + + + + + + + + + + + + + + An intrinsic genotype that specifies variation from a defined reference genome. + variant genomic genotype + + + + + + + + + An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities. + eliminating classes that are not necessary or add uneeded complexity. + obsolete_sequence information entity + + + + + + + + + + + + + + 1 + + + + + biological sequence residue + monomeric residue + biological sequence unit + + + + + + + + + deoxyribonucleic acid residue + DNA residue + + + + + + + + + ribonucleic acid residue + RNA residue + + + + + + + + + amino acid residue + + + + + + + + + An attribute, quality, or state of a sequence feature or collection. + http://purl.obolibrary.org/obo/SO_0000400 + Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity. + sequence feature attribute + + + + + + + + + + The location of a sequence feature as defined by its start and end position on some reference coordinate system. + 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). + +2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there. + sequence feature location + + + + + + + + + + A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature) + modification-qualified sequence feature + + + + + + + + + + + + + + + + + + + 1. The zebrafish "fgf8a<ti282a>/fgf8a<+>" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state). + +2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308. + + ##fileformat=VCFv4.2 + ##FORMAT=<ID=GT, Description="Genotype, 0=REF, 1=ALT"> + #CHROM POS REF ALT FILTER FORMAT SAMP001 + 20 2300608 C T PASS GT 0/1 + 20 2301308 T G PASS GT 1/1 + (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html) + +3. Some allelic genotype formats encode the genotype as a single string - e.g. "GRCh38 Chr12:258635(A;T)" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12. + A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes. + single locus genotype + An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location. + +This contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background. + allelic genotype + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each. + genotype-phenotype association + + + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + + + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + true + + + + + + + + + + + + + + + knockdown reagent targeted gene complement + + + + + + + + + + A sequence alteration within the coding sequence of a gene. + Not required at this poitn, so marked exploratory and obsoleted. +Asserted under sequence_alteration. + obsolete_coding sequence alteration + + + + + + + + + A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome. + P-element construct + + + + + + + + + An engineered region that is used to transfer foreign genetic material into a host cell. + engineered_genetic_vector + Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. + +Constructs are typically packaged as part of delivery systems such as plasmids or viral vectors. + engineered genetic construct + + + + + + + + + A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct. + non-integrated transgene + extra-chromosomal transgene + + + + + + + + + A collection of more than one sequence feature. + http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection + obsolete_sequence feature collection + + + + + + + + + + + + + + + A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block. + Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block. + +Instead, we can create an 'allele set' class as the haplotype parent? + Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype. + A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. + +As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': + +1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. + +2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). "Star alleles" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/). + +3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. + +Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. + haplotype + + + + + + + + + A set of genomic sequences (a biological sequence that is of genomic origin). + copy number complement + A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. + genomic sequence set + + + + + + + + + A relation used to describe an environment contextualizing the identity of an entity. + microsatellite alteration + + + + + + + + + A relation used to describe a process contextualizing the identity of an entity. + repeat region alteration + + + + + + + + + A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism + allelic state + + + + + + + + + allelic dosage + an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome. + gene dosage + Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute. + Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. + +Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. + obsolete_genetic dosage + + + + + + + + + A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent. + genetic origin + variant origin + allele origin + + + + + + + + + Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg. + maternally inherited + maternal allele origin + + + + + + + + + Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm. + paternally inherited + paternal allele origin + + + + + + + + + Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis. + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. + +De novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder. + de novo allele origin + + + + + + + + + Describes an allele whose origin is not known. + unknown allele origin + + + + + + + + + Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body. + acquired + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells. + +These acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations. + somatic allele origin + + + + + + + + + a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells). + germ-line + replaced by GENO:0000900 ! 'germline' + obsolete_gametic + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement') + +Alt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome. + "Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes." +From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/ +https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/ + diplotype + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes. + allelic phase + + + + + + + + + + + + + + + + + + + + + oryzias latipes strain + + + + + + + + + Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg). + hereditary + parental origin + parentally inherited + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells. + germline allele origin + + + + + + + + + An inheritance pattern that is not determined or not known. + unknown inheritance + undetermined inheritance + + + + + + + + + The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”. + One of a set of sequence features or haplotypes that exist at a particular genetic locus. <see ClinGen Allele Model> + The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. + http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/ + No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. + ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) + As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. + +In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) + obsolete_canonical allele + + + + + + + + + An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence. + The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. + http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ + No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. + +Former axiom: denotes some 'obsolete_canonical allele' + ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) + The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. + obsolete_contextual allele + + + + + + + + + A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not. + heteroplasmic mitochondrial inheritance + + + + + + + + + A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited. + homoplasmic mitochondrial inheritance + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + An generically dependent continuant that carries biological sequence that is part of or derived from a genome. + An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities. + genomic entity + + + + + + + + + A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations. + Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as +"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations." Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location. + +Current definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele. + Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424. + A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. + haplotype block + + + + + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. + 'Genomic Genotype' vs 'Genome' in GENO: +A genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome. + complete genotype + 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. + +2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. + genomic genotype + + + + + + + + + A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells) + decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin + Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. + obsolete_allele cellular context + + + + + + + + + The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system + In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. + +We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences. + In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. + +For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus). + genomic location + genomic locus + VMC:Location + 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. + +2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. + +3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there. + genomic feature location + + + + + + + + + + + + + + + + + + + + + + + + true + A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc). + useful organizational term to collect entities that have genomes/genotypes. + organismal entity + + + + + + + + + The molecular product resulting from transcription of a single gene (either a protein or RNA molecule) + gene product + + + + + + + + + reporter role + + + + + + + + + selectable marker role + + + + + + + + + selectable marker region + + + + + + + + + + + + + + + A genome whose sequence is identical to that of a genome sequence considered to be the reference. + reference genome + + + + + + + + + A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it. + Former comment: "Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project." + Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype. + Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. + +Former SC axioms: +- is_allele_of some 'haplotype block' +- 'has part' some sequence_alteration + 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene). + +2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. + +GENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. + +3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': + +a. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. +b. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. +c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. + +The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. + obsolete_haplotype + + + + + + + + + A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations. + Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block. + Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. + A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. + +The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. + +----------------------- + +* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. + obsolete_haplotype block + + + + + + + + + An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell. + Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene. + organellar plasmy + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes). + A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification. + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes. + qualified sequence feature + + + + + + + + + + + + + + + + + + + + + A set of qualified seqeunce features. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'. + qualified sequence feature set + + + + + + + + + A biolocical sequence, or set of such sequences. + biological sequence or collection + biological sequence or set + + + + + + + + + A set of biological sequences. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. + +A set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence. + biological sequence set + + + + + + + + + A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome. + Formerly considered modeling this as an informational entity, defined as "An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome." + functional feature complement + genetic dosage + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963. + As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). + The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. + obsolete_functional copy number complement + + + + + + + + + A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form. + obsolete_intrinsic sequence feature attribute + + + + + + + + + A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.) + obsolete_extrinsic sequence feature attribute + + + + + + + + + A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism). + allelic cellular distribution + + + + + + + + + A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin. + constitutional + + + + + + + + + A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin. + clonal + + + + + + + + + An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors. + complex inherritance + multi-factorial inheritance + multi-genic inheritance + multi-locus inheritance + multigenic inheritance + http://purl.obolibrary.org/obo/HP_0001426 + Diseases inherited in this manner are termed 'complex diseases'. + multifactorial inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes. + http://purl.obolibrary.org/obo/HP_0010984 + digenic inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes. + http://purl.obolibrary.org/obo/HP_0010983 + It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform. + oligogenic inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes. + http://purl.obolibrary.org/obo/HP_0010982 + Typically used for traits/conditions governed by more than three gene loci. + polygenic inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors. + single-gene inheritance + monogenic inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome. + autosomal inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome. + gonosomal inheritance + http://purl.obolibrary.org/obo/HP_0010985 + allosomal inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome. + http://purl.obolibrary.org/obo/HP_0001417 + X-linked inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + complete X-linked dominant inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + semi-dominant X-linked inheritance + incomplete X-linked dominant inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant X-linked inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome. + holandric inheritance + http://purl.obolibrary.org/obo/HP_0001450 + Y-linked inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome. + Z-linked inheritance + + + + + + + + + A Z-linked inheritance pattern wherein the trait manifests in heterozygotes. + Z-linked dominant inheritance + + + + + + + + + A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + complete Z-linked dominant inheritance + + + + + + + + + A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + semi-dominant Z-linked inheritance + incomplete Z-linked dominant inheritance + + + + + + + + + An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant Z-linked inheritance + + + + + + + + + A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals. + Z-linked reccessive inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome. + W-linked inheritance + + + + + + + + + An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome. + http://purl.obolibrary.org/obo/HP_0001427 + Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy). + mitochondrial inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females). + http://purl.obolibrary.org/obo/HP_0001470 + sex-limited autosomal dominant inheritance + + + + + + + + + An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females). + http://purl.obolibrary.org/obo/HP_0031362 + sex-limited autosomal recessive inheritance + + + + + + + + + A set of discrete alleles within a particular genome. + 'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An "Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'. + allele set + + + + + + + + + A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s). + copy number variation + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. + In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). + +Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. + obsolete_variant copy number complement + + + + + + + + + A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger. + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961. + 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. + +2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. + +3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. + obsolete_copy number complement + + + + + + + + + + + + + + + A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism). + A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. + genomic sequence + + + + + + + + + A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome. + The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome. + +We represent the notion of copy number at the "sequence level" (as opposed to the "sequence feature level") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The "sequence level" representation here supports this use case. By contrast, a "feature level" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity). + The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result. + +A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. + +The fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. + The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence. + copy number complement + + + + + + + + + A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s). + Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a "sequence feature level" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred). + +For example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains. + 'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome. + variant copy number complement + + + + + + + + + A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome. + functional genetic dosage + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence. + +'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. + +As we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele. + functional copy complement + + + + + + + + + A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type. + mosaic + + + + + + + + + A pair of integers representing start and end position of a location on a sequence coordinate system. + sequence interval + + + + + + + + + molecular function + + + + + + + + + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete] + developmental process + + + + + + + + + pulling in HP 'phenotypic abnormality' root here + human phenotypic abnormality + + + + + + + + + Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology. + A spatiotemporal region encompassing some part of the life cycle of an organism. + human life cycle stage + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + information content entity + + + + + + + + + ontology metadata + data about an ontology part + + + + + + + + + where to place this depends on if we take the organismal view or the quality centric view. + mammalian phenotype + + + + + + + + + Mus musculus + + + + + + + + + Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies. + Viruses + + + + + + + + + Danio rerio + + + + + + + + + Oryzias latipes + + + + + + + + + Homo sapiens + + + + + + + + + A processual entity that realizes a plan which is the concretization of a plan specification. + Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO. + planned process + + + + + + + + + reagent role + + + + + + + + + a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area + population + + + + + + + + + An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. + genotyping assay + + + + + + + + + A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. + A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. + targeted gene knock-out technique + + + + + + + + + targeted gene knock-in technique + + + + + + + + + Stub class to serve as root of hierarchy for imports from NCBI Taxonomy. + organism + + + + + + + + + + + + + + + + + + + + + + + + + the introduction. alteration or integration of genetic material into a cell or organism + genetic modification technique + + + + + + + + + 'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html + Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute. + color value + obsolete_color brightness + + + + + + + + + female + + + + + + + + + male + + + + + + + + + phenotypic sex + + + + + + + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role). + collection of organisms + + + + + + + + + A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. + family + + + + + + + + + Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. + morpholino_oligo + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. + Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosome arm + + + + + + + + + + + + + + + + + + + + + Any extent of continuous biological sequence. + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome. + sequence_feature + + + + + + + + + + + true + Formalizes the first identity criteria for a sequence feature of its sequence. + + + + + + + + + + + true + Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property). + + + + + + + + + A region of known length which may be used to manufacture a longer region. + obsolete_assembly_component + + + + + + + + + A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. + obsolete_contig + + + + + + + + + + + + 0 + + + The point at which one or more contiguous nucleotides were excised. + deleted_sequence + nucleotide deletion + nucleotide_deletion + + SO:1000033 + SO:0000159 + SOFA + http://en.wikipedia.org/wiki/Nucleotide_deletion + deletion + + + + + + + + + enhancer + + + + + + + + + A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. + promoter + + + + + + + + + A region of nucleotide sequence that has translocated to a new position. + transchr + translocated sequence + + SO:0000199 + DBVAR + translocation + + + + + + + + + SSLP + simple sequence length polymorphism + simple sequence length variation + + SO:0000207 + simple_sequence_length_variation + + + + + + + + + sequence length variation + + SO:0000248 + sequence_length_variation + + + + + + + + + + + + + + + See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25. + +Includes things like loxP sites, inducible promoters, ires elements, etc. + engineered_foreign_gene + + + + + + + + + A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. + http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29 + A defined feature that includes any type of VNTR or SSLP locus. + microsatellite + + + + + + + + + RNAi_reagent + + + + + + + + + Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. + A complete chromosome sequence. + chromosome + + + + + + + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + + "Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. + chromosome band + + + + + + + + + centromere + + + + + + + + + Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct. + obsolete_engineered_plasmid + + + + + + + + + The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. + insertion + nucleotide insertion + nucleotide_insertion + + SO:1000034 + SO:0000667 + DBVAR + SOFA + insertion + + + + + + + + + SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. + single nucleotide polymorphism + + SO:0000694 + SOFA + SNP + + + + + + + + + A junction is a boundary between regions. A boundary has an extent of zero. + junction + + + + + + + + + A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. + Regarding the distinction between a 'gene' and a 'gene allele': +Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment). + A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion. + gene + + + + + + + + + A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. + quantitative trait locus + QTL + + + + + + + + + An attribute to describe a region that was modified in vitro. + engineered + + + + + + + + + + + + + + + + + + + construct + engineered_region + + + + + + + + + + + + + + + + + + + An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'. + chromosomal feature + gross chromosomal part + chromosome part + + + + + + + + + A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome). + On the relationship between 'transgenic insertions', 'transgenes', and 'alleles' +Transgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete. + +In addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. + +For the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach. + Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism). + +Note that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome. + transgene + + + + + + + + + A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. + multiple nucleotide polymorphism + + SO:0001013 + MNP + + + + + + + + + A variation that increases or decreases the copy number of a given region. + CNP + CNV + copy number polymorphism + copy number variation + + SO:0001019 + SOFA + http://en.wikipedia.org/wiki/Copy_number_variation + copy_number_variation + + + + + + + + + + + + + + + A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny) + Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. + 'genome sequence' + A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'. + genome + + + + + + + + + + + + + + + + + + + A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': + +1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871. + +2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112. + +3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112. + A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. + sequence variation + + SO:1000004 + SO:1000007 + SO:0001059 + SOFA + 1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. + +Alleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part. + +2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. + +For a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference. + +3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism. + sequence_alteration + + + + + + + + + + + + + + + An insertion that derives from another organism, via the use of recombinant DNA technology. + transgenic insertion + + SO:0001218 + transgenic_insertion + + + + + + + + + A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. + not currently needed to support modeling use cases. can re-introduce if becomes necessary. + obsolete_experimental_feature + + + + + + + + + A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. + gene_trap_construct + + + + + + + + + A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. + promoter_trap_construct + + + + + + + + + A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. + enhancer_trap_construct + + + + + + + + + SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist. + single nucleotide variant + + kareneilbeck + Thu Oct 08 11:37:49 PDT 2009 + SO:0001483 + SOFA + SNV + + + + + + + + + A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. + heritable_phenotypic_marker + + + + + + + + + + + + + + + 'GRCh37.p10' (a human reference genome build) + A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced. + reference genome sequence + + + + + + + + + A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. + copy number gain + gain + + kareneilbeck + Mon Feb 28 01:54:09 PST 2011 + SO:0001742 + DBVAR + copy_number_gain + + + + + + + + + A sequence alteration whereby the copy number of a given region is less than the reference sequence. + copy number loss + loss + + kareneilbeck + Mon Feb 28 01:55:02 PST 2011 + SO:0001743 + DBVAR + copy_number_loss + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. + UPD + uniparental disomy + + kareneilbeck + Mon Feb 28 02:01:05 PST 2011 + SO:0001744 + DBVAR + http:http\://en.wikipedia.org/wiki/Uniparental_disomy + UPD + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. + maternal uniparental disomy + + kareneilbeck + Mon Feb 28 02:03:01 PST 2011 + SO:0001745 + maternal_uniparental_disomy + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. + paternal uniparental disomy + + kareneilbeck + Mon Feb 28 02:03:30 PST 2011 + SO:0001746 + paternal_uniparental_disomy + + + + + + + + + A structural sequence alteration where there are multiple equally plausible explanations for the change. + complex + + kareneilbeck + Wed Mar 23 03:21:19 PDT 2011 + SO:0001784 + DBVAR + complex_structural_alteration + + + + + + + + + + kareneilbeck + Fri Mar 25 02:27:41 PDT 2011 + SO:0001785 + DBVAR + structural_alteration + + + + + + + + + Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term. + regulatory element + regulatory gene region + regulatory_region + + + + + + + + + Any change in genomic DNA caused by a single event. + + SO:1000002 + SOFA + substitution + + + + + + + + + When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change. + complex substitution + + SO:1000005 + SOFA + complex_substitution + + + + + + + + + A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. + point mutation + + SO:1000008 + SOFA + http://en.wikipedia.org/wiki/Point_mutation + point_mutation + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. + + SO:1000009 + transition + + + + + + + + + A substitution of a pyrimidine, C or T, for another pyrimidine. + pyrimidine transition + + SO:1000010 + pyrimidine_transition + + + + + + + + + A transition of a cytidine to a thymine. + C to T transition + + SO:1000011 + C_to_T_transition + + + + + + + + + The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine. + C to T transition at pCpG site + + SO:1000012 + C_to_T_transition_at_pCpG_site + + + + + + + + + T to C transition + + SO:1000013 + T_to_C_transition + + + + + + + + + A substitution of a purine, A or G, for another purine. + purine transition + + SO:1000014 + purine_transition + + + + + + + + + A transition of an adenine to a guanine. + A to G transition + + SO:1000015 + A_to_G_transition + + + + + + + + + A transition of a guanine to an adenine. + G to A transition + + SO:1000016 + G_to_A_transition + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. + + SO:1000017 + http://en.wikipedia.org/wiki/Transversion + transversion + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. + pyrimidine to purine transversion + + SO:1000018 + pyrimidine_to_purine_transversion + + + + + + + + + A transversion from cytidine to adenine. + C to A transversion + + SO:1000019 + C_to_A_transversion + + + + + + + + + C to G transversion + + SO:1000020 + C_to_G_transversion + + + + + + + + + A transversion from T to A. + T to A transversion + + SO:1000021 + T_to_A_transversion + + + + + + + + + A transversion from T to G. + T to G transversion + + SO:1000022 + T_to_G_transversion + + + + + + + + + Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. + purine to pyrimidine transversion + + SO:1000023 + purine_to_pyrimidine_transversion + + + + + + + + + A transversion from adenine to cytidine. + A to C transversion + + SO:1000024 + A_to_C_transversion + + + + + + + + + A transversion from adenine to thymine. + A to T transversion + + SO:1000025 + A_to_T_transversion + + + + + + + + + A transversion from guanine to cytidine. + G to C transversion + + SO:1000026 + G_to_C_transversion + + + + + + + + + A transversion from guanine to thymine. + G to T transversion + + SO:1000027 + G_to_T_transversion + + + + + + + + + A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. + + SO:1000032 + http://en.wikipedia.org/wiki/Indel + Indels can have a different number of bases than the corresponding reference sequence. + indel + + + + + + + + + One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point. + nucleotide duplication + nucleotide_duplication + + SO:1000035 + duplication + + + + + + + + + A continuous nucleotide sequence is inverted in the same position. + inversion + + SO:1000036 + DBVAR + SOFA + inversion + + + + + + + + + A tandem duplication where the individual regions are in the same orientation. + direct tandem duplication + + SO:1000039 + direct_tandem_duplication + + + + + + + + + A tandem duplication where the individual regions are not in the same orientation. + inverted tandem duplication + mirror duplication + + SO:1000040 + inverted_tandem_duplication + + + + + + + + + A duplication consisting of 2 identical adjacent regions. + erverted + tandem duplication + + SO:1000173 + DBVAR + tandem_duplication + + + + + + + + + Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms) + life cycle stage + + + + + + + + + + + + + + + Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies. + http://purl.obolibrary.org/obo/CARO_0000000 + anatomical entity + + + + + + + + + Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework. + 1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition) + +2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment + Phenotype + + + + + + + + + Animals exhibit variations compared to a given control. + 'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes. + Variant + c. elegans phenotype + worm phenotype + + + + + + + + + abnormal(ly) malformed endocardium cell + + + + + + + + + abnormal(ly) absent dorso-rostral cluster + + + + + + + + + abnormal(ly) disrupted diencephalon development + + + + + + + + + abnormal(ly) disrupted neutrophil aggregation + + + + + + + + + abnormal(ly) absent adaxial cell + + + + + + + + + association + + + + + + + + + + + + + + + + Equivalent to: http://www.informatics.jax.org/marker/MGI:98297 + mus musculus shh gene + + + + + + + + + + http://zfin.org/ZDB-GENE-980526-166 + danio rerio shha gene + + + + + + + + + + http://zfin.org/ZDB-GENE-040123-1 + danio rerio cdkn1ca gene + + + + + + + + + + Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690 + +Codes for: http://www.uniprot.org/uniprot/Q15465 + homo sapiens SHH gene + + + + + + + + + + + + + + exploratory term + + + + + + + + + exemplar term + + + + + + + + + + + + + + + + + Initially created such that integrated transgene infers as child of sequence_alteration. + + + + + + + diff --git a/geno-full.json b/geno-full.json new file mode 100644 index 0000000..3f48f2f --- /dev/null +++ b/geno-full.json @@ -0,0 +1,11682 @@ +{ + "graphs" : [ { + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/SO_0000165", + "type" : "CLASS", + "lbl" : "enhancer" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000167", + "meta" : { + "definition" : { + "val" : "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "promoter" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001013", + "meta" : { + "definition" : { + "val" : "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001013" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multiple nucleotide polymorphism" + } ] + }, + "type" : "CLASS", + "lbl" : "MNP" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000281", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25.\n\nIncludes things like loxP sites, inducible promoters, ires elements, etc." + } ] + }, + "type" : "CLASS", + "lbl" : "engineered_foreign_gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000060", + "meta" : { + "definition" : { + "val" : "A version/allele of a gene that serves as a standard against which variant genes are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development.\nhttp://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690\n\nNote that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference gene" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reference gene allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000057", + "meta" : { + "definition" : { + "val" : "A gene that originates from the genome of a mus musculus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "mus musculus gene" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10090", + "type" : "CLASS", + "lbl" : "Mus musculus" + }, { + "id" : "http://purl.obolibrary.org/obo/ERO_0000007", + "meta" : { + "definition" : { + "val" : "A technique is a planned process used to accomplish a specific activity or task.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "technique" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000159", + "meta" : { + "definition" : { + "val" : "The point at which one or more contiguous nucleotides were excised.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Nucleotide_deletion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000033" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide deletion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "deleted_sequence" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide_deletion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000159" + } ] + }, + "type" : "CLASS", + "lbl" : "deletion" + }, { + "id" : "http://purl.obolibrary.org/obo/PCO_0000020", + "meta" : { + "definition" : { + "val" : "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "family" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000034", + "meta" : { + "definition" : { + "val" : "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "morpholino_oligo" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001483", + "meta" : { + "definition" : { + "val" : "SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single nucleotide variant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001483" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Thu Oct 08 11:37:49 PDT 2009" + } ] + }, + "type" : "CLASS", + "lbl" : "SNV" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000173", + "type" : "CLASS", + "lbl" : "promoter trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000172", + "type" : "CLASS", + "lbl" : "gene trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000054", + "meta" : { + "definition" : { + "val" : "A gene that originates from the genome of a homo sapiens.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "homo sapiens gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000175", + "type" : "CLASS", + "lbl" : "random transgene insertion technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000174", + "type" : "CLASS", + "lbl" : "targeted knock-in technique" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "color value" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_color brightness" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000435", + "meta" : { + "definition" : { + "val" : "An assay which generates data about a genotype from a specimen of genomic DNA. 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Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "gene_trap_construct" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000149", + "meta" : { + "definition" : { + "val" : "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_contig" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001479", + "meta" : { + "definition" : { + "val" : "A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "enhancer_trap_construct" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000409", + "meta" : { + "definition" : { + "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Barry Smith, Werner Ceusters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "CLASS", + "lbl" : "denotator type" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000020", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:48Z" + } ] + }, + "type" : "CLASS", + "lbl" : "EL++ ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000019", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:28Z" + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module subsetted by OWL profile" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0000383", + "type" : "CLASS", + "lbl" : "female" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0000384", + "type" : "CLASS", + "lbl" : "male" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000011", + "meta" : { + "definition" : { + "val" : "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:00:14Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "external import" + } ] + }, + "type" : "CLASS", + "lbl" : "external import ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000012", + "meta" : { + "definition" : { + "val" : "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "taxon subset" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:14:16Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + }, + "type" : "CLASS", + "lbl" : "species subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000411", + "meta" : { + "definition" : { + "val" : "relates an class defined in an ontology, to the type of it's denotator", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is denotator type" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is denotator type" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000013", + "meta" : { + "definition" : { + "val" : "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/reason" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:20:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "reasoned ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000014", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:21:12Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" + } ] + }, + "type" : "CLASS", + "lbl" : "generated ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000412", + "meta" : { + "definition" : { + "val" : "For external terms/classes, the ontology from which the term was imported", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "imported from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + }, + "type" : "PROPERTY", + "lbl" : "imported from" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0000386", + "type" : "CLASS", + "lbl" : "abnormal(ly) absent dorso-rostral cluster" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000015", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/template" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://doi.org/10.1186/s13326-017-0126-0" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:21:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "template generated ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:28:15Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "taxonomic bridge ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001026", + "meta" : { + "definition" : { + "val" : "A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "'genome sequence'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "genome" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "universal" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000017", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:15:54Z" + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module subsetted by expressivity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000018", + "meta" : { + "definition" : { + "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:10Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "obo basic subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "meta" : { + "definition" : { + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term replaced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term replaced by" + }, { + "id" : "http://purl.obolibrary.org/obo/PCO_0000000", + "meta" : { + "definition" : { + "val" : "A material entity that consists of two or more organisms, viruses, or viroids.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)." + } ] + }, + "type" : "CLASS", + "lbl" : "collection of organisms" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000010", + "meta" : { + "definition" : { + "val" : "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "antislim" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:59:57Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "exclusion subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "type" : "PROPERTY", + "lbl" : "has_role" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has quality" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000008", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended for usage in analysis or discovery applications.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:49Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "analysis subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000009", + "meta" : { + "definition" : { + "val" : "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ribbon subset" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:59:19Z" + } ] + }, + "type" : "CLASS", + "lbl" : "single layer subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand expression to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "expand expression to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:03Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology file" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001019", + "meta" : { + "definition" : { + "val" : "A variation that increases or decreases the copy number of a given region.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number polymorphism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Copy_number_variation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001019" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number variation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "CNP" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "CNV" + } ] + }, + "type" : "CLASS", + "lbl" : "copy_number_variation" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000425", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand assertion to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "expand assertion to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000001", + "meta" : { + "definition" : { + "val" : "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:30Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "base ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000002", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:47Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "source ontology module" + } ] + }, + "type" : "CLASS", + "lbl" : "editors ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000003", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:13Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" + } ] + }, + "type" : "CLASS", + "lbl" : "main release ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "meta" : { + "definition" : { + "val" : "Terms with this status should eventually replaced with a term from another ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "to be replaced with external ontology term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000004", + "meta" : { + "definition" : { + "val" : "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:23Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "bridge ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "meta" : { + "definition" : { + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "defined class" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0100026", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy." + } ] + }, + "type" : "CLASS", + "lbl" : "organism" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "meta" : { + "definition" : { + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "named class expression" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000289", + "meta" : { + "definition" : { + "val" : "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A defined feature that includes any type of VNTR or SSLP locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29" + } ] + }, + "type" : "CLASS", + "lbl" : "microsatellite" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000005", + "meta" : { + "definition" : { + "val" : "A subset ontology module that is intended to be imported from another ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "import file" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add axioms that indicate this is the output of a module extraction process." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/extract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:47Z" + } ] + }, + "type" : "CLASS", + "lbl" : "import ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000006", + "meta" : { + "definition" : { + "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/filter" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:11Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "subset ontology" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology slim" + } ] + }, + "type" : "CLASS", + "lbl" : "subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000007", + "meta" : { + "definition" : { + "val" : "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:38Z" + } ] + }, + "type" : "CLASS", + "lbl" : "curation subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002131", + "meta" : { + "definition" : { + "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "overlaps" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0001894", + "type" : "CLASS", + "lbl" : "phenotypic sex" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006011", + "meta" : { + "definition" : { + "val" : "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "VFB" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "#40" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-21T16:43:39Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "may be identical to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006012", + "meta" : { + "definition" : { + "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "GO ontology" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/15532" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/32" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall, Jie Zheng" + } ] + }, + "type" : "PROPERTY", + "lbl" : "scheduled for obsoletion on or after" + }, { + "id" : "http://purl.org/oban/association", + "type" : "CLASS", + "lbl" : "association" + }, { + "id" : "http://purl.obolibrary.org/obo/CHEBI_23367", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology." + } ] + }, + "type" : "CLASS", + "lbl" : "molecular entity" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000199", + "meta" : { + "definition" : { + "val" : "A region of nucleotide sequence that has translocated to a new position.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000199" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "transchr" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "translocated sequence" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + } ] + }, + "type" : "CLASS", + "lbl" : "translocation" + }, { + "id" : "http://biohackathon.org/resource/faldo#BothStrandsPosition", + "type" : "CLASS", + "lbl" : "Both strands" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0032502", + "meta" : { + "definition" : { + "val" : "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete]", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "developmental process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000092", + "type" : "CLASS", + "lbl" : "gene trap insertion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000091", + "type" : "CLASS", + "lbl" : "obsolete_experimental insertion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000093", + "meta" : { + "definition" : { + "val" : "A transgene that has been integrated into a chrromosome in the host genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion.\n\nAn 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome." + } ] + }, + "type" : "CLASS", + "lbl" : "integrated transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_000244", + "meta" : { + "definition" : { + "val" : "Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "molecularly controls" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "meta" : { + "definition" : { + "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + } ] + }, + "type" : "PROPERTY", + "lbl" : "concretizes" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has participant" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000600", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "elucidation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Barry Smith" + } ] + }, + "type" : "PROPERTY", + "lbl" : "elucidation" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000601", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(nl)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom associated with a term expressed using natural language" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has associated axiom(nl)" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000602", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom expressed in first order logic using CLIF syntax" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(fol)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has associated axiom(fol)" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000603", + "meta" : { + "definition" : { + "val" : "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\"", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is allocated id range" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is allocated id range" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "type" : "PROPERTY", + "lbl" : "input of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "inheres_in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "type" : "PROPERTY", + "lbl" : "output of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has input" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "type" : "PROPERTY", + "lbl" : "obsolete_formed as result of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has output" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "participates in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "type" : "PROPERTY", + "lbl" : "is member of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "meta" : { + "definition" : { + "val" : "has member is a mereological relation between a collection and an item.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes\n\nExample 2: a collection of information entities such as a genotype being comprised of a background component and a variant component" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has member" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "bearer of" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000105", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms)" + } ] + }, + "type" : "CLASS", + "lbl" : "life cycle stage" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "type" : "PROPERTY", + "lbl" : "temporally related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003307", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is preventative for condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003306", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to penetrance of condition" + } ] + }, + "type" : "PROPERTY", + "lbl" : "contributes to frequency of condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003308", + "meta" : { + "definition" : { + "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "correlated with condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003303", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "causes condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003302", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." + } ] + }, + "type" : "PROPERTY", + "lbl" : "causes or contributes to condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to expressivity of condition" + } ] + }, + "type" : "PROPERTY", + "lbl" : "contributes to severity of condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003304", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "contributes to condition" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_8090", + "type" : "CLASS", + "lbl" : "Oryzias latipes" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001059", + "meta" : { + "definition" : { + "val" : "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001059" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence variation" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. \n\nAlleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part.\n\n2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. \n\nFor a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference.\n\n3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': \n\n1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871.\n\n2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112.\n\n3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000007" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + } ] + }, + "type" : "CLASS", + "lbl" : "sequence_alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "term imported" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "term split" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "type" : "PROPERTY", + "lbl" : "derives from" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "meta" : { + "definition" : { + "val" : "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Brush" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is model of" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0005531", + "type" : "CLASS", + "lbl" : "abnormal(ly) disrupted neutrophil aggregation" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "meta" : { + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "editor note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "meta" : { + "definition" : { + "val" : "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term editor" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term editor" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000281" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has curation status" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has curation status" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000598", + "meta" : { + "definition" : { + "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID policy for" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000599", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID prefix" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "meta" : { + "definition" : { + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "meta" : { + "definition" : { + "val" : "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + }, + "type" : "PROPERTY", + "lbl" : "example of usage" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000596", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID digit count" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The 'tracker item' can associate a tracker with a specific ontology term." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term tracker item" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term tracker item" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000234", + "meta" : { + "definition" : { + "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The 'term requester' can credit the person, organization or project who request the ontology term." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "ontology term requester" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000113", + "meta" : { + "definition" : { + "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "in branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000277" + } ] + }, + "type" : "PROPERTY", + "lbl" : "in branch" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000597", + "meta" : { + "definition" : { + "val" : "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID range allocated to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "meta" : { + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has obsolescence reason" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has obsolescence reason" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "meta" : { + "definition" : { + "val" : "An administrative note of use for a curator but of no use for a user", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curator note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "curator note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "meta" : { + "definition" : { + "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + } ] + }, + "type" : "PROPERTY", + "lbl" : "editor preferred term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "alternative term" + } ] + }, + "type" : "PROPERTY", + "lbl" : "alternative term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "meta" : { + "definition" : { + "val" : "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition source" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition source" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "type" : "PROPERTY", + "lbl" : "phenotype of" + }, { + "id" : "http://biohackathon.org/resource/faldo#end", + "type" : "PROPERTY", + "lbl" : "end" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "metadata complete" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "pending final vetting" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "metadata incomplete" + }, { + "id" : "http://www.ncbi.nlm.nih.gov/gene/20423", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Equivalent to: http://www.informatics.jax.org/marker/MGI:98297" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000514" + } ] + }, + "type" : "CLASS", + "lbl" : "mus musculus shh gene" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "type" : "INDIVIDUAL", + "lbl" : "example to be eventually removed" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "uncurated" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "meta" : { + "definition" : { + "val" : "term created to ease viewing/sort terms for development purpose, and will not be included in a release", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "organizational term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "ready for release" + }, { + "id" : "http://www.ncbi.nlm.nih.gov/gene/30269", + "meta" : { + "xrefs" : [ { + "val" : "http://zfin.org/ZDB-GENE-980526-166" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000514" + } ] + }, + "type" : "CLASS", + "lbl" : "danio rerio shha gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000919", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000918", + "meta" : { + "definition" : { + "val" : "An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene." + } ] + }, + "type" : "CLASS", + "lbl" : "organellar plasmy" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000915", + "meta" : { + "definition" : { + "val" : "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_haplotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000914", + "meta" : { + "definition" : { + "val" : "A genome whose sequence is identical to that of a genome sequence considered to be the reference.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "reference genome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000917", + "meta" : { + "definition" : { + "val" : "Describes the number of members in some set.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_count" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_member_count" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000136", + "meta" : { + "definition" : { + "val" : "is_about is a (currently) primitive relation that relates an information artifact to an entity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is about" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000916", + "meta" : { + "definition" : { + "val" : "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.\n\nThe boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.\n\n-----------------------\n\n* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_haplotype block" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000911", + "type" : "CLASS", + "lbl" : "selectable marker role" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000910", + "type" : "CLASS", + "lbl" : "reporter role" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000912", + "type" : "CLASS", + "lbl" : "selectable marker region" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000293", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_specified_input" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000907", + "meta" : { + "definition" : { + "val" : "The molecular product resulting from transcription of a single gene (either a protein or RNA molecule)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "gene product" + }, { + "id" : "http://biohackathon.org/resource/faldo#reference", + "meta" : { + "definition" : { + "val" : "The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "reference" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000909", + "type" : "PROPERTY", + "lbl" : "gene symbol" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000299", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_specified_output" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0001148", + "meta" : { + "definition" : { + "val" : "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a \"targeted\" insertion." + } ] + }, + "type" : "CLASS", + "lbl" : "targeted gene knock-out technique" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0001149", + "type" : "CLASS", + "lbl" : "targeted gene knock-in technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000904", + "meta" : { + "definition" : { + "val" : "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "useful organizational term to collect entities that have genomes/genotypes." + }, { + "pred" : "http://purl.obolibrary.org/obo/GENO_0000905", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "organismal entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000903", + "meta" : { + "definition" : { + "val" : "A relation linking a sequence feature to the location it occupies on some reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occupies" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000906", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from." + } ] + }, + "type" : "PROPERTY", + "lbl" : "on strand" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000027", + "type" : "CLASS", + "lbl" : "data item" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000905", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models." + } ] + }, + "type" : "PROPERTY", + "lbl" : "mixin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000902", + "meta" : { + "definition" : { + "val" : "The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "VMC:Location" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed.\n\nFor example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future.\n\nWe don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic location" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. \n\t\n2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus.\n\n3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic locus" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic feature location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000901", + "meta" : { + "definition" : { + "val" : "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_allele cellular context" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "requires discussion" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "first order logic expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "first order logic expression" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000427", + "meta" : { + "definition" : { + "val" : "use boolean value xsd:true to indicate that the property is an antisymmetric property", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "antisymmetric property" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part_of antisymmetric property xsd:true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "antisymmetric property" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "type" : "PROPERTY", + "lbl" : "is subsequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "meta" : { + "definition" : { + "val" : "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + }, + "type" : "PROPERTY", + "lbl" : "overlaps sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000931", + "meta" : { + "definition" : { + "val" : "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010983" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform." + } ] + }, + "type" : "CLASS", + "lbl" : "oligogenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "meta" : { + "definition" : { + "val" : "inverse of downstream of sequence of", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is upstream of sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000930", + "meta" : { + "definition" : { + "val" : "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010984" + } ] + }, + "type" : "CLASS", + "lbl" : "digenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "meta" : { + "definition" : { + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "bounds sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "meta" : { + "definition" : { + "val" : "x has subsequence y iff all of the sequence parts of x are sequence parts of y", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has subsequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000937", + "meta" : { + "definition" : { + "val" : "An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "complete X-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000936", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001417" + } ] + }, + "type" : "CLASS", + "lbl" : "X-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000815", + "meta" : { + "definition" : { + "val" : "The location of a sequence feature as defined by its start and end position on some reference coordinate system.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms).\n\n2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000818", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "modification-qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000939", + "meta" : { + "definition" : { + "val" : "An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "co-dominant X-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000938", + "meta" : { + "definition" : { + "val" : "An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "semi-dominant X-linked inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "incomplete X-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000933", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single-gene inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "monogenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "meta" : { + "definition" : { + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is downstream of sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000932", + "meta" : { + "definition" : { + "val" : "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010982" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Typically used for traits/conditions governed by more than three gene loci." + } ] + }, + "type" : "CLASS", + "lbl" : "polygenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000935", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010985" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gonosomal inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "allosomal inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000934", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "autosomal inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000929", + "meta" : { + "definition" : { + "val" : "An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001426" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complex inherritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-factorial inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multigenic inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-locus inheritance" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Diseases inherited in this manner are termed 'complex diseases'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-genic inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "multifactorial inheritance" + }, { + "id" : "http://biohackathon.org/resource/faldo#ReverseStrandPosition", + "type" : "CLASS", + "lbl" : "Negative strand" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0010000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has axiom id" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has axiom label" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000920", + "meta" : { + "definition" : { + "val" : "A set of qualified seqeunce features.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified sequence feature set" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000902", + "meta" : { + "definition" : { + "val" : "A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism).\n\nNote that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "On the relationship between 'transgenic insertions', 'transgenes', and 'alleles'\nTransgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete.\n\nIn addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. \n\nFor the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach." + } ] + }, + "type" : "CLASS", + "lbl" : "transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000926", + "meta" : { + "definition" : { + "val" : "A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "allelic cellular distribution" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000925", + "meta" : { + "definition" : { + "val" : "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_extrinsic sequence feature attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000928", + "meta" : { + "definition" : { + "val" : "A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "clonal" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000927", + "meta" : { + "definition" : { + "val" : "A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "constitutional" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000922", + "meta" : { + "definition" : { + "val" : "A set of biological sequences.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. \n\nA set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000921", + "meta" : { + "definition" : { + "val" : "A biolocical sequence, or set of such sequences.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "biological sequence or collection" + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence or set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000924", + "meta" : { + "definition" : { + "val" : "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_intrinsic sequence feature attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000923", + "meta" : { + "definition" : { + "val" : "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genetic dosage" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "functional feature complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_functional copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000953", + "meta" : { + "definition" : { + "val" : "An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0031362" + } ] + }, + "type" : "CLASS", + "lbl" : "sex-limited autosomal recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000952", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001470" + } ] + }, + "type" : "CLASS", + "lbl" : "sex-limited autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/HsapDv_0000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A spatiotemporal region encompassing some part of the life cycle of an organism." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology." + } ] + }, + "type" : "CLASS", + "lbl" : "human life cycle stage" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000959", + "meta" : { + "definition" : { + "val" : "Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference.\n\nFor copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_defining_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000958", + "meta" : { + "definition" : { + "val" : "Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_defining_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000719", + "meta" : { + "definition" : { + "val" : "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons." + } ] + }, + "type" : "CLASS", + "lbl" : "intrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000839", + "type" : "CLASS", + "lbl" : "knockdown reagent targeted gene complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000834", + "meta" : { + "definition" : { + "val" : "Used to annotation axioms that define identity criteria for instances of a class.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_identity_criteria" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000955", + "meta" : { + "definition" : { + "val" : "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number variation" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_variant copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000713", + "meta" : { + "definition" : { + "val" : "A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "qualified sequence feature or collection" + }, { + "id" : "http://biohackathon.org/resource/faldo#ExactPosition", + "meta" : { + "definition" : { + "val" : "A position that is exactly known.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Exact position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000712", + "type" : "PROPERTY", + "lbl" : "ObsoleteDataProperty" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000954", + "meta" : { + "definition" : { + "val" : "A set of discrete alleles within a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An \"Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'." + } ] + }, + "type" : "CLASS", + "lbl" : "allele set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000833", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each." + } ] + }, + "type" : "CLASS", + "lbl" : "genotype-phenotype association" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000957", + "meta" : { + "definition" : { + "val" : "Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location.\n\nFor copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_defining_location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000715", + "meta" : { + "definition" : { + "val" : "A set of qualified sequence features that carry genomic sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele.\n\nA complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified genomic feature set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000956", + "meta" : { + "definition" : { + "val" : "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000714", + "meta" : { + "definition" : { + "val" : "A qualified sequence feature that carries sequence derived from the genome of a cell or organism.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified genomic feature" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000219", + "meta" : { + "definition" : { + "val" : "Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of." + } ] + }, + "type" : "PROPERTY", + "lbl" : "denotes" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7955", + "type" : "CLASS", + "lbl" : "Danio rerio" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000011", + "meta" : { + "definition" : { + "val" : "A processual entity that realizes a plan which is the concretization of a plan specification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO." + } ] + }, + "type" : "CLASS", + "lbl" : "planned process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000942", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Z-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000941", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001450" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "holandric inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "Y-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000804", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "construct" + } ] + }, + "type" : "CLASS", + "lbl" : "engineered_region" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "type" : "INDIVIDUAL", + "lbl" : "placeholder removed" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which is unique across the OBO Foundry.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "OBO foundry unique label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBO Foundry " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." + } ] + }, + "type" : "PROPERTY", + "lbl" : "OBO foundry unique label" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000948", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "W-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "terms merged" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000947", + "meta" : { + "definition" : { + "val" : "A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Z-linked reccessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000224", + "meta" : { + "definition" : { + "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "core" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000708", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "organizational property to hold imports from faldo." + } ] + }, + "type" : "PROPERTY", + "lbl" : "faldo properties" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "meta" : { + "definition" : { + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "failed exploratory term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "meta" : { + "definition" : { + "val" : "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obsolescence reason specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolescence reason specification" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0000199", + "type" : "CLASS", + "lbl" : "abnormal(ly) malformed endocardium cell" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000949", + "meta" : { + "definition" : { + "val" : "An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy)." + } ] + }, + "type" : "CLASS", + "lbl" : "mitochondrial inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000823", + "meta" : { + "definition" : { + "val" : "A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location.\n\nThis contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single locus genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "1. The zebrafish \"fgf8a/fgf8a<+>\" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state).\n\n2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308.\n\n ##fileformat=VCFv4.2\n ##FORMAT=\n #CHROM POS REF ALT FILTER FORMAT SAMP001\n 20 2300608 C T PASS GT\t 0/1\t\n 20 2301308 T G PASS GT\t 1/1\n (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html)\n\n3. Some allelic genotype formats encode the genotype as a single string - e.g. \"GRCh38 Chr12:258635(A;T)\" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12." + } ] + }, + "type" : "CLASS", + "lbl" : "allelic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000702", + "meta" : { + "definition" : { + "val" : "A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "VMC:State" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "biomacromolecular sequence" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "state" + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000944", + "meta" : { + "definition" : { + "val" : "A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "complete Z-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000943", + "meta" : { + "definition" : { + "val" : "A Z-linked inheritance pattern wherein the trait manifests in heterozygotes.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Z-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000701", + "meta" : { + "definition" : { + "val" : "A sequence feature or a set of such features.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence feature or collection" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature or set" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000102", + "meta" : { + "definition" : { + "val" : "data about an ontology part is a data item about a part of an ontology, for example a term", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology metadata" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "CLASS", + "lbl" : "data about an ontology part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000946", + "meta" : { + "definition" : { + "val" : "An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "co-dominant Z-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000703", + "meta" : { + "definition" : { + "val" : "Shortcut relation linking a sequence feature directly to a string representing the 'state' of its sequence - i.e. the ordering of units that comprise it (e.g. 'atgcagctagctaccgtcgatcg').", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_string" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000945", + "meta" : { + "definition" : { + "val" : "A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "semi-dominant Z-linked inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "incomplete Z-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000016", + "meta" : { + "definition" : { + "val" : "A transition of a guanine to an adenine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "G to A transition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000016" + } ] + }, + "type" : "CLASS", + "lbl" : "G_to_A_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000015", + "meta" : { + "definition" : { + "val" : "A transition of an adenine to a guanine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : 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"pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "T to C transition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000013" + } ] + }, + "type" : "CLASS", + "lbl" : "T_to_C_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0003674", + "type" : "CLASS", + "lbl" : "molecular function" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000019", + "meta" : { + "definition" : { + "val" : "A transversion from cytidine to adenine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "C to A transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "C_to_A_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000018", + "meta" : { + "definition" : { + "val" : "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000018" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "pyrimidine to purine transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "pyrimidine_to_purine_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000017", + "meta" : { + "definition" : { + "val" : "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000610", + "meta" : { + "definition" : { + "val" : "A relationship between a reference locus/allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_reference_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies." + } ] + }, + "type" : "CLASS", + "lbl" : "cell" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000611", + "meta" : { + "definition" : { + "val" : "A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "background genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic background" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000850", + "meta" : { + "definition" : { + "val" : "A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "P-element construct" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000618", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "chromosomal band brightness" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal band intensity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000619", + "type" : "CLASS", + "lbl" : "gpos" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000614", + "meta" : { + "definition" : { + "val" : "An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "New term request for SO." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal region" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000023", + "meta" : { + "definition" : { + "val" : "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000023" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "purine to pyrimidine transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "purine_to_pyrimidine_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000856", + "meta" : { + "definition" : { + "val" : "An engineered region that is used to transfer foreign genetic material into a host cell.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "engineered_genetic_vector" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. \n\nConstructs are typically packaged as part of delivery systems such as plasmids or viral vectors." + } ] + }, + "type" : "CLASS", + "lbl" : "engineered genetic construct" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000022", + "meta" : { + "definition" : { + "val" : "A transversion from T to G.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "T to G transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000022" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "T_to_G_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000616", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome sub-band" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000737", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "expression-qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000021", + "meta" : { + "definition" : { + "val" : "A transversion from T to A.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000021" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "T to A transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "T_to_A_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000830", + "meta" : { + "definition" : { + "val" : "An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "chromosomal feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gross chromosomal part" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome part" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000078", + "meta" : { + "definition" : { + "val" : "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curation status specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000266" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "CLASS", + "lbl" : "curation status specification" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000020", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "C to G transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "C_to_G_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000736", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "location-qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000005", + "meta" : { + "definition" : { + "val" : "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\\"complex\\\" should be used. Usually there are multiple equally plausible explanations for the change.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complex substitution" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000005" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "complex_substitution" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000002", + "meta" : { + "definition" : { + "val" : "Any change in genomic DNA caused by a single event.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "substitution" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000009", + "meta" : { + "definition" : { + "val" : "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000009" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "transition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000008", + "meta" : { + "definition" : { + "val" : "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "point mutation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Point_mutation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000008" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "point_mutation" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000962", + "meta" : { + "definition" : { + "val" : "A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a \"sequence feature level\" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred).\n\nFor example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome." + } ] + }, + "type" : "CLASS", + "lbl" : "variant copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000720", + "type" : "CLASS", + "lbl" : "DNA sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000841", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA26332-9" + } ] + }, + "type" : "PROPERTY", + "lbl" : "likely_pathogenic_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000840", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA6668-3" + } ] + }, + "type" : "PROPERTY", + "lbl" : "pathogenic_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000961", + "meta" : { + "definition" : { + "val" : "A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result.\n\nA 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. \n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome.\n\nWe represent the notion of copy number at the \"sequence level\" (as opposed to the \"sequence feature level\") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The \"sequence level\" representation here supports this use case. By contrast, a \"feature level\" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000964", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type." + } ] + }, + "type" : "CLASS", + "lbl" : "mosaic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000843", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA6675-8" + } ] + }, + "type" : "PROPERTY", + "lbl" : "benign_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000722", + "type" : "CLASS", + "lbl" : "amino acid sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000721", + "type" : "CLASS", + "lbl" : "RNA sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000963", + "meta" : { + "definition" : { + "val" : "A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "functional genetic dosage" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence.\n\n'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nAs we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele." + } ] + }, + "type" : "CLASS", + "lbl" : "functional copy complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000842", + "meta" : { + "definition" : { + "val" : "Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "non-causal_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000704", + "meta" : { + "definition" : { + "val" : "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Regarding the distinction between a 'gene' and a 'gene allele': \nEvery zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment)." + } ] + }, + "type" : "CLASS", + "lbl" : "gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000960", + "meta" : { + "definition" : { + "val" : "A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000849", + "type" : "PROPERTY", + "lbl" : "is_candidate_variant_for" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000848", + "meta" : { + "definition" : { + "val" : "A sequence alteration within the coding sequence of a gene.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_coding sequence alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000606", + "type" : "CLASS", + "lbl" : "hemizygous insertion-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000608", + "meta" : { + "definition" : { + "val" : "a relation to link a single locus complement to its zygosity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000845", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA26333-7" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_uncertain_significance_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000012", + "meta" : { + "definition" : { + "val" : "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000012" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "C to T transition at pCpG site" + } ] + }, + "type" : "CLASS", + "lbl" : "C_to_T_transition_at_pCpG_site" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000966", + "meta" : { + "definition" : { + "val" : "Relates a sequence feature location to an interval that defines its start and end position.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_interval" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000724", + "type" : "CLASS", + "lbl" : "obsolete_biological sequence or collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000603", + "meta" : { + "definition" : { + "val" : "an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "heteroplasmic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000602", + "meta" : { + "definition" : { + "val" : "an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "homoplasmic" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000011", + "meta" : { + "definition" : { + "val" : "A transition of a cytidine to a thymine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "C to T transition" + } ] + }, + "type" : "CLASS", + "lbl" : "C_to_T_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000965", + "meta" : { + "definition" : { + "val" : "A pair of integers representing start and end position of a location on a sequence coordinate system.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "sequence interval" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000844", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA26334-5" + } ] + }, + "type" : "PROPERTY", + "lbl" : "likely_benign_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000010", + "meta" : { + "definition" : { + "val" : "A substitution of a pyrimidine, C or T, for another pyrimidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "pyrimidine transition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000010" + } ] + }, + "type" : "CLASS", + "lbl" : "pyrimidine_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000726", + "meta" : { + "definition" : { + "val" : "A relation linking a qualified sequence feature to its component sequence feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_sequence_feature_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000847", + "meta" : { + "definition" : { + "val" : "A relation used to describe an environment contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_qualifying_environment" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000605", + "type" : "CLASS", + "lbl" : "hemizygous Y-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000967", + "meta" : { + "definition" : { + "val" : "Relates a 'sequence feature location' to a sequence that it is anchored to.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_reference_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000725", + "type" : "CLASS", + "lbl" : "obsolete_biological sequence collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000604", + "type" : "CLASS", + "lbl" : "hemizygous X-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000846", + "meta" : { + "definition" : { + "val" : "A relation used to describe a process contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_qualifying_process" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000036", + "meta" : { + "definition" : { + "val" : "A continuous nucleotide sequence is inverted in the same position.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000036" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inversion" + } ] + }, + "type" : "CLASS", + "lbl" : "inversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000035", + "meta" : { + "definition" : { + "val" : "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide_duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000035" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide duplication" + } ] + }, + "type" : "CLASS", + "lbl" : "duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000039", + "meta" : { + "definition" : { + "val" : "A tandem duplication where the individual regions are in the same orientation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "direct tandem duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000039" + } ] + }, + "type" : "CLASS", + "lbl" : "direct_tandem_duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000874", + "meta" : { + "definition" : { + "val" : "A relation used to describe a process contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "repeat region alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000632", + "type" : "CLASS", + "lbl" : "gpos66" + }, { + "id" : "http://biohackathon.org/resource/faldo#ForwardStrandPosition", + "type" : "CLASS", + "lbl" : "Positive strand" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000511", + "meta" : { + "definition" : { + "val" : "An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "wild-type" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000873", + "meta" : { + "definition" : { + "val" : "A relation used to describe an environment contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "microsatellite alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000634", + "meta" : { + "definition" : { + "val" : "relation between an molecular agent and its molecular target", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_targeted_by" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000513", + "meta" : { + "definition" : { + "val" : "a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "aneusomic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000876", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allelic dosage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gene dosage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_genetic dosage" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000875", + "meta" : { + "definition" : { + "val" : "A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "allelic state" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000512", + "meta" : { + "definition" : { + "val" : "One of a set of sequence features known to exist at a particular genomic location.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations).\n\nAlleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variable feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene.\n\nTo be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene.\n\t\n[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17)\n[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17)\n[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17)\n[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17)\n[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17)\n[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17)\n[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483\n[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17)\n[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17)\n[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17)\n[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17)\n[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)" + } ] + }, + "type" : "CLASS", + "lbl" : "allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000633", + "type" : "CLASS", + "lbl" : "gpos33" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000870", + "meta" : { + "definition" : { + "val" : "A collection of more than one sequence feature.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence feature collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000872", + "meta" : { + "definition" : { + "val" : "A set of genomic sequences (a biological sequence that is of genomic origin).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number complement" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic sequence set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000871", + "meta" : { + "definition" : { + "val" : "A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. \n\nAs highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\n1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \n\n2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). \"Star alleles\" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/).\n\n3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. \n\nEach of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block.\n\nInstead, we can create an 'allele set' class as the haplotype parent?" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype." + } ] + }, + "type" : "CLASS", + "lbl" : "haplotype" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000040", + "meta" : { + "definition" : { + "val" : "A tandem duplication where the individual regions are not in the same orientation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inverted tandem duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "mirror duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000040" + } ] + }, + "type" : "CLASS", + "lbl" : "inverted_tandem_duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000639", + "meta" : { + "definition" : { + "val" : "Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. \n\n2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds.\n\n3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "sequence_derives_from" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000878", + "meta" : { + "definition" : { + "val" : "Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "maternally inherited" + } ] + }, + "type" : "CLASS", + "lbl" : "maternal allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000515", + "meta" : { + "definition" : { + "val" : "An allele of a gene that contains some sequence alteration.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset." + } ] + }, + "type" : "CLASS", + "lbl" : "variant gene allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000877", + "meta" : { + "definition" : { + "val" : "A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genetic origin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variant origin" + } ] + }, + "type" : "CLASS", + "lbl" : "allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000514", + "type" : "INDIVIDUAL", + "lbl" : "exemplar term" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000638", + "meta" : { + "definition" : { + "val" : "A transgene part whose sequence is expressed in a gene product through transcription and/or translation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "coding transgene feature" + } ] + }, + "type" : "CLASS", + "lbl" : "expressed transgene region" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000879", + "meta" : { + "definition" : { + "val" : "Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "paternally inherited" + } ] + }, + "type" : "CLASS", + "lbl" : "paternal allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000516", + "meta" : { + "definition" : { + "val" : "A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allelic complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "homologous allele complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single locus feature complement" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes.\n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a.\n\nThe collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome." + } ] + }, + "type" : "CLASS", + "lbl" : "single locus complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000637", + "meta" : { + "definition" : { + "val" : "A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "regulatory transgene region" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000027", + "meta" : { + "definition" : { + "val" : "A transversion from guanine to thymine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000027" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "G to T transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "G_to_T_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000026", + "meta" : { + "definition" : { + "val" : "A transversion from guanine to cytidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000026" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "G to C transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "G_to_C_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000025", + "meta" : { + "definition" : { + "val" : "A transversion from adenine to thymine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "A to T transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000025" + } ] + }, + "type" : "CLASS", + "lbl" : "A_to_T_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000024", + "meta" : { + "definition" : { + "val" : "A transversion from adenine to cytidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000024" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "A to C transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "A_to_C_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000742", + "meta" : { + "definition" : { + "val" : "A relation linking a sequence_alteration to the gene it alters.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_within_allele_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_alteration_within" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000500", + "meta" : { + "definition" : { + "val" : "A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral allele" + } ] + }, + "type" : "CLASS", + "lbl" : "ancestral polymorphic allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000621", + "type" : "CLASS", + "lbl" : "gvar" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000741", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_has_regulatory_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000620", + "type" : "CLASS", + "lbl" : "gneg" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000623", + "type" : "CLASS", + "lbl" : "gpos75" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000502", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "wild-type gene allele" + } ] + }, + "type" : "CLASS", + "lbl" : "wild-type gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000501", + "meta" : { + "definition" : { + "val" : "An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain.\n\nThe notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "wild-type allele" + } ] + }, + "type" : "CLASS", + "lbl" : "wild-type allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000622", + "type" : "CLASS", + "lbl" : "gpos100" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000743", + "type" : "PROPERTY", + "lbl" : "has_asserted_phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000740", + "type" : "PROPERTY", + "lbl" : "has_inferred_phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000861", + "meta" : { + "definition" : { + "val" : "A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "non-integrated transgene" + } ] + }, + "type" : "CLASS", + "lbl" : "extra-chromosomal transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000629", + "meta" : { + "definition" : { + "val" : "A chromosome arm that is the longer of the two arms of a given chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "q-arm" + } ] + }, + "type" : "CLASS", + "lbl" : "long chromosome arm" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000628", + "meta" : { + "definition" : { + "val" : "A chromosome arm that is the shorter of the two arms of a given chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "stalk" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "p-arm" + } ] + }, + "type" : "CLASS", + "lbl" : "short chromosome arm" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000625", + "type" : "CLASS", + "lbl" : "gpos25" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000504", + "meta" : { + "definition" : { + "val" : "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position." + } ] + }, + "type" : "CLASS", + "lbl" : "reagent targeted gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000867", + "type" : "PROPERTY", + "lbl" : "proabalistic_quantifier" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000624", + "type" : "CLASS", + "lbl" : "gpos50" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000866", + "meta" : { + "definition" : { + "val" : "Property to link an assertion or association with some value quantifying its relevance or ranking.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The 'rank' quantifier in Bgee gene-anatomy associations, that indicates the imporatnace/specificity of a gene expression in a given anatommy relative to expressionin other anatomies for the same gene." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_quantifier" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000506", + "meta" : { + "definition" : { + "val" : "A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "extrinsic transgene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "experimentally-expressed transgene" + } ] + }, + "type" : "CLASS", + "lbl" : "transiently-expressed transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000032", + "meta" : { + "definition" : { + "val" : "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Indels can have a different number of bases than the corresponding reference sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Indel" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000032" + } ] + }, + "type" : "CLASS", + "lbl" : "indel" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000626", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_color_value" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_staining_intensity" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000181", + "meta" : { + "definition" : { + "val" : "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "population" + }, { + "id" : "http://biohackathon.org/resource/faldo#Region", + "meta" : { + "definition" : { + "val" : "A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "Region" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000780", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "deoxyribonucleic acid residue" + } ] + }, + "type" : "CLASS", + "lbl" : "DNA residue" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000896", + "meta" : { + "definition" : { + "val" : "Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg').", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_string" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000533", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gene targeting reagent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence targeting reagent" + } ] + }, + "type" : "CLASS", + "lbl" : "gene knockdown reagent" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000654", + "meta" : { + "definition" : { + "val" : "An organizational class to hold relations of parthood between sequences/features.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000411", + "meta" : { + "definition" : { + "val" : "A relation linking a gene class to a sequence-varaint or expression-variant of the gene.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Domain = punned gene class\nRange = genomic feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_variant_instance" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_has_genetic_variant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000653", + "meta" : { + "definition" : { + "val" : "A relationship between a wild-type allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_wild_type_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000895", + "meta" : { + "definition" : { + "val" : "The ending position of a sequence feature or interval.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "end_position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000414", + "meta" : { + "definition" : { + "val" : "A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets." + } ] + }, + "type" : "PROPERTY", + "lbl" : "targets_gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000898", + "meta" : { + "definition" : { + "val" : "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as \n\"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.\" Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location.\n\nCurrent definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424." + } ] + }, + "type" : "CLASS", + "lbl" : "haplotype block" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000777", + "meta" : { + "definition" : { + "val" : "An intrinsic genotype that specifies variation from a defined reference genome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "variant genomic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000030", + "meta" : { + "definition" : { + "val" : "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000142" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples of information content entites include journal articles, data, graphical layouts, and graphs." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Chris Stoeckert" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "information content entity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." + } ] + }, + "type" : "CLASS", + "lbl" : "information content entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000534", + "meta" : { + "definition" : { + "val" : "A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "targeted gene segment" + } ] + }, + "type" : "CLASS", + "lbl" : "reagent-targeted gene subregion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000897", + "meta" : { + "definition" : { + "val" : "An generically dependent continuant that carries biological sequence that is part of or derived from a genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/GENO_0000905", + "val" : "true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000655", + "type" : "PROPERTY", + "lbl" : "is_sequence_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000413", + "meta" : { + "definition" : { + "val" : "A relation linking a gene class to one of its sequence-variant alleles.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = punned gene class\nRange = allele" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_sequence_variant" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000892", + "meta" : { + "definition" : { + "val" : "A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "heteroplasmic mitochondrial inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000650", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sex_agnostic_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000770", + "type" : "CLASS", + "lbl" : "phenotypic inheritance process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000891", + "meta" : { + "definition" : { + "val" : "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/source", + "val" : "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.\n\nFormer axiom: denotes some 'obsolete_canonical allele'" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_contextual allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000410", + "meta" : { + "definition" : { + "val" : "A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_variant_instance_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Domain = genomic feature instance\nRange = punned gene class IRI" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_genetic_variant_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000652", + "meta" : { + "definition" : { + "val" : "A relationship between a polymorphic allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_polymorphic_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000894", + "meta" : { + "definition" : { + "val" : "The starting position of a sequence feature or interval.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "start_position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000773", + "meta" : { + "definition" : { + "val" : "An attribute describing a type of variation inhering in a sequence feature or collection.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allele attribute" + } ] + }, + "type" : "CLASS", + "lbl" : "variation attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000893", + "meta" : { + "definition" : { + "val" : "A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "homoplasmic mitochondrial inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0005692", + "type" : "CLASS", + "lbl" : "abnormal(ly) absent adaxial cell" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000651", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_mutant_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000772", + "meta" : { + "definition" : { + "val" : "A sequence attribute inhering in a feature whose identity is not specified.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_unspecified" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000637", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_engineered_plasmid" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000779", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "biological sequence residue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "monomeric residue" + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence unit" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000415", + "meta" : { + "definition" : { + "val" : "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "replaced with SO:engineered_region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "extra-genomic sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reagent sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000778", + "meta" : { + "definition" : { + "val" : "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "eliminating classes that are not necessary or add uneeded complexity." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence information entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000536", + "meta" : { + "definition" : { + "val" : "A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Scope of 'Genetic State': \n'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs.\n\n2. Genotype Subtypes:\nIn GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. \n\nTwo more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features.\n\n3. The Genotype Partonomy: \n'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype \"fgf8a; fgf3[AB]\", described at zfin.org/ZDB-FISH-150901-9362, include the following elements:\n\n - GVC: fgf8a; fgf3 (total intrinsic variation in the genome)\n - Genomic Background: AB (the reference against which the GVC is variant)\n - VSLC1: fgf8a (homozygous complement of gene alleles at one known variant locus)\n - VSLC2: fgf3 (heterozygous complement of gene alleles at another known variant locus)\n - Allele 1: fgf8a (variant version of the fgf8a gene, present in two copies)\n - Allele 2: fgf3 (variant version of the fgf3 gene, present in one copy)\n - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy)\n - Sequence Alteration1: (the specific mutation within the fgf8a gene that makes it variant)\n - Sequence Alteration2: (the specific mutation within the fgf3 gene that makes it variant)\n\nA graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md\n\nOne reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to \"propagate phenotypes\" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). \nNote however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above." + } ] + }, + "type" : "CLASS", + "lbl" : "genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000899", + "meta" : { + "definition" : { + "val" : "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "'Genomic Genotype' vs 'Genome' in GENO: \nA genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complete genotype" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000418", + "meta" : { + "definition" : { + "val" : "A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_affected_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000659", + "meta" : { + "definition" : { + "val" : "A set of sequence features.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus\n\n2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele.\n\n3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature).\n\nThe notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3].\n\n[1] https://www.snpedia.com/index.php/APOE-%CE%B54\n[2] https://www.snpedia.com/index.php/APOE-%CE%B52\n[3] https://www.snpedia.com/index.php/Gs270" + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature set" + }, { + "id" : "http://biohackathon.org/resource/faldo#StrandedPosition", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'." + } ] + }, + "type" : "CLASS", + "lbl" : "Stranded position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000890", + "meta" : { + "definition" : { + "val" : "One of a set of sequence features or haplotypes that exist at a particular genetic locus. ", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand.\n\nIn the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references)" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_canonical allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000885", + "meta" : { + "definition" : { + "val" : "An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement')\n\nAlt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "\"Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes.\"\nFrom https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/" + } ] + }, + "type" : "CLASS", + "lbl" : "diplotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000642", + "meta" : { + "definition" : { + "val" : "A transgene whose product is used as a selectable marker.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "selectable marker transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000524", + "meta" : { + "definition" : { + "val" : "A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment.\n\nThe 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "experimental genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "expression genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. \n\nOur rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. \n\nFinally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as:\n\n shha; shhb\n\nThis notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct." + } ] + }, + "type" : "CLASS", + "lbl" : "extrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000645", + "meta" : { + "definition" : { + "val" : "A genomic genotype where the genomic background specifies a male or female sex chromosome complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sex-qualified genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "intrinsic genotype (sex-specific)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances.\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nIn the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sex-qualified intrinsic genotype" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic genotype (sex-qualified)" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000887", + "type" : "CLASS", + "lbl" : "oryzias latipes strain" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000402", + "meta" : { + "definition" : { + "val" : "A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a/fgf8a)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "trans-heterozygous" + } ] + }, + "type" : "CLASS", + "lbl" : "compound heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000644", + "meta" : { + "definition" : { + "val" : "A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). \n\nA base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation)." + } ] + }, + "type" : "CLASS", + "lbl" : "karyotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000886", + "meta" : { + "definition" : { + "val" : "A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "allelic phase" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000881", + "meta" : { + "definition" : { + "val" : "Describes an allele whose origin is not known.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "unknown allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000880", + "meta" : { + "definition" : { + "val" : "Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. \n\t\t\nDe novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" + } ] + }, + "type" : "CLASS", + "lbl" : "de novo allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000883", + "meta" : { + "definition" : { + "val" : "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "replaced by GENO:0000900 ! 'germline'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "germ-line" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_gametic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000641", + "meta" : { + "definition" : { + "val" : "A relationship between a variant allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_variant_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000882", + "meta" : { + "definition" : { + "val" : "Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells.\n\t\t\nThese acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "acquired" + } ] + }, + "type" : "CLASS", + "lbl" : "somatic allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000761", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Proposal for a property linking regulatory elements to larger features of which they are a part." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_regulatory_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000640", + "type" : "CLASS", + "lbl" : "reporter region" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000173", + "meta" : { + "definition" : { + "val" : "A duplication consisting of 2 identical adjacent regions.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tandem duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000173" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "erverted" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + } ] + }, + "type" : "CLASS", + "lbl" : "tandem_duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000529", + "meta" : { + "definition" : { + "val" : "A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism).\n\nThe identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "expression allele" + } ] + }, + "type" : "CLASS", + "lbl" : "expression-variant gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000408", + "meta" : { + "definition" : { + "val" : "A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_sequence_variant_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size).\n\nWhile conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like \"fgf8a is an allele of the Danio rerio fgf8a gene\", and we may create data where fgf8a is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene).\n\nIt is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. \n\nThis departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\\GAL4 gene.\n\nAt the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = allele \nRange = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that the allele is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " is_allele_of the 'danio rerio fgf8a' gene locus." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000768", + "meta" : { + "definition" : { + "val" : "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "remodeling notion of sequence feature position around the idea of a 'genomic locus'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic coordinates" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_genomic position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000647", + "meta" : { + "definition" : { + "val" : "A genomic genotype here the genomic background specifies a female sex chromosome complement.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "female intrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000889", + "meta" : { + "definition" : { + "val" : "An inheritance pattern that is not determined or not known.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unknown inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "undetermined inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000646", + "meta" : { + "definition" : { + "val" : "A genomic genotype here the genomic background specifies a male sex chromosome complement.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "male intrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000525", + "meta" : { + "definition" : { + "val" : "A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" + } ] + }, + "type" : "CLASS", + "lbl" : "effective genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000888", + "meta" : { + "definition" : { + "val" : "Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parental origin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parentally inherited" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "hereditary" + } ] + }, + "type" : "CLASS", + "lbl" : "germline allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000767", + "meta" : { + "definition" : { + "val" : "A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_has_position_component" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000649", + "meta" : { + "definition" : { + "val" : "A background genotype whose sequence or identity is not known or specified.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unspecified background genotype" + } ] + }, + "type" : "CLASS", + "lbl" : "unspecified genomic background" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000528", + "meta" : { + "definition" : { + "val" : "The set of all transgenes trransiently expressed in a biological system in the context of a given experiment.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "experimental transgene complement" + } ] + }, + "type" : "CLASS", + "lbl" : "transiently-expressed transgene complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000527", + "meta" : { + "definition" : { + "val" : "A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment." + } ] + }, + "type" : "CLASS", + "lbl" : "reagent-targeted gene complement" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000783", + "meta" : { + "definition" : { + "val" : "An attribute to describe a region that was modified in vitro.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "engineered" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000086", + "type" : "CLASS", + "lbl" : "reagent role" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000681", + "meta" : { + "definition" : { + "val" : "An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "transgenic extrachromosomal replicon" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "exogenous extrachromosomal replicon" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "aberrant extrachromosomal replicon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'." + } ] + }, + "type" : "CLASS", + "lbl" : "novel extrachromosomal replicon" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000680", + "meta" : { + "definition" : { + "val" : "A genomic feature that has an extent of zero.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Former logical def: \n'genomic feature'\n and (has_extent value 0)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A junction between bases, a deletion variant, a terminus at the end of a chromosome." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_null feature" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", + "type" : "CLASS", + "lbl" : "Homo sapiens" + }, { + "id" : "http://purl.obolibrary.org/obo/MP_0000001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "where to place this depends on if we take the organismal view or the quality centric view." + } ] + }, + "type" : "CLASS", + "lbl" : "mammalian phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000678", + "meta" : { + "definition" : { + "val" : "Property linking a sequence or sequence feature to an integer representing its length in terms of the number of units in the sequence.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_extent" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000793", + "type" : "PROPERTY", + "lbl" : "inferred_to_contribute_to_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000794", + "type" : "PROPERTY", + "lbl" : "inferred_to_correlate_with_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001746", + "meta" : { + "definition" : { + "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001746" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "paternal uniparental disomy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 02:03:30 PST 2011" + } ] + }, + "type" : "CLASS", + "lbl" : "paternal_uniparental_disomy" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001745", + "meta" : { + "definition" : { + "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 02:03:01 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001745" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "maternal uniparental disomy" + } ] + }, + "type" : "CLASS", + "lbl" : "maternal_uniparental_disomy" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001505", + "meta" : { + "definition" : { + "val" : "A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'GRCh37.p10' (a human reference genome build)" + } ] + }, + "type" : "CLASS", + "lbl" : "reference genome sequence" + }, { + "id" : "http://www.ncbi.nlm.nih.gov/gene/399483", + "meta" : { + "xrefs" : [ { + "val" : "http://zfin.org/ZDB-GENE-040123-1" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000514" + } ] + }, + "type" : "CLASS", + "lbl" : "danio rerio cdkn1ca gene" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001742", + "meta" : { + "definition" : { + "val" : "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 01:54:09 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number gain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001742" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + } ] + }, + "type" : "CLASS", + "lbl" : "copy_number_gain" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001500", + "meta" : { + "definition" : { + "val" : "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "heritable_phenotypic_marker" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001744", + "meta" : { + "definition" : { + "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "uniparental disomy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "UPD" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http:http\\://en.wikipedia.org/wiki/Uniparental_disomy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 02:01:05 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001744" + } ] + }, + "type" : "CLASS", + "lbl" : "UPD" + }, { + "id" : "http://purl.obolibrary.org/obo/WBPhenotype_0000886", + "meta" : { + "definition" : { + "val" : "Animals exhibit variations compared to a given control.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "c. elegans phenotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "Variant" + } ] + }, + "type" : "CLASS", + "lbl" : "worm phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001743", + "meta" : { + "definition" : { + "val" : "A sequence alteration whereby the copy number of a given region is less than the reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001743" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 01:55:02 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "loss" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number loss" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + } ] + }, + "type" : "CLASS", + "lbl" : "copy_number_loss" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#Subset", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000771", + "meta" : { + "definition" : { + "val" : "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quantitative trait locus" + } ] + }, + "type" : "CLASS", + "lbl" : "QTL" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000791", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains.\n\nBelow are the different kinds/paths of propagation we desire:\n1. Propagation 'down' a genotype (from larger components to smaller ones)\n2. Propagation 'up' a genotype (from smaller components to larger ones)\n3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype).\n4. From an effective genotype to its intrinsic and extrinsic components.\n5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele).\n6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this.\n\nNote that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha/shha [AB] to shha/shha [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition')" + } ] + }, + "type" : "PROPERTY", + "lbl" : "inferred_to_cause_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000790", + "type" : "PROPERTY", + "lbl" : "related_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000788", + "meta" : { + "definition" : { + "val" : "An attribute, quality, or state of a sequence feature or collection.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0000400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000667", + "meta" : { + "definition" : { + "val" : "A transgene that codes for a product used as a reporter of gene expression or activity.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "reporter transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000666", + "meta" : { + "definition" : { + "val" : "A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "SO:0000831 (gene member region)" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "defined gene part" + } ] + }, + "type" : "CLASS", + "lbl" : "gene part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000661", + "meta" : { + "definition" : { + "val" : "Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_sex_agnostic_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000782", + "type" : "CLASS", + "lbl" : "amino acid residue" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000781", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ribonucleic acid residue" + } ] + }, + "type" : "CLASS", + "lbl" : "RNA residue" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000660", + "meta" : { + "definition" : { + "val" : "A set of genomic features (i.e. sequence features that are of genomic origin).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature.\n\nThe notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic locus complement" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic feature set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000784", + "meta" : { + "definition" : { + "val" : "A relation between two seqeunces or features that are considered variant with each other along their entire extents.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "completely_varies_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000783", + "meta" : { + "definition" : { + "val" : "A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues)", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_unit" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001410", + "meta" : { + "definition" : { + "val" : "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "not currently needed to support modeling use cases. can re-introduce if becomes necessary." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_experimental_feature" + }, { + "id" : "http://biohackathon.org/resource/faldo#location", + "type" : "PROPERTY", + "lbl" : "location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000580", + "meta" : { + "definition" : { + "val" : "A relation used to describe a context or conditions that define and/or identify an entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_qualifying_context" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association.\n\nUsed in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_qualifier" + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000118", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "pulling in HP 'phenotypic abnormality' root here" + } ] + }, + "type" : "CLASS", + "lbl" : "human phenotypic abnormality" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000460", + "meta" : { + "definition" : { + "val" : "A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "transgene part" + }, { + "id" : "http://purl.org/oban/association_has_subject", + "type" : "PROPERTY", + "lbl" : "association has subject" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000458", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a)" + } ] + }, + "type" : "CLASS", + "lbl" : "simple heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "type" : "PROPERTY", + "lbl" : "is part of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000575", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl\nThis ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes." + } ] + }, + "type" : "CLASS", + "lbl" : "zebrafish phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000211", + "meta" : { + "definition" : { + "val" : "A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "materializes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence." + } ] + }, + "type" : "PROPERTY", + "lbl" : "bears_concretization_of" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "type" : "PROPERTY", + "lbl" : "has part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000339", + "meta" : { + "definition" : { + "val" : "A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as \"the point at which one or more contiguous nucleotides were excised\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "absent aneusomic chromosome" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "lost aneusomic chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000338", + "meta" : { + "definition" : { + "val" : "A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "duplicate chromosome" + } ] + }, + "type" : "CLASS", + "lbl" : "gained aneusomic chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000445", + "meta" : { + "definition" : { + "val" : "A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "class_to_feature_relation" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_feature_affected_by" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000324", + "meta" : { + "definition" : { + "val" : "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_chromosome complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000447", + "meta" : { + "definition" : { + "val" : "A relation between a gene class and a gene targeting reagent that targets it.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Domain = punned gene class\nRange = gene knockdown reagent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_target_of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_gene_target_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000688", + "meta" : { + "definition" : { + "val" : "A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "terminus" + }, { + "id" : "http://biohackathon.org/resource/faldo#position", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is." + } ] + }, + "type" : "PROPERTY", + "lbl" : "position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000683", + "meta" : { + "definition" : { + "val" : "A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "varies_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000443", + "meta" : { + "definition" : { + "val" : "A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = expression variant feature.\nRange = punned gene class" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_expression_variant_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000685", + "meta" : { + "definition" : { + "val" : "An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "novel" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000684", + "meta" : { + "definition" : { + "val" : "A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles." + } ] + }, + "type" : "CLASS", + "lbl" : "novel replicon" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000667", + "meta" : { + "definition" : { + "val" : "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000034" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide_insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000667" + } ] + }, + "type" : "CLASS", + "lbl" : "insertion" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an epidemic" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a human being" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a hurricane" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a flame" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a sea wave" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a tornado" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an aggregate of human beings." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the undetached arm of a human being" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a forest fire" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an energy wave" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a puff of smoke" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a photon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "material entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000449", + "meta" : { + "definition" : { + "val" : "A relation linking a gene class to one of an expression-variant of that gene..", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = punned gene class\nRange = expression variant feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_expression_variant_instance" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_expression_variant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000207", + "meta" : { + "definition" : { + "val" : "A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/so_has_quality" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000341", + "meta" : { + "definition" : { + "val" : "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "\"Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band\n" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome band" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000340", + "meta" : { + "definition" : { + "val" : "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A complete chromosome sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000481", + "meta" : { + "definition" : { + "val" : "A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. \n\n2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). \n\n3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic feature" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10239", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies." + } ] + }, + "type" : "CLASS", + "lbl" : "Viruses" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000480", + "meta" : { + "definition" : { + "val" : "An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "mutant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000482", + "meta" : { + "definition" : { + "val" : "A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "genetic material" + }, { + "id" : "http://purl.obolibrary.org/obo/ERO_0002003", + "meta" : { + "definition" : { + "val" : "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "stem cell line" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000477", + "meta" : { + "definition" : { + "val" : "An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "polymorphic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000359", + "meta" : { + "definition" : { + "val" : "shortcut relation used to link a phenotype directly to a genotype of an organism", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "phenotype_has_genotype" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Might expand to something like:\n\nphenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype)))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_phenotype_of_organism_with_genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_phenotype_with_genotype" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_phenotype_of_genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/CHEBI_33696", + "type" : "CLASS", + "lbl" : "nucleic acid" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000111", + "meta" : { + "definition" : { + "val" : "a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider http://semanticscience.org/resource/SIO_001062 ! human population (\"A human population refers to a collection of human beings\")." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "homo sapiens population" + } ] + }, + "type" : "CLASS", + "lbl" : "human population" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000231", + "meta" : { + "definition" : { + "val" : "An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO)", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://semanticscience.org/resource/SIO_000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "No proper part relation anymore in RO/BFO?" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_proper_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000113", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon)" + } ] + }, + "type" : "CLASS", + "lbl" : "taxonomic group" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000476", + "meta" : { + "definition" : { + "val" : "An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "variant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000112", + "meta" : { + "definition" : { + "val" : "A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "organism strain or breed" + } ] + }, + "type" : "CLASS", + "lbl" : "strain or breed" + }, { + "id" : "http://purl.obolibrary.org/obo/ERO_0002002", + "meta" : { + "definition" : { + "val" : "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "embryonic stem cell line" + }, { + "id" : "http://purl.obolibrary.org/obo/UPHENO_0001001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition)\n\n2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework." + } ] + }, + "type" : "CLASS", + "lbl" : "Phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000337", + "type" : "CLASS", + "lbl" : "RNAi_reagent" + }, { + "id" : "http://biohackathon.org/resource/faldo#begin", + "type" : "PROPERTY", + "lbl" : "begin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000119", + "type" : "CLASS", + "lbl" : "danio rerio strain" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001785", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001785" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Fri Mar 25 02:27:41 PDT 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + } ] + }, + "type" : "CLASS", + "lbl" : "structural_alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000239", + "meta" : { + "definition" : { + "val" : "A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "VMC:state" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_sequence_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_state" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000118", + "type" : "CLASS", + "lbl" : "mus musculus strain" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000699", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A junction is a boundary between regions. A boundary has an extent of zero." + } ] + }, + "type" : "CLASS", + "lbl" : "junction" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0600043", + "meta" : { + "definition" : { + "val" : "the introduction. alteration or integration of genetic material into a cell or organism", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "genetic modification technique" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000577", + "type" : "CLASS", + "lbl" : "centromere" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001784", + "meta" : { + "definition" : { + "val" : "A structural sequence alteration where there are multiple equally plausible explanations for the change.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001784" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Wed Mar 23 03:21:19 PDT 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + } ] + }, + "type" : "CLASS", + "lbl" : "complex_structural_alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000694", + "meta" : { + "definition" : { + "val" : "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single nucleotide polymorphism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000694" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + } ] + }, + "type" : "CLASS", + "lbl" : "SNP" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000351", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of biological processes from GO-BP." + } ] + }, + "type" : "CLASS", + "lbl" : "biological process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000346", + "meta" : { + "definition" : { + "val" : "A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complete aneusomic chromosome" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism.\n\nSimilarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication." + } ] + }, + "type" : "CLASS", + "lbl" : "aneusomic chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000345", + "meta" : { + "definition" : { + "val" : "A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome.\n\nLoss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "dropped partial anneuploid chromosomal element" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "translocated absent chromosomal segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "truncated chromosome terminus" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement" + } ] + }, + "type" : "CLASS", + "lbl" : "lost aneusomic chromosomal segment" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000106", + "meta" : { + "definition" : { + "val" : "A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic material" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000220", + "type" : "PROPERTY", + "lbl" : "is_genotype_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000344", + "meta" : { + "definition" : { + "val" : "A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "translocated duplicate chromosomal segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "translocated duplicate chromosomal element" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "duplicate partial aneuploid chromosomal element" + } ] + }, + "type" : "CLASS", + "lbl" : "gained aneusomic chromosomal segment" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000222", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and some level of genetic variation present in its genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000343", + "meta" : { + "definition" : { + "val" : "A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "aneuploid chromosomal segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "aneusomic chromosomal subregion/segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Aneusomic chromosomal parts are examples of \"partial aneuploidy\" as described in http://en.wikipedia.org/wiki/Aneuploidy: \"The terms \"partial monosomy\" and \"partial trisomy\" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "partial aneusomic chromosomal element" + } ] + }, + "type" : "CLASS", + "lbl" : "aneusomic chromosomal part" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000207", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "simple sequence length polymorphism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "SSLP" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "simple sequence length variation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000207" + } ] + }, + "type" : "CLASS", + "lbl" : "simple_sequence_length_variation" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000108", + "meta" : { + "definition" : { + "val" : "A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "physical genome" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements.\n\nNote that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome." + } ] + }, + "type" : "CLASS", + "lbl" : "material genome" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mass of this piece of gold." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the length of the circumference of your waist" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of your nose" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the color of a tomato" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the ambient temperature of this portion of air" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of your nostril" + } ] + }, + "type" : "CLASS", + "lbl" : "quality" + }, { + "id" : "http://purl.org/oban/association_has_predicate", + "type" : "PROPERTY", + "lbl" : "association has predicate" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "type" : "PROPERTY", + "lbl" : "starts during" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "type" : "PROPERTY", + "lbl" : "ends during" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "meta" : { + "definition" : { + "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the life of an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the flight of a bird" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of cell-division, \\ a beating of the heart" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of sleeping" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of meiosis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "your process of aging." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the course of a disease" + } ] + }, + "type" : "CLASS", + "lbl" : "process" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an atom of element X has the disposition to decay to an atom of element Y" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the cell wall is disposed to filter chemicals in endocitosis and exocitosis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "children are innately disposed to categorize objects in certain ways." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "certain people have a predisposition to colon cancer" + } ] + }, + "type" : "CLASS", + "lbl" : "disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of your blood to coagulate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of being a doctor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of your reproductive organs" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of this piece of metal to conduct electricity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of this boundary to delineate where Utah and Colorado meet" + } ] + }, + "type" : "CLASS", + "lbl" : "realizable entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000382", + "meta" : { + "definition" : { + "val" : "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_variant_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000140", + "type" : "CLASS", + "lbl" : "non-heritable" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000142", + "meta" : { + "definition" : { + "val" : "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000141", + "meta" : { + "definition" : { + "val" : "The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/NCIT_C45827" + }, { + "val" : "http://purl.obolibrary.org/obo/HP_0000005" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, \"genetic context\" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. \n\nThese genetic and environmental \"interactions\" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "mode of inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "phenotypic inheritance pattern" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family." + } ] + }, + "type" : "CLASS", + "lbl" : "inheritance pattern" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000383", + "type" : "PROPERTY", + "lbl" : "is_variant_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000137", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "no-call zygosity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indeterminite zygosity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unknown zygosity" + } ] + }, + "type" : "CLASS", + "lbl" : "unspecified zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000499", + "meta" : { + "definition" : { + "val" : "A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "minor allele" + } ] + }, + "type" : "CLASS", + "lbl" : "minor polymorphic allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000136", + "type" : "CLASS", + "lbl" : "homozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000139", + "type" : "CLASS", + "lbl" : "heritable" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000017", + "meta" : { + "definition" : { + "val" : "A sequence that serves as a standard against which other sequences at the same location are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "reference sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000138", + "meta" : { + "definition" : { + "val" : "The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells).\n\nWe can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms." + } ] + }, + "type" : "CLASS", + "lbl" : "heritabililty" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000133", + "meta" : { + "definition" : { + "val" : "An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://semanticscience.org/resource/SIO_001263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allelic state" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "derived from https://en.wikipedia.org/wiki/Zygosity" + } ] + }, + "type" : "CLASS", + "lbl" : "zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000495", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "expression construct feature" + } ] + }, + "type" : "CLASS", + "lbl" : "expression construct" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000132", + "meta" : { + "definition" : { + "val" : "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "in trans" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000253", + "type" : "PROPERTY", + "lbl" : "obsolete_is_specified_by" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000498", + "meta" : { + "definition" : { + "val" : "A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "major allele" + } ] + }, + "type" : "CLASS", + "lbl" : "major polymorphic allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000014", + "meta" : { + "definition" : { + "val" : "A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene)", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0001023 ! allele" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The \"mn004Gt\" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome.\n\nhttp://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722\n\nhttp://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion.\n\nA genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment).\n\nThis design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not." + } ] + }, + "type" : "CLASS", + "lbl" : "gene allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000135", + "type" : "CLASS", + "lbl" : "heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000497", + "meta" : { + "definition" : { + "val" : "An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "PMID: 25741868 ACMG Guidelines" + } ] + }, + "type" : "CLASS", + "lbl" : "polymorphic allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000134", + "type" : "CLASS", + "lbl" : "hemizygous" + }, { + "id" : "http://purl.org/oban/association_has_object", + "type" : "PROPERTY", + "lbl" : "association has object" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000019", + "meta" : { + "definition" : { + "val" : "a collection more than one sequence features (ie a collection of discontinuous sequence features)", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one)" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence feature collection" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000110", + "meta" : { + "definition" : { + "val" : "Any extent of continuous biological sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", + "meta" : { + "definition" : { + "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an atom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a heart" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the interior of your mouth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a chair" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a spatial region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a leg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an orchestra." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the bottom right portion of a human torso" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a molecule" + } ] + }, + "type" : "CLASS", + "lbl" : "independent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000492", + "meta" : { + "definition" : { + "val" : "A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "mutation" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000491", + "meta" : { + "definition" : { + "val" : "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required for any specific use case at this point so removed for simplicity. \nFormely asserted as allele and inferred as varaint allele. \nEq class definition:\nallele\n and (mutation or ('has subsequence' some mutation))" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_mutant allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000010", + "meta" : { + "definition" : { + "val" : "A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "OBI:genetic population background information" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic background" + } ] + }, + "type" : "CLASS", + "lbl" : "background genome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000131", + "meta" : { + "definition" : { + "val" : "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "in cis" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000494", + "meta" : { + "definition" : { + "val" : "A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "episomal replicon" + } ] + }, + "type" : "CLASS", + "lbl" : "extrachromosomal replicon" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000252", + "type" : "PROPERTY", + "lbl" : "is_subject_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000251", + "type" : "PROPERTY", + "lbl" : "is_sequence_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000368", + "meta" : { + "definition" : { + "val" : "A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Exploratory/temporary property, as we formalize our phenotypic inheritance model." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_participates_in_inheritance_process" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "meta" : { + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/CARO_0000000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies." + } ] + }, + "type" : "CLASS", + "lbl" : "anatomical entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000125", + "meta" : { + "definition" : { + "val" : "sequence attribute that can inhere only in a collection of more than one sequence features", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence feature collection attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000488", + "meta" : { + "definition" : { + "val" : "A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways).", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_expression_variant_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000248", + "meta" : { + "definition" : { + "val" : "An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://semanticscience.org/resource/SIO_000093" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_proper_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/CLO_0000031", + "meta" : { + "definition" : { + "val" : "A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "cell line" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000243", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_approximates_sequence" + }, { + "id" : "http://biohackathon.org/resource/faldo#Position", + "meta" : { + "definition" : { + "val" : "Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "FALDO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region)." + } ] + }, + "type" : "CLASS", + "lbl" : "Position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000000", + "meta" : { + "definition" : { + "val" : "A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sex-agnostic intrinsic genotype" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "organismal genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Example zebrafish intrinsic genotype:\n\nGenotype = fgf8a; shha (AB)\nreference component (genomic background) = AB \nvariant component ('genomic variation complement') = fgf8a; shha\n\n. . . and within this variant component, there are two 'variant single locus complements' represented:\n\nallele complement 1 = fgf8a\nallele complement 2 = shha\n\nand within each of these 'variant single locus complements' there is one or more variant gene locus member:\n\nin complement 1: fgf8a\nin complement 2: shha" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic genotype (sex-agnostic)" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000242", + "meta" : { + "definition" : { + "val" : "A relationship between an information content entity representing a specification, and the entity it specifies.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A geno:intrinnsic genotype 'specifies' a SO:genome.\nA geno:karyotype 'specifies' a geno:karyotype feature collection." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_specifies" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000484", + "type" : "INDIVIDUAL", + "lbl" : "exploratory term" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000002", + "meta" : { + "definition" : { + "val" : "An allele that varies in it sequence from what is considered the reference or canonical sequence at that location.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variant feature" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another.\n\nA variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "alternate allele" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence-variant feature" + } ] + }, + "type" : "CLASS", + "lbl" : "variant allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000486", + "meta" : { + "definition" : { + "val" : "A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_variant_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000244", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_resolves_to_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Julius Caesar" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Verdi’s Requiem" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the Second World War" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "your body mass index" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" + } ] + }, + "type" : "CLASS", + "lbl" : "entity" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000002", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" + } ] + }, + "type" : "CLASS", + "lbl" : "continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." + } ] + }, + "type" : "CLASS", + "lbl" : "occurrent" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000009", + "meta" : { + "definition" : { + "val" : "A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation.\n\nIn model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene))." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic variation complement" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000105", + "meta" : { + "definition" : { + "val" : "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome arm" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000143", + "meta" : { + "definition" : { + "val" : "A region of known length which may be used to manufacture a longer region.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_assembly_component" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000164", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "objective is to insert some specified sequence into the genome of a cell or virus" + } ] + }, + "type" : "CLASS", + "lbl" : "genetic insertion technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000042", + "meta" : { + "definition" : { + "val" : "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "hemizygous reference junction" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction.\n\nThe junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reference junction" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000160", + "type" : "CLASS", + "lbl" : "unspecified life cycle stage" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000037", + "meta" : { + "definition" : { + "val" : "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class def: 'genomic feature'\n and (has_sequence_attribute some unspecified)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele)." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_unspecified feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000033", + "meta" : { + "definition" : { + "val" : "A genome that varies at one or more loci from the sequence of some reference genome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here)" + } ] + }, + "type" : "CLASS", + "lbl" : "variant genome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000036", + "meta" : { + "definition" : { + "val" : "An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.\n\nIn model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared." + } ] + }, + "type" : "CLASS", + "lbl" : "reference allele" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of a hammer to drive in nails" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of amylase in saliva to break down starch into sugar" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" + } ] + }, + "type" : "CLASS", + "lbl" : "function" + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions.\n\n2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class \"system\". The relation \"environed_by\" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised." + } ] + }, + "type" : "CLASS", + "lbl" : "environmental system" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000031", + "meta" : { + "definition" : { + "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." + } ] + }, + "type" : "CLASS", + "lbl" : "generically dependent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000393", + "type" : "CLASS", + "lbl" : "trisomic homozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000030", + "meta" : { + "definition" : { + "val" : "A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variant allelic complement" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members.\n\nNote that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant." + } ] + }, + "type" : "CLASS", + "lbl" : "variant single locus complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000392", + "type" : "CLASS", + "lbl" : "aneusomic zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000150", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "duplicate term, use GENO:0000148" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_autosomal recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000394", + "type" : "CLASS", + "lbl" : "trisomic heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000152", + "meta" : { + "definition" : { + "val" : "An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another." + } ] + }, + "type" : "CLASS", + "lbl" : "reference" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000391", + "type" : "CLASS", + "lbl" : "disomic zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000148", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "autosomal recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000147", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0000006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "vertical inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000029", + "meta" : { + "definition" : { + "val" : "A single locus complement that serves as a standard against which 'variant' sequences are compared", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference allelic complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference single locus feature complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'single locus complement'\n and (has_sequence_attribute some reference)\n\nSC axioms:\n'has member' exactly 0 'variant allele'\n'has member' only 'reference genomic feature'\n'has member' some 'reference genomic feature'" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reference single locus complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000149", + "meta" : { + "definition" : { + "val" : "An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001419" + } ] + }, + "type" : "CLASS", + "lbl" : "X-linked recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000144", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "pure dominant inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "complete autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000022", + "meta" : { + "definition" : { + "val" : "A sequence feature collection comprised of discontiguous sequences from a single genome", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic feature collection" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_genomic feature collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000143", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "co-dominant autosomal inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000385", + "meta" : { + "definition" : { + "val" : "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_reference_sequence_part" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_reference_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000146", + "meta" : { + "definition" : { + "val" : "An X-linked inheritance pattern wherein the trait manifests in heterozygotes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001423" + } ] + }, + "type" : "CLASS", + "lbl" : "X-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000145", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "intermediate dominant autosomal inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "semi-dominant autosomal inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "incomplete autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000387", + "type" : "PROPERTY", + "lbl" : "is_reference_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001218", + "meta" : { + "definition" : { + "val" : "An insertion that derives from another organism, via the use of recombinant DNA technology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001218" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "transgenic insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "transgenic_insertion" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000023", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a boundary to demarcate two neighboring administrative territories" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a stone in marking a property boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a building in serving as a military target" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of subject in a clinical trial" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the priest role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the student role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." + } ] + }, + "type" : "CLASS", + "lbl" : "role" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0000755", + "type" : "CLASS", + "lbl" : "abnormal(ly) disrupted diencephalon development" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000020", + "meta" : { + "definition" : { + "val" : "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "of one-sided specifically dependent continuants: the mass of this tomato" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of being a doctor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of this fish to decay" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the pink color of a medium rare piece of grilled filet mignon at its center" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the smell of this portion of mozzarella" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of this heart: to pump blood" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of this hole." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mutual dependence of proton donors and acceptors in chemical reactions [79" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" + } ] + }, + "type" : "CLASS", + "lbl" : "specifically dependent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000248", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000248" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence length variation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : 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"http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000481", + "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000903", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000902" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000777", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000899" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000219", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000033" + } ] + } ], + "domainRangeAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002200", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002201", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000251", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" + } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000368", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000141" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000610", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000036" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000653", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000501" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000359", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000641", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000652", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000497" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000651", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000491" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000959", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000903", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000815" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000958", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000408", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000481" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000608", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000516" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000133" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000966", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000815" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000239", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000726", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000957", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000815" ] + } ], + "propertyChainAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000449", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000639", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/GENO_0000639" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000418", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/GENO_0000418" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000211", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000053", "http://purl.obolibrary.org/obo/RO_0000059" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000449", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000445", "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000418", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000418" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000445", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000742", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000408" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000445", "http://purl.obolibrary.org/obo/RO_0003303" ] + } ] + } ] +} \ No newline at end of file diff --git a/geno-full.obo b/geno-full.obo new file mode 100644 index 0000000..f0b2a6a --- /dev/null +++ b/geno-full.obo @@ -0,0 +1,4218 @@ +format-version: 1.2 +data-version: geno/releases/2019-09-09/geno-full.owl +ontology: geno/geno-full +property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string +property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string +property_value: http://purl.org/dc/terms/license "Unspecified" xsd:string + +[Term] +id: BFO:0000001 +name: entity +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +is_a: BFO:0000001 ! entity +property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] +is_a: BFO:0000002 ! continuant +property_value: IAO:0000112 "a chair" xsd:string +property_value: IAO:0000112 "a heart" xsd:string +property_value: IAO:0000112 "a leg" xsd:string +property_value: IAO:0000112 "a molecule" xsd:string +property_value: IAO:0000112 "a spatial region" xsd:string +property_value: IAO:0000112 "an atom" xsd:string +property_value: IAO:0000112 "an orchestra." xsd:string +property_value: IAO:0000112 "an organism" xsd:string +property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string +property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] +is_a: BFO:0000003 ! occurrent +property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string +property_value: IAO:0000112 "a process of meiosis" xsd:string +property_value: IAO:0000112 "a process of sleeping" xsd:string +property_value: IAO:0000112 "the course of a disease" xsd:string +property_value: IAO:0000112 "the flight of a bird" xsd:string +property_value: IAO:0000112 "the life of an organism" xsd:string +property_value: IAO:0000112 "your process of aging." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role +property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string +property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string +property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string +property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocitosis and exocitosis" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89" xsd:string +property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000017 +name: realizable entity +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality +property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string +property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string +property_value: IAO:0000112 "the function of your reproductive organs" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string +property_value: IAO:0000112 "the color of a tomato" xsd:string +property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string +property_value: IAO:0000112 "the mass of this piece of gold." xsd:string +property_value: IAO:0000112 "the shape of your nose" xsd:string +property_value: IAO:0000112 "the shape of your nostril" xsd:string +property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] +is_a: BFO:0000002 ! continuant +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string +property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000023 +name: role +is_a: BFO:0000017 ! realizable entity +property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string +property_value: IAO:0000112 "the priest role" xsd:string +property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string +property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string +property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string +property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string +property_value: IAO:0000112 "the student role" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string +property_value: IAO:0000600 "b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] +is_a: BFO:0000002 ! continuant +property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition +property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string +property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string +property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string +property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +is_a: BFO:0000004 ! independent continuant +property_value: IAO:0000112 "a flame" xsd:string +property_value: IAO:0000112 "a forest fire" xsd:string +property_value: IAO:0000112 "a human being" xsd:string +property_value: IAO:0000112 "a hurricane" xsd:string +property_value: IAO:0000112 "a photon" xsd:string +property_value: IAO:0000112 "a puff of smoke" xsd:string +property_value: IAO:0000112 "a sea wave" xsd:string +property_value: IAO:0000112 "a tornado" xsd:string +property_value: IAO:0000112 "an aggregate of human beings." xsd:string +property_value: IAO:0000112 "an energy wave" xsd:string +property_value: IAO:0000112 "an epidemic" xsd:string +property_value: IAO:0000112 "the undetached arm of a human being" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BothStrandsPosition +name: Both strands +is_a: StrandedPosition ! Stranded position + +[Term] +id: CHEBI:23367 +name: molecular entity +is_a: BFO:0000040 ! material entity +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology." xsd:string + +[Term] +id: CHEBI:33696 +name: nucleic acid +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CL:0000000 +name: cell +comment: Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies. +is_a: UBERON:0001062 ! anatomical entity + +[Term] +id: CLO:0000031 +name: cell line +def: "A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture)." [] +is_a: GENO:0000904 ! organismal entity +relationship: RO:0001000 OBI:0100026 ! derives from organism + +[Term] +id: DbXref +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Definition +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: ENVO:01000254 +name: environmental system +comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. +is_a: BFO:0000040 ! material entity +property_value: IAO:0000116 "1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions.\n\n2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity)." xsd:string + +[Term] +id: ERO:0000007 +name: technique +def: "A technique is a planned process used to accomplish a specific activity or task." [] +is_a: OBI:0000011 ! planned process + +[Term] +id: ERO:0002002 +name: embryonic stem cell line +def: "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo." [] +is_a: ERO:0002003 ! stem cell line + +[Term] +id: ERO:0002003 +name: stem cell line +def: "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types." [] +is_a: CLO:0000031 ! cell line + +[Term] +id: ExactPosition +name: Exact position +def: "A position that is exactly known." [] +is_a: Position ! Position + +[Term] +id: ForwardStrandPosition +name: Positive strand +is_a: StrandedPosition ! Stranded position + +[Term] +id: GENO:0000000 +name: genomic genotype (sex-agnostic) +def: "A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement)" [] +comment: In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances). +is_a: GENO:0000899 ! genomic genotype +property_value: IAO:0000112 "Example zebrafish intrinsic genotype:\n\nGenotype = fgf8a; shha (AB)\nreference component (genomic background) = AB \nvariant component ('genomic variation complement') = fgf8a; shha\n\n. . . and within this variant component, there are two 'variant single locus complements' represented:\n\nallele complement 1 = fgf8a\nallele complement 2 = shha\n\nand within each of these 'variant single locus complements' there is one or more variant gene locus member:\n\nin complement 1: fgf8a\nin complement 2: shha" xsd:string +property_value: IAO:0000116 "This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype." xsd:string +property_value: IAO:0000118 "genotype" xsd:string +property_value: IAO:0000118 "organismal genotype" xsd:string +property_value: IAO:0000118 "sex-agnostic intrinsic genotype" xsd:string + +[Term] +id: GENO:0000002 +name: variant allele +def: "An allele that varies in it sequence from what is considered the reference or canonical sequence at that location." [] +comment: Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another.\n\nA variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence. +is_a: GENO:0000512 ! allele +intersection_of: GENO:0000512 ! allele +intersection_of: GENO:0000683 GENO:0000036 ! varies_with reference allele +relationship: GENO:0000683 GENO:0000036 ! varies_with reference allele +property_value: IAO:0000116 "The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles." xsd:string +property_value: IAO:0000118 "alternate allele" xsd:string +property_value: IAO:0000118 "sequence-variant feature" xsd:string +property_value: IAO:0000118 "variant feature" xsd:string + +[Term] +id: GENO:0000009 +name: genomic variation complement +def: "A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation.\n\nIn model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)). +is_a: GENO:0000660 ! genomic feature set +intersection_of: GENO:0000660 ! genomic feature set +intersection_of: GENO:0000382 GENO:0000030 ! has_variant_part variant single locus complement +relationship: GENO:0000382 GENO:0000030 ! has_variant_part variant single locus complement +property_value: IAO:0000116 "Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases." xsd:string + +[Term] +id: GENO:0000010 +name: background genome +def: "A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations)." [] +xref: OBI:genetic population background information +is_a: GENO:0000914 ! reference genome +property_value: IAO:0000112 "The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB)" xsd:string +property_value: IAO:0000116 "Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it." xsd:string +property_value: IAO:0000118 "genomic background" xsd:string + +[Term] +id: GENO:0000014 +name: gene allele +def: "A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene)" [] +comment: In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion.\n\nA genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene. +xref: http://purl.obolibrary.org/obo/SO_0001023 ! allele +is_a: GENO:0000512 ! allele +relationship: GENO:0000408 SO:0000704 ! is_allele_of gene +property_value: IAO:0000112 "The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The \"mn004Gt\" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome.\n\nhttp://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722\n\nhttp://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8" xsd:string +property_value: IAO:0000116 "Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment).\n\nThis design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not." xsd:string + +[Term] +id: GENO:0000017 +name: reference sequence +def: "A sequence that serves as a standard against which other sequences at the same location are compared." [] +comment: A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence. +is_a: GENO:0000702 ! biological sequence +intersection_of: GENO:0000702 ! biological sequence +intersection_of: RO:0000087 GENO:0000152 ! has_role reference +relationship: RO:0000087 GENO:0000152 ! has_role reference +property_value: IAO:0000116 "The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant." xsd:string +property_value: IAO:0000118 "reference sequence" xsd:string + +[Term] +id: GENO:0000019 +name: obsolete_sequence feature collection +def: "a collection more than one sequence features (ie a collection of discontinuous sequence features)" [] +comment: 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. +xref: perhaps not same as SO:sequence collection\, as here we explicitly include features that can have an extent of zero (and SO\:sequence collection is a collection of regions that have an extent of at least one) +is_a: ObsoleteClass + +[Term] +id: GENO:0000022 +name: obsolete_genomic feature collection +def: "A sequence feature collection comprised of discontiguous sequences from a single genome" [] +comment: Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. +is_a: ObsoleteClass +property_value: IAO:0000116 "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system." xsd:string +property_value: IAO:0000118 "genomic feature collection" xsd:string + +[Term] +id: GENO:0000029 +name: obsolete_reference single locus complement +def: "A single locus complement that serves as a standard against which 'variant' sequences are compared" [] +is_a: ObsoleteClass +property_value: IAO:0000118 "reference allelic complement" xsd:string +property_value: IAO:0000118 "reference single locus feature complement" xsd:string +property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'single locus complement'\n and (has_sequence_attribute some reference)\n\nSC axioms:\n'has member' exactly 0 'variant allele'\n'has member' only 'reference genomic feature'\n'has member' some 'reference genomic feature'" xsd:string + +[Term] +id: GENO:0000030 +name: variant single locus complement +def: "A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13)." [] +comment: Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members.\n\nNote that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant. +is_a: GENO:0000516 ! single locus complement +intersection_of: GENO:0000516 ! single locus complement +intersection_of: GENO:0000382 GENO:0000002 ! has_variant_part variant allele +relationship: GENO:0000382 GENO:0000002 ! has_variant_part variant allele +property_value: IAO:0000118 "variant allelic complement" xsd:string + +[Term] +id: GENO:0000033 +name: variant genome +def: "A genome that varies at one or more loci from the sequence of some reference genome." [] +xref: http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here) +is_a: SO:0001026 ! genome +intersection_of: SO:0001026 ! genome +intersection_of: GENO:0000683 GENO:0000914 ! varies_with reference genome +relationship: GENO:0000382 SO:0001059 ! has_variant_part sequence_alteration +relationship: GENO:0000683 GENO:0000914 ! varies_with reference genome + +[Term] +id: GENO:0000036 +name: reference allele +def: "An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome." [] +comment: Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.\n\nIn model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared. +is_a: GENO:0000512 ! allele +intersection_of: GENO:0000512 ! allele +intersection_of: RO:0000087 GENO:0000152 ! has_role reference +relationship: RO:0000087 GENO:0000152 ! has_role reference + +[Term] +id: GENO:0000037 +name: obsolete_unspecified feature +def: "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus)." [] +comment: An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). +is_a: ObsoleteClass +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '." xsd:string +property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class def: 'genomic feature'\n and (has_sequence_attribute some unspecified)" xsd:string + +[Term] +id: GENO:0000042 +name: obsolete_reference junction +def: "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature." [] +comment: In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction.\n\nThe junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. +is_a: ObsoleteClass +property_value: IAO:0000118 "hemizygous reference junction" xsd:string +property_value: IAO:0000231 "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" xsd:string + +[Term] +id: GENO:0000047 +name: danio rerio gene +def: "A gene that originates from the genome of a danio rerio." [] +is_a: SO:0000704 ! gene +intersection_of: SO:0000704 ! gene +intersection_of: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio +relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio + +[Term] +id: GENO:0000054 +name: homo sapiens gene +def: "A gene that originates from the genome of a homo sapiens." [] +is_a: SO:0000704 ! gene +intersection_of: SO:0000704 ! gene +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens + +[Term] +id: GENO:0000057 +name: mus musculus gene +def: "A gene that originates from the genome of a mus musculus." [] +is_a: SO:0000704 ! gene +intersection_of: SO:0000704 ! gene +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus + +[Term] +id: GENO:0000060 +name: obsolete_reference gene allele +def: "A version/allele of a gene that serves as a standard against which variant genes are compared." [] +comment: Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. +is_a: ObsoleteClass +property_value: IAO:0000112 "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development.\nhttp://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690\n\nNote that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469" xsd:string +property_value: IAO:0000118 "reference gene" xsd:string +property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" xsd:string + +[Term] +id: GENO:0000091 +name: obsolete_experimental insertion +is_a: ObsoleteClass + +[Term] +id: GENO:0000092 +name: gene trap insertion +is_a: SO:0000667 ! insertion +relationship: RO:0002353 GENO:0000172 ! output of gene trapping technique + +[Term] +id: GENO:0000093 +name: integrated transgene +def: "A transgene that has been integrated into a chrromosome in the host genome." [] +comment: An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion.\n\nAn 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome. +is_a: SO:0000902 ! transgene +relationship: BFO:0000050 SO:0001218 ! is part of transgenic_insertion + +[Term] +id: GENO:0000106 +name: genomic material +def: "A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny." [] +comment: 1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms. +is_a: GENO:0000482 ! genetic material +relationship: BFO:0000050 GENO:0000108 ! is part of material genome +relationship: RO:0000091 GENO:0000139 ! has disposition heritable +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way." xsd:string + +[Term] +id: GENO:0000108 +name: material genome +def: "A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion." [] +comment: A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements.\n\nNote that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome. +is_a: BFO:0000040 ! material entity +property_value: IAO:0000118 "physical genome" xsd:string + +[Term] +id: GENO:0000111 +name: human population +def: "a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)" [] +is_a: OBI:0000181 ! population +property_value: IAO:0000116 "Consider http://semanticscience.org/resource/SIO_001062 ! human population (\"A human population refers to a collection of human beings\")." xsd:string +property_value: IAO:0000118 "homo sapiens population" xsd:string + +[Term] +id: GENO:0000112 +name: strain or breed +def: "A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical." [] +comment: Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR) +is_a: GENO:0000113 ! taxonomic group +relationship: RO:0002162 OBI:0100026 ! in taxon organism +property_value: IAO:0000118 "organism strain or breed" xsd:string + +[Term] +id: GENO:0000113 +name: taxonomic group +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000116 "A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon)" xsd:string + +[Term] +id: GENO:0000118 +name: mus musculus strain +is_a: GENO:0000112 ! strain or breed + +[Term] +id: GENO:0000119 +name: danio rerio strain +is_a: GENO:0000112 ! strain or breed +relationship: RO:0002351 NCBITaxon:7955 ! has member Danio rerio +relationship: RO:0002351 NCBITaxon:7955 ! has member Danio rerio + +[Term] +id: GENO:0000125 +name: obsolete_sequence feature collection attribute +def: "sequence attribute that can inhere only in a collection of more than one sequence features" [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000131 +name: in cis +def: "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes)." [] +is_a: GENO:0000886 ! allelic phase + +[Term] +id: GENO:0000132 +name: in trans +def: "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes)." [] +is_a: GENO:0000886 ! allelic phase + +[Term] +id: GENO:0000133 +name: zygosity +def: "An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different)." [] +xref: http://semanticscience.org/resource/SIO_001263 +is_a: GENO:0000875 ! allelic state +relationship: RO:0000052 GENO:0000516 ! inheres_in single locus complement +property_value: IAO:0000118 "allelic state" xsd:string +property_value: IAO:0000119 "derived from https://en.wikipedia.org/wiki/Zygosity" xsd:string + +[Term] +id: GENO:0000134 +name: hemizygous +is_a: GENO:0000391 ! disomic zygosity + +[Term] +id: GENO:0000135 +name: heterozygous +is_a: GENO:0000391 ! disomic zygosity + +[Term] +id: GENO:0000136 +name: homozygous +is_a: GENO:0000391 ! disomic zygosity + +[Term] +id: GENO:0000137 +name: unspecified zygosity +is_a: GENO:0000133 ! zygosity +property_value: IAO:0000118 "indeterminite zygosity" xsd:string {comment="MGI uses this term when zygosity is not known."} +property_value: IAO:0000118 "no-call zygosity" xsd:string {comment="(this is how the GVF10 format/standard refers to loci without enough data to make an accurate call . . . see http://www.sequenceontology.org/resources/gvf.html#quick_gvf_examples)"} +property_value: IAO:0000118 "unknown zygosity" xsd:string + +[Term] +id: GENO:0000138 +name: heritabililty +def: "The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event." [] +comment: We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells).\n\nWe can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms. +is_a: BFO:0000016 ! disposition + +[Term] +id: GENO:0000139 +name: heritable +is_a: GENO:0000138 ! heritabililty + +[Term] +id: GENO:0000140 +name: non-heritable +is_a: GENO:0000138 ! heritabililty + +[Term] +id: GENO:0000141 +name: inheritance pattern +def: "The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment." [] +comment: An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, "genetic context" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. \n\nThese genetic and environmental "interactions" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y. +xref: http://purl.obolibrary.org/obo/HP_0000005 +xref: http://purl.obolibrary.org/obo/NCIT_C45827 +is_a: BFO:0000016 ! disposition +property_value: IAO:0000116 "The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family." xsd:string +property_value: IAO:0000118 "mode of inheritance" xsd:string +property_value: IAO:0000118 "phenotypic inheritance pattern" xsd:string + +[Term] +id: GENO:0000142 +name: obsolete_dominant inheritance +def: "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes" [] +is_a: ObsoleteClass +property_value: IAO:0000231 "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." xsd:string + +[Term] +id: GENO:0000143 +name: co-dominant autosomal inheritance +def: "An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." [] +is_a: GENO:0000147 ! autosomal dominant inheritance + +[Term] +id: GENO:0000144 +name: complete autosomal dominant inheritance +def: "An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." [] +is_a: GENO:0000147 ! autosomal dominant inheritance +property_value: IAO:0000118 "pure dominant inheritance" xsd:string + +[Term] +id: GENO:0000145 +name: incomplete autosomal dominant inheritance +def: "An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." [] +is_a: GENO:0000147 ! autosomal dominant inheritance +property_value: IAO:0000118 "intermediate dominant autosomal inheritance" xsd:string +property_value: IAO:0000118 "semi-dominant autosomal inheritance" xsd:string + +[Term] +id: GENO:0000146 +name: X-linked dominant inheritance +def: "An X-linked inheritance pattern wherein the trait manifests in heterozygotes." [] +xref: http://purl.obolibrary.org/obo/HP_0001423 +is_a: GENO:0000936 ! X-linked inheritance + +[Term] +id: GENO:0000147 +name: autosomal dominant inheritance +def: "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes." [] +xref: http://purl.obolibrary.org/obo/HP_0000006 +is_a: GENO:0000934 ! autosomal inheritance +property_value: IAO:0000118 "vertical inheritance" xsd:string + +[Term] +id: GENO:0000148 +name: autosomal recessive inheritance +def: "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals." [] +is_a: GENO:0000934 ! autosomal inheritance + +[Term] +id: GENO:0000149 +name: X-linked recessive inheritance +def: "An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals." [] +xref: http://purl.obolibrary.org/obo/HP_0001419 +is_a: GENO:0000936 ! X-linked inheritance + +[Term] +id: GENO:0000150 +name: obsolete_autosomal recessive inheritance +is_a: ObsoleteClass +property_value: IAO:0000231 "duplicate term, use GENO:0000148" xsd:string + +[Term] +id: GENO:0000152 +name: reference +def: "An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared." [] +comment: Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another. +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000160 +name: unspecified life cycle stage +is_a: UBERON:0000105 ! life cycle stage + +[Term] +id: GENO:0000164 +name: genetic insertion technique +comment: objective is to insert some specified sequence into the genome of a cell or virus +is_a: OBI:0600043 ! genetic modification technique + +[Term] +id: GENO:0000165 +name: mutagen treatment technique +is_a: OBI:0600043 ! genetic modification technique + +[Term] +id: GENO:0000166 +name: targeted gene mutation technique +def: "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping)." [] +comment: This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. +is_a: OBI:0600043 ! genetic modification technique +relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele + +[Term] +id: GENO:0000169 +name: random genetic insertion technique +comment: Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. +is_a: GENO:0000164 ! genetic insertion technique + +[Term] +id: GENO:0000170 +name: targeted genetic insertion technique +is_a: GENO:0000164 ! genetic insertion technique +relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele + +[Term] +id: GENO:0000171 +name: enhancer trapping technique +is_a: GENO:0000170 ! targeted genetic insertion technique + +[Term] +id: GENO:0000172 +name: gene trapping technique +is_a: GENO:0000170 ! targeted genetic insertion technique + +[Term] +id: GENO:0000173 +name: promoter trapping technique +is_a: GENO:0000170 ! targeted genetic insertion technique + +[Term] +id: GENO:0000174 +name: targeted knock-in technique +is_a: GENO:0000170 ! targeted genetic insertion technique + +[Term] +id: GENO:0000175 +name: random transgene insertion technique +is_a: GENO:0000169 ! random genetic insertion technique + +[Term] +id: GENO:0000324 +name: obsolete_chromosome complement +def: "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome" [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000338 +name: gained aneusomic chromosome +def: "A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation" [] +comment: This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome. +is_a: GENO:0000346 ! aneusomic chromosome +relationship: GENO:0000207 GENO:0000685 ! has_sequence_attribute novel +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "duplicate chromosome" xsd:string + +[Term] +id: GENO:0000339 +name: lost aneusomic chromosome +def: "A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation." [] +is_a: GENO:0000346 ! aneusomic chromosome +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as \"the point at which one or more contiguous nucleotides were excised\"." xsd:string +property_value: IAO:0000118 "absent aneusomic chromosome" xsd:string + +[Term] +id: GENO:0000343 +name: aneusomic chromosomal part +def: "A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation." [] +comment: Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome." +is_a: SO:0000830 ! chromosome part +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000207 GENO:0000513 ! has_sequence_attribute aneusomic +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism." xsd:string +property_value: IAO:0000118 "aneuploid chromosomal segment" xsd:string +property_value: IAO:0000118 "aneusomic chromosomal subregion/segment" xsd:string +property_value: IAO:0000118 "partial aneusomic chromosomal element" xsd:string + +[Term] +id: GENO:0000344 +name: gained aneusomic chromosomal segment +def: "A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event." [] +comment: Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location. +is_a: GENO:0000343 ! aneusomic chromosomal part +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "duplicate partial aneuploid chromosomal element" xsd:string +property_value: IAO:0000118 "translocated duplicate chromosomal element" xsd:string +property_value: IAO:0000118 "translocated duplicate chromosomal segment" xsd:string + +[Term] +id: GENO:0000345 +name: lost aneusomic chromosomal segment +def: "A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome." [] +comment: This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome.\n\nLoss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus. +is_a: GENO:0000343 ! aneusomic chromosomal part +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement" xsd:string +property_value: IAO:0000118 "dropped partial anneuploid chromosomal element" xsd:string +property_value: IAO:0000118 "translocated absent chromosomal segment" xsd:string +property_value: IAO:0000118 "truncated chromosome terminus" xsd:string + +[Term] +id: GENO:0000346 +name: aneusomic chromosome +def: "A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation" [] +comment: Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism.\n\nSimilarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication. +is_a: SO:0000340 ! chromosome +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000207 GENO:0000513 ! has_sequence_attribute aneusomic +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "complete aneusomic chromosome" xsd:string + +[Term] +id: GENO:0000351 +name: biological process +is_a: BFO:0000015 ! process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of biological processes from GO-BP." xsd:string + +[Term] +id: GENO:0000391 +name: disomic zygosity +is_a: GENO:0000133 ! zygosity + +[Term] +id: GENO:0000392 +name: aneusomic zygosity +is_a: GENO:0000133 ! zygosity + +[Term] +id: GENO:0000393 +name: trisomic homozygous +is_a: GENO:0000392 ! aneusomic zygosity + +[Term] +id: GENO:0000394 +name: trisomic heterozygous +is_a: GENO:0000392 ! aneusomic zygosity + +[Term] +id: GENO:0000402 +name: compound heterozygous +def: "A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a/fgf8a)" [] +is_a: GENO:0000135 ! heterozygous +property_value: IAO:0000118 "trans-heterozygous" xsd:string + +[Term] +id: GENO:0000415 +name: obsolete_reagent sequence feature +def: "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)" [] +is_a: ObsoleteClass +property_value: IAO:0000116 "replaced with SO:engineered_region" xsd:string +property_value: IAO:0000118 "extra-genomic sequence" xsd:string + +[Term] +id: GENO:0000458 +name: simple heterozygous +comment: a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a) +is_a: GENO:0000135 ! heterozygous + +[Term] +id: GENO:0000460 +name: transgene part +def: "A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc)" [] +is_a: GENO:0000666 ! gene part +intersection_of: GENO:0000666 ! gene part +intersection_of: RO:0002525 SO:0000902 ! is subsequence of transgene +relationship: RO:0002525 SO:0000902 ! is subsequence of transgene + +[Term] +id: GENO:0000476 +name: variant +def: "An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level" [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000477 +name: polymorphic +def: "An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000480 +name: mutant +def: "An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000481 +name: genomic feature +def: "A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)" [] +comment: 1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. \n\n2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). \n\n3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome. +is_a: GENO:0000897 ! genomic entity +is_a: SO:0000110 ! sequence_feature +intersection_of: SO:0000110 ! sequence_feature +intersection_of: GENO:0000903 GENO:0000902 ! has_location genomic feature location +relationship: BFO:0000050 SO:0001026 ! is part of genome +relationship: GENO:0000239 GENO:0000960 ! has_sequence genomic sequence +relationship: GENO:0000903 GENO:0000902 ! has_location genomic feature location +property_value: IAO:0000116 "This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology." xsd:string + +[Term] +id: GENO:0000482 +name: genetic material +def: "A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion)." [] +comment: This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material. +is_a: CHEBI:33696 ! nucleic acid +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000491 +name: obsolete_mutant allele +def: "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain." [] +comment: 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. +is_a: ObsoleteClass +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000119 "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" xsd:string +property_value: IAO:0000231 "Not required for any specific use case at this point so removed for simplicity. \nFormely asserted as allele and inferred as varaint allele. \nEq class definition:\nallele\n and (mutation or ('has subsequence' some mutation))" xsd:string + +[Term] +id: GENO:0000492 +name: mutation +def: "A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain." [] +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000683 GENO:0000501 ! varies_with wild-type allele + +[Term] +id: GENO:0000494 +name: extrachromosomal replicon +def: "A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon)" [] +is_a: GENO:0000481 ! genomic feature +relationship: GENO:0000207 GENO:0000139 ! has_sequence_attribute heritable +property_value: IAO:0000116 "Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element" xsd:string +property_value: IAO:0000118 "episomal replicon" xsd:string +property_value: IAO:0000231 "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'." xsd:string + +[Term] +id: GENO:0000495 +name: expression construct +is_a: GENO:0000856 ! engineered genetic construct +property_value: IAO:0000118 "expression construct feature" xsd:string + +[Term] +id: GENO:0000497 +name: polymorphic allele +def: "An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population." [] +comment: Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%). +is_a: GENO:0000512 ! allele +property_value: IAO:0000119 "PMID: 25741868 ACMG Guidelines" xsd:string + +[Term] +id: GENO:0000498 +name: major polymorphic allele +def: "A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location." [] +is_a: GENO:0000497 ! polymorphic allele +property_value: IAO:0000118 "major allele" xsd:string + +[Term] +id: GENO:0000499 +name: minor polymorphic allele +def: "A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location)." [] +is_a: GENO:0000497 ! polymorphic allele +property_value: IAO:0000118 "minor allele" xsd:string + +[Term] +id: GENO:0000500 +name: ancestral polymorphic allele +def: "A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree." [] +is_a: GENO:0000497 ! polymorphic allele +property_value: IAO:0000118 "ancestral allele" xsd:string + +[Term] +id: GENO:0000501 +name: wild-type allele +def: "An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared." [] +comment: 'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain.\n\nThe notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis. +is_a: GENO:0000512 ! allele +property_value: IAO:0000118 "wild-type allele" xsd:string + +[Term] +id: GENO:0000502 +name: wild-type gene +comment: A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation. +is_a: GENO:0000501 ! wild-type allele +is_a: SO:0000704 ! gene +property_value: IAO:0000118 "wild-type gene allele" xsd:string + +[Term] +id: GENO:0000504 +name: reagent targeted gene +def: "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." [] +comment: The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position. +is_a: GENO:0000529 ! expression-variant gene +relationship: GENO:0000231 GENO:0000534 ! has_proper_part reagent-targeted gene subregion +relationship: GENO:0000447 GENO:0000533 ! is_gene_target_of gene knockdown reagent + +[Term] +id: GENO:0000506 +name: transiently-expressed transgene +def: "A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome)." [] +is_a: GENO:0000529 ! expression-variant gene +property_value: IAO:0000118 "experimentally-expressed transgene" xsd:string +property_value: IAO:0000118 "extrinsic transgene" xsd:string + +[Term] +id: GENO:0000511 +name: wild-type +def: "An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000512 +name: allele +def: "One of a set of sequence features known to exist at a particular genomic location." [] +comment: An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations).\n\nAlleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence). +is_a: GENO:0000481 ! genomic feature +intersection_of: GENO:0000481 ! genomic feature +intersection_of: GENO:0000683 GENO:0000481 ! varies_with genomic feature +relationship: GENO:0000683 GENO:0000481 ! varies_with genomic feature +property_value: IAO:0000116 "A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene.\n\nTo be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene.\n \n[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17)\n[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17)\n[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17)\n[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17)\n[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17)\n[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17)\n[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483\n[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17)\n[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17)\n[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17)\n[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17)\n[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)" xsd:string +property_value: IAO:0000118 "variable feature" xsd:string + +[Term] +id: GENO:0000513 +name: aneusomic +def: "a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation." [] +is_a: GENO:0000773 ! variation attribute +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000515 +name: variant gene allele +def: "An allele of a gene that contains some sequence alteration." [] +comment: A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset. +is_a: GENO:0000002 ! variant allele +is_a: GENO:0000014 ! gene allele +intersection_of: GENO:0000014 ! gene allele +intersection_of: GENO:0000683 GENO:0000036 ! varies_with reference allele +relationship: GENO:0000382 SO:0001059 ! has_variant_part sequence_alteration +relationship: GENO:0000641 SO:0000704 ! is_variant_allele_of gene + +[Term] +id: GENO:0000516 +name: single locus complement +def: "A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes.\n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. +is_a: GENO:0000660 ! genomic feature set +property_value: IAO:0000112 "The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a.\n\nThe collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome." xsd:string +property_value: IAO:0000116 "TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label." xsd:string +property_value: IAO:0000118 "allelic complement" xsd:string +property_value: IAO:0000118 "homologous allele complement" xsd:string +property_value: IAO:0000118 "single locus feature complement" xsd:string + +[Term] +id: GENO:0000524 +name: extrinsic genotype +def: "A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state." [] +comment: An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment.\n\nThe 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations. +is_a: GENO:0000536 ! genotype +property_value: IAO:0000112 "In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as:\n\n shha; shhb\n\nThis notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct." xsd:string +property_value: IAO:0000116 "We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. \n\nOur rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. \n\nFinally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" xsd:string +property_value: IAO:0000118 "experimental genotype" xsd:string +property_value: IAO:0000118 "expression genotype" xsd:string + +[Term] +id: GENO:0000525 +name: effective genotype +def: "A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs)." [] +comment: An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment. +is_a: GENO:0000536 ! genotype +relationship: BFO:0000051 GENO:0000524 ! has part extrinsic genotype +relationship: BFO:0000051 GENO:0000719 ! has part intrinsic genotype +property_value: IAO:0000116 "Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" xsd:string + +[Term] +id: GENO:0000527 +name: reagent-targeted gene complement +def: "A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes)." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment. +is_a: GENO:0000715 ! qualified genomic feature set +relationship: RO:0002351 GENO:0000504 ! has member reagent targeted gene + +[Term] +id: GENO:0000528 +name: transiently-expressed transgene complement +def: "The set of all transgenes trransiently expressed in a biological system in the context of a given experiment." [] +is_a: GENO:0000715 ! qualified genomic feature set +relationship: GENO:0000382 GENO:0000506 ! has_variant_part transiently-expressed transgene +property_value: IAO:0000118 "experimental transgene complement" xsd:string + +[Term] +id: GENO:0000529 +name: expression-variant gene +def: "A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism)." [] +comment: Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism).\n\nThe identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system. +is_a: GENO:0000737 ! expression-qualified sequence feature +relationship: GENO:0000443 SO:0000704 ! is_expression_variant_of gene +property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes)." xsd:string +property_value: IAO:0000116 "See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself." xsd:string +property_value: IAO:0000118 "expression allele" xsd:string + +[Term] +id: GENO:0000533 +name: gene knockdown reagent +is_a: SO:0000804 ! engineered_region +property_value: IAO:0000118 "gene targeting reagent" xsd:string +property_value: IAO:0000118 "sequence targeting reagent" xsd:string + +[Term] +id: GENO:0000534 +name: reagent-targeted gene subregion +def: "A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent." [] +is_a: GENO:0000737 ! expression-qualified sequence feature +property_value: IAO:0000118 "targeted gene segment" xsd:string + +[Term] +id: GENO:0000536 +name: genotype +def: "A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference." [] +comment: 1. Scope of 'Genetic State': \n'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs.\n\n2. Genotype Subtypes:\nIn GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. \n\nTwo more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features.\n\n3. The Genotype Partonomy: \n'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a; fgf3[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements:\n\n - GVC: fgf8a; fgf3 (total intrinsic variation in the genome)\n - Genomic Background: AB (the reference against which the GVC is variant)\n - VSLC1: fgf8a (homozygous complement of gene alleles at one known variant locus)\n - VSLC2: fgf3 (heterozygous complement of gene alleles at another known variant locus)\n - Allele 1: fgf8a (variant version of the fgf8a gene, present in two copies)\n - Allele 2: fgf3 (variant version of the fgf3 gene, present in one copy)\n - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy)\n - Sequence Alteration1: (the specific mutation within the fgf8a gene that makes it variant)\n - Sequence Alteration2: (the specific mutation within the fgf3 gene that makes it variant)\n\nA graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md\n\nOne reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data. +is_a: IAO:0000030 ! information content entity +property_value: IAO:0000116 "As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above." xsd:string +property_value: IAO:0000119 "Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). \nNote however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO." xsd:string + +[Term] +id: GENO:0000575 +name: zebrafish phenotype +comment: ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl\nThis ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes. +is_a: UPHENO:0001001 ! Phenotype + +[Term] +id: GENO:0000602 +name: homoplasmic +def: "an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism." [] +is_a: GENO:0000918 ! organellar plasmy + +[Term] +id: GENO:0000603 +name: heteroplasmic +def: "an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism." [] +is_a: GENO:0000918 ! organellar plasmy + +[Term] +id: GENO:0000604 +name: hemizygous X-linked +is_a: GENO:0000134 ! hemizygous + +[Term] +id: GENO:0000605 +name: hemizygous Y-linked +is_a: GENO:0000134 ! hemizygous + +[Term] +id: GENO:0000606 +name: hemizygous insertion-linked +is_a: GENO:0000134 ! hemizygous + +[Term] +id: GENO:0000611 +name: genomic background +def: "A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations)." [] +is_a: GENO:0000899 ! genomic genotype +intersection_of: GENO:0000899 ! genomic genotype +intersection_of: RO:0000087 GENO:0000152 ! has_role reference +relationship: IAO:0000219 GENO:0000010 ! denotes background genome +relationship: RO:0000087 GENO:0000152 ! has_role reference +property_value: IAO:0000116 "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it." xsd:string +property_value: IAO:0000118 "background genotype" xsd:string + +[Term] +id: GENO:0000614 +name: chromosomal region +def: "An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band." [] +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 SO:0000105 ! is part of chromosome arm +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000116 "New term request for SO." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string + +[Term] +id: GENO:0000616 +name: chromosome sub-band +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 SO:0000341 ! is part of chromosome band +relationship: GENO:0000207 GENO:0000618 ! has_sequence_attribute chromosomal band intensity +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string + +[Term] +id: GENO:0000618 +name: chromosomal band intensity +is_a: GENO:0000788 ! sequence feature attribute +property_value: IAO:0000118 "chromosomal band brightness" xsd:string + +[Term] +id: GENO:0000619 +name: gpos +is_a: GENO:0000618 ! chromosomal band intensity + +[Term] +id: GENO:0000620 +name: gneg +is_a: GENO:0000618 ! chromosomal band intensity + +[Term] +id: GENO:0000621 +name: gvar +is_a: GENO:0000618 ! chromosomal band intensity + +[Term] +id: GENO:0000622 +name: gpos100 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000623 +name: gpos75 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000624 +name: gpos50 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000625 +name: gpos25 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000628 +name: short chromosome arm +def: "A chromosome arm that is the shorter of the two arms of a given chromosome." [] +is_a: SO:0000105 ! chromosome arm +property_value: IAO:0000118 "p-arm" xsd:string +property_value: IAO:0000118 "stalk" xsd:string + +[Term] +id: GENO:0000629 +name: long chromosome arm +def: "A chromosome arm that is the longer of the two arms of a given chromosome." [] +is_a: SO:0000105 ! chromosome arm +property_value: IAO:0000118 "q-arm" xsd:string + +[Term] +id: GENO:0000632 +name: gpos66 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000633 +name: gpos33 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000637 +name: regulatory transgene region +def: "A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed." [] +is_a: GENO:0000460 ! transgene part +is_a: SO:0005836 ! regulatory_region + +[Term] +id: GENO:0000638 +name: expressed transgene region +def: "A transgene part whose sequence is expressed in a gene product through transcription and/or translation." [] +is_a: GENO:0000460 ! transgene part +property_value: IAO:0000118 "coding transgene feature" xsd:string + +[Term] +id: GENO:0000640 +name: reporter region +is_a: GENO:0000638 ! expressed transgene region + +[Term] +id: GENO:0000642 +name: selectable marker transgene +def: "A transgene whose product is used as a selectable marker." [] +is_a: SO:0000804 ! engineered_region +is_a: SO:0000902 ! transgene +intersection_of: SO:0000902 ! transgene +intersection_of: RO:0000087 GENO:0000911 ! has_role selectable marker role +relationship: RO:0000087 GENO:0000911 ! has_role selectable marker role + +[Term] +id: GENO:0000644 +name: karyotype +def: "A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell." [] +comment: Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). \n\nA base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation). +is_a: GENO:0000899 ! genomic genotype +property_value: IAO:0000119 "Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28)" xsd:string + +[Term] +id: GENO:0000645 +name: genomic genotype (sex-qualified) +def: "A genomic genotype where the genomic background specifies a male or female sex chromosome complement." [] +comment: We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances.\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. +is_a: GENO:0000899 ! genomic genotype +relationship: GENO:0000650 GENO:0000000 ! has_sex_agnostic_part genomic genotype (sex-agnostic) +property_value: IAO:0000116 "This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nIn the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former." xsd:string +property_value: IAO:0000118 "intrinsic genotype (sex-specific)" xsd:string +property_value: IAO:0000118 "sex-qualified genotype" xsd:string +property_value: IAO:0000118 "sex-qualified intrinsic genotype" xsd:string + +[Term] +id: GENO:0000646 +name: male intrinsic genotype +def: "A genomic genotype here the genomic background specifies a male sex chromosome complement." [] +is_a: GENO:0000645 ! genomic genotype (sex-qualified) + +[Term] +id: GENO:0000647 +name: female intrinsic genotype +def: "A genomic genotype here the genomic background specifies a female sex chromosome complement." [] +is_a: GENO:0000645 ! genomic genotype (sex-qualified) + +[Term] +id: GENO:0000649 +name: unspecified genomic background +def: "A background genotype whose sequence or identity is not known or specified." [] +is_a: GENO:0000611 ! genomic background +property_value: IAO:0000118 "unspecified background genotype" xsd:string + +[Term] +id: GENO:0000659 +name: sequence feature set +def: "A set of sequence features." [] +comment: 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature).\n\nThe notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles \{rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3].\n\n[1] https://www.snpedia.com/index.php/APOE-%CE%B54\n[2] https://www.snpedia.com/index.php/APOE-%CE%B52\n[3] https://www.snpedia.com/index.php/Gs270 +is_a: GENO:0000701 ! sequence feature or set +relationship: RO:0002351 SO:0000110 ! has member sequence_feature +property_value: IAO:0000112 "1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus\n\n2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele.\n\n3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y}" xsd:string + +[Term] +id: GENO:0000660 +name: genomic feature set +def: "A set of genomic features (i.e. sequence features that are of genomic origin)." [] +comment: A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature.\n\nThe notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. +is_a: GENO:0000659 ! sequence feature set +is_a: GENO:0000897 ! genomic entity +relationship: RO:0002351 GENO:0000481 ! has member genomic feature +property_value: IAO:0000116 "In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member." xsd:string +property_value: IAO:0000118 "genomic locus complement" xsd:string + +[Term] +id: GENO:0000666 +name: gene part +def: "A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc)." [] +xref: SO:0000831 (gene member region) +is_a: GENO:0000481 ! genomic feature +intersection_of: GENO:0000481 ! genomic feature +intersection_of: RO:0002525 GENO:0000014 ! is subsequence of gene allele +relationship: RO:0002525 GENO:0000014 ! is subsequence of gene allele +property_value: IAO:0000118 "defined gene part" xsd:string + +[Term] +id: GENO:0000667 +name: reporter transgene +def: "A transgene that codes for a product used as a reporter of gene expression or activity." [] +is_a: SO:0000804 ! engineered_region +is_a: SO:0000902 ! transgene +intersection_of: SO:0000902 ! transgene +intersection_of: RO:0000087 GENO:0000910 ! has_role reporter role +relationship: BFO:0000051 GENO:0000640 ! has part reporter region +relationship: RO:0000087 GENO:0000910 ! has_role reporter role + +[Term] +id: GENO:0000680 +name: obsolete_null feature +def: "A genomic feature that has an extent of zero." [] +is_a: ObsoleteClass +property_value: IAO:0000112 "A junction between bases, a deletion variant, a terminus at the end of a chromosome." xsd:string +property_value: IAO:0000116 "Former logical def: \n'genomic feature'\n and (has_extent value 0)" xsd:string + +[Term] +id: GENO:0000681 +name: novel extrachromosomal replicon +def: "An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found." [] +comment: Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. +is_a: GENO:0000494 ! extrachromosomal replicon +is_a: GENO:0000684 ! novel replicon +property_value: IAO:0000118 "aberrant extrachromosomal replicon" xsd:string +property_value: IAO:0000118 "exogenous extrachromosomal replicon" xsd:string +property_value: IAO:0000118 "transgenic extrachromosomal replicon" xsd:string + +[Term] +id: GENO:0000684 +name: novel replicon +def: "A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome." [] +comment: Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles. +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000207 GENO:0000685 ! has_sequence_attribute novel +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature." xsd:string + +[Term] +id: GENO:0000685 +name: novel +def: "An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000688 +name: terminus +def: "A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide)." [] +is_a: SO:0000110 ! sequence_feature + +[Term] +id: GENO:0000701 +name: sequence feature or set +def: "A sequence feature or a set of such features." [] +comment: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location. +is_a: BFO:0000031 ! generically dependent continuant +union_of: GENO:0000701 ! sequence feature or set +union_of: SO:0000110 ! sequence_feature +property_value: IAO:0000118 "sequence feature or collection" xsd:string + +[Term] +id: GENO:0000702 +name: biological sequence +def: "A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides)." [] +comment: 'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome. +xref: VMC:State +is_a: GENO:0000921 ! biological sequence or set +disjoint_from: GENO:0000815 ! sequence feature location +disjoint_from: SO:0000110 ! sequence_feature +property_value: IAO:0000116 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." xsd:string +property_value: IAO:0000118 "biomacromolecular sequence" xsd:string +property_value: IAO:0000118 "state" xsd:string {http://purl.obolibrary.org/obo/IAO_0000116="In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele."} + +[Term] +id: GENO:0000713 +name: qualified sequence feature or collection +def: "A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification." [] +is_a: BFO:0000031 ! generically dependent continuant + +[Term] +id: GENO:0000714 +name: qualified genomic feature +def: "A qualified sequence feature that carries sequence derived from the genome of a cell or organism." [] +is_a: GENO:0000897 ! genomic entity +is_a: GENO:0000919 ! qualified sequence feature +relationship: GENO:0000726 GENO:0000481 {http://purl.obolibrary.org/obo/GENO_0000834="true", comment="Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position)."} ! has_sequence_feature genomic feature +property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." xsd:string + +[Term] +id: GENO:0000715 +name: qualified genomic feature set +def: "A set of qualified sequence features that carry genomic sequence." [] +comment: A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles \{rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele.\n\nA complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome. +is_a: GENO:0000897 ! genomic entity +is_a: GENO:0000920 ! qualified sequence feature set +relationship: GENO:0000726 GENO:0000660 ! has_sequence_feature genomic feature set +relationship: RO:0002351 GENO:0000714 ! has member qualified genomic feature +property_value: IAO:0000116 "Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member." xsd:string + +[Term] +id: GENO:0000719 +name: intrinsic genotype +def: "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype." [] +comment: 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. +is_a: GENO:0000536 ! genotype +property_value: IAO:0000116 "Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome." xsd:string + +[Term] +id: GENO:0000720 +name: DNA sequence +is_a: GENO:0000702 ! biological sequence +intersection_of: GENO:0000702 ! biological sequence +intersection_of: GENO:0000783 GENO:0000780 ! has_sequence_unit DNA residue +intersection_of: GENO:0000783 GENO:0000780 {all_only="true"} ! has_sequence_unit DNA residue +relationship: GENO:0000783 GENO:0000780 ! has_sequence_unit DNA residue + +[Term] +id: GENO:0000721 +name: RNA sequence +is_a: GENO:0000702 ! biological sequence +intersection_of: GENO:0000702 ! biological sequence +intersection_of: GENO:0000783 GENO:0000781 ! has_sequence_unit RNA residue +intersection_of: GENO:0000783 GENO:0000781 {all_only="true"} ! has_sequence_unit RNA residue +relationship: GENO:0000783 GENO:0000781 ! has_sequence_unit RNA residue + +[Term] +id: GENO:0000722 +name: amino acid sequence +is_a: GENO:0000702 ! biological sequence +intersection_of: GENO:0000702 ! biological sequence +intersection_of: GENO:0000783 GENO:0000782 ! has_sequence_unit amino acid residue +intersection_of: GENO:0000783 GENO:0000782 {all_only="true"} ! has_sequence_unit amino acid residue +relationship: GENO:0000783 GENO:0000782 ! has_sequence_unit amino acid residue + +[Term] +id: GENO:0000724 +name: obsolete_biological sequence or collection +is_a: ObsoleteClass + +[Term] +id: GENO:0000725 +name: obsolete_biological sequence collection +is_a: GENO:0000724 ! obsolete_biological sequence or collection + +[Term] +id: GENO:0000736 +name: location-qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature." [] +comment: As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell). +is_a: GENO:0000714 ! qualified genomic feature +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000737 +name: expression-qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct)" [] +is_a: GENO:0000714 ! qualified genomic feature + +[Term] +id: GENO:0000768 +name: obsolete_genomic position +def: "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence." [] +is_a: ObsoleteClass +property_value: IAO:0000116 "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature." xsd:string +property_value: IAO:0000118 "genomic coordinates" xsd:string +property_value: IAO:0000231 "remodeling notion of sequence feature position around the idea of a 'genomic locus'" xsd:string + +[Term] +id: GENO:0000770 +name: phenotypic inheritance process +is_a: GENO:0000351 ! biological process + +[Term] +id: GENO:0000772 +name: obsolete_unspecified +def: "A sequence attribute inhering in a feature whose identity is not specified." [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000773 +name: variation attribute +def: "An attribute describing a type of variation inhering in a sequence feature or collection." [] +is_a: GENO:0000788 ! sequence feature attribute +property_value: IAO:0000118 "allele attribute" xsd:string + +[Term] +id: GENO:0000777 +name: variant genomic genotype +def: "An intrinsic genotype that specifies variation from a defined reference genome." [] +is_a: GENO:0000899 ! genomic genotype +intersection_of: GENO:0000899 ! genomic genotype +intersection_of: IAO:0000219 GENO:0000033 ! denotes variant genome +relationship: IAO:0000219 GENO:0000033 ! denotes variant genome + +[Term] +id: GENO:0000778 +name: obsolete_sequence information entity +def: "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities." [] +is_a: ObsoleteClass +property_value: IAO:0000231 "eliminating classes that are not necessary or add uneeded complexity." xsd:string + +[Term] +id: GENO:0000779 +name: biological sequence unit +is_a: GENO:0000702 ! biological sequence +property_value: IAO:0000118 "biological sequence residue" xsd:string +property_value: IAO:0000118 "monomeric residue" xsd:string + +[Term] +id: GENO:0000780 +name: DNA residue +is_a: GENO:0000779 ! biological sequence unit +property_value: IAO:0000118 "deoxyribonucleic acid residue" xsd:string + +[Term] +id: GENO:0000781 +name: RNA residue +is_a: GENO:0000779 ! biological sequence unit +property_value: IAO:0000118 "ribonucleic acid residue" xsd:string + +[Term] +id: GENO:0000782 +name: amino acid residue +is_a: GENO:0000779 ! biological sequence unit + +[Term] +id: GENO:0000788 +name: sequence feature attribute +def: "An attribute, quality, or state of a sequence feature or collection." [] +comment: Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity. +xref: http://purl.obolibrary.org/obo/SO_0000400 +is_a: BFO:0000020 ! specifically dependent continuant + +[Term] +id: GENO:0000815 +name: sequence feature location +def: "The location of a sequence feature as defined by its start and end position on some reference coordinate system." [] +comment: 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms).\n\n2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there. +is_a: BFO:0000031 ! generically dependent continuant +disjoint_from: SO:0000110 ! sequence_feature + +[Term] +id: GENO:0000818 +name: modification-qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature)" [] +is_a: GENO:0000714 ! qualified genomic feature +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000823 +name: allelic genotype +def: "A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes." [] +comment: An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location.\n\nThis contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background. +is_a: GENO:0000719 ! intrinsic genotype +is_a: GENO:0000897 ! genomic entity +intersection_of: GENO:0000719 ! intrinsic genotype +intersection_of: IAO:0000219 GENO:0000516 ! denotes single locus complement +relationship: IAO:0000219 GENO:0000516 ! denotes single locus complement +property_value: IAO:0000112 "1. The zebrafish \"fgf8a/fgf8a<+>\" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state).\n\n2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308.\n\n ##fileformat=VCFv4.2\n ##FORMAT=\n #CHROM POS REF ALT FILTER FORMAT SAMP001\n 20 2300608 C T PASS GT 0/1 \n 20 2301308 T G PASS GT 1/1\n (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html)\n\n3. Some allelic genotype formats encode the genotype as a single string - e.g. \"GRCh38 Chr12:258635(A;T)\" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12." xsd:string +property_value: IAO:0000118 "single locus genotype" xsd:string + +[Term] +id: GENO:0000833 +name: genotype-phenotype association +is_a: http://purl.org/oban/association ! association +relationship: GENO:0000580 ENVO:01000254 {http://purl.obolibrary.org/obo/GENO_0000834="true"} ! has_qualifier environmental system +relationship: http://purl.org/oban/association_has_object UPHENO:0001001 {http://purl.obolibrary.org/obo/GENO_0000834="true"} ! Phenotype +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each." xsd:string + +[Term] +id: GENO:0000839 +name: knockdown reagent targeted gene complement +is_a: GENO:0000527 ! reagent-targeted gene complement +relationship: GENO:0000382 GENO:0000504 ! has_variant_part reagent targeted gene + +[Term] +id: GENO:0000848 +name: obsolete_coding sequence alteration +def: "A sequence alteration within the coding sequence of a gene." [] +is_a: ObsoleteClass +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000231 "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." xsd:string + +[Term] +id: GENO:0000850 +name: P-element construct +def: "A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: GENO:0000856 +name: engineered genetic construct +def: "An engineered region that is used to transfer foreign genetic material into a host cell." [] +comment: Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. \n\nConstructs are typically packaged as part of delivery systems such as plasmids or viral vectors. +is_a: SO:0000804 ! engineered_region +property_value: IAO:0000118 "engineered_genetic_vector" xsd:string + +[Term] +id: GENO:0000861 +name: extra-chromosomal transgene +def: "A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct." [] +is_a: SO:0000902 ! transgene +property_value: IAO:0000118 "non-integrated transgene" xsd:string + +[Term] +id: GENO:0000870 +name: obsolete_sequence feature collection +def: "A collection of more than one sequence feature." [] +xref: http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection +is_a: ObsoleteClass + +[Term] +id: GENO:0000871 +name: haplotype +def: "A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block." [] +comment: A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. \n\nAs highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\n1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \n\n2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). "Star alleles" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/).\n\n3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. \n\nEach of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. +is_a: GENO:0000660 ! genomic feature set +relationship: RO:0002351 GENO:0000512 ! has member allele +property_value: http://purl.org/dc/terms/source "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype." xsd:string +property_value: IAO:0000116 "Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block.\n\nInstead, we can create an 'allele set' class as the haplotype parent?" xsd:string + +[Term] +id: GENO:0000872 +name: genomic sequence set +def: "A set of genomic sequences (a biological sequence that is of genomic origin)." [] +comment: A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. +is_a: GENO:0000922 ! biological sequence set +property_value: IAO:0000118 "copy number complement" xsd:string + +[Term] +id: GENO:0000873 +name: microsatellite alteration +def: "A relation used to describe an environment contextualizing the identity of an entity." [] +is_a: GENO:0000874 ! repeat region alteration + +[Term] +id: GENO:0000874 +name: repeat region alteration +def: "A relation used to describe a process contextualizing the identity of an entity." [] +is_a: SO:0001059 ! sequence_alteration + +[Term] +id: GENO:0000875 +name: allelic state +def: "A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism" [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: GENO:0000876 +name: obsolete_genetic dosage +comment: Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. +is_a: ObsoleteClass +property_value: IAO:0000118 "allelic dosage" xsd:string +property_value: IAO:0000118 "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome." xsd:string +property_value: IAO:0000118 "gene dosage" xsd:string +property_value: IAO:0000231 "Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute." xsd:string + +[Term] +id: GENO:0000877 +name: allele origin +def: "A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent." [] +is_a: GENO:0000788 ! sequence feature attribute +property_value: IAO:0000118 "genetic origin" xsd:string +property_value: IAO:0000118 "variant origin" xsd:string + +[Term] +id: GENO:0000878 +name: maternal allele origin +def: "Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg." [] +is_a: GENO:0000888 ! germline allele origin +property_value: IAO:0000118 "maternally inherited" xsd:string + +[Term] +id: GENO:0000879 +name: paternal allele origin +def: "Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm." [] +is_a: GENO:0000888 ! germline allele origin +property_value: IAO:0000118 "paternally inherited" xsd:string + +[Term] +id: GENO:0000880 +name: de novo allele origin +def: "Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis." [] +comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. \n \nDe novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder. +is_a: GENO:0000877 ! allele origin +property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string + +[Term] +id: GENO:0000881 +name: unknown allele origin +def: "Describes an allele whose origin is not known." [] +is_a: GENO:0000877 ! allele origin + +[Term] +id: GENO:0000882 +name: somatic allele origin +def: "Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body." [] +comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells.\n \nThese acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations. +is_a: GENO:0000877 ! allele origin +property_value: IAO:0000118 "acquired" xsd:string +property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string + +[Term] +id: GENO:0000883 +name: obsolete_gametic +def: "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells)." [] +is_a: ObsoleteClass +property_value: IAO:0000118 "germ-line" xsd:string +property_value: IAO:0000231 "replaced by GENO:0000900 ! 'germline'" xsd:string + +[Term] +id: GENO:0000885 +name: diplotype +def: "An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement')\n\nAlt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome." [] +comment: "Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes."\nFrom https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/ +is_a: GENO:0000823 ! allelic genotype + +[Term] +id: GENO:0000886 +name: allelic phase +def: "A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes." [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: GENO:0000887 +name: oryzias latipes strain +is_a: GENO:0000112 ! strain or breed +relationship: RO:0002351 NCBITaxon:8090 ! has member Oryzias latipes +relationship: RO:0002351 NCBITaxon:8090 ! has member Oryzias latipes + +[Term] +id: GENO:0000888 +name: germline allele origin +def: "Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg)." [] +comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells. +is_a: GENO:0000877 ! allele origin +property_value: IAO:0000118 "hereditary" xsd:string +property_value: IAO:0000118 "parental origin" xsd:string +property_value: IAO:0000118 "parentally inherited" xsd:string +property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string + +[Term] +id: GENO:0000889 +name: undetermined inheritance +def: "An inheritance pattern that is not determined or not known." [] +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000118 "unknown inheritance" xsd:string + +[Term] +id: GENO:0000890 +name: obsolete_canonical allele +def: "One of a set of sequence features or haplotypes that exist at a particular genetic locus. " [] +comment: As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand.\n\nIn the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) +is_a: ObsoleteClass +property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string +property_value: IAO:0000112 "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." xsd:string +property_value: IAO:0000116 "The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string +property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/ xsd:string +property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs." xsd:string + +[Term] +id: GENO:0000891 +name: obsolete_contextual allele +def: "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence." [] +comment: The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. +is_a: ObsoleteClass +property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string +property_value: IAO:0000116 "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string +property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ xsd:string +property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.\n\nFormer axiom: denotes some 'obsolete_canonical allele'" xsd:string + +[Term] +id: GENO:0000892 +name: heteroplasmic mitochondrial inheritance +def: "A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not." [] +is_a: GENO:0000949 ! mitochondrial inheritance + +[Term] +id: GENO:0000893 +name: homoplasmic mitochondrial inheritance +def: "A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited." [] +is_a: GENO:0000949 ! mitochondrial inheritance + +[Term] +id: GENO:0000897 +name: genomic entity +def: "An generically dependent continuant that carries biological sequence that is part of or derived from a genome." [] +is_a: BFO:0000031 ! generically dependent continuant +relationship: RO:0002162 OBI:0100026 ! in taxon organism +property_value: GENO:0000905 "true" xsd:boolean +property_value: IAO:0000116 "An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities." xsd:string + +[Term] +id: GENO:0000898 +name: haplotype block +def: "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations." [] +comment: A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000116 "Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as \n\"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.\" Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location.\n\nCurrent definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele." xsd:string +property_value: IAO:0000119 "Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424." xsd:string + +[Term] +id: GENO:0000899 +name: genomic genotype +def: "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype." [] +comment: 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. +is_a: GENO:0000719 ! intrinsic genotype +is_a: GENO:0000897 ! genomic entity +intersection_of: GENO:0000719 ! intrinsic genotype +intersection_of: IAO:0000219 SO:0001026 ! denotes genome +relationship: GENO:0000385 GENO:0000611 ! has_reference_part genomic background +relationship: IAO:0000219 SO:0001026 ! denotes genome +property_value: IAO:0000116 "'Genomic Genotype' vs 'Genome' in GENO: \nA genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome." xsd:string +property_value: IAO:0000118 "complete genotype" xsd:string + +[Term] +id: GENO:0000901 +name: obsolete_allele cellular context +def: "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)" [] +comment: Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. +is_a: ObsoleteClass +property_value: IAO:0000231 "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin" xsd:string + +[Term] +id: GENO:0000902 +name: genomic feature location +def: "The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system" [] +comment: 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. \n \n2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus.\n\n3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there. +xref: VMC:Location +is_a: GENO:0000815 ! sequence feature location +property_value: IAO:0000116 "In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future.\n\nWe don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences." xsd:string +property_value: IAO:0000116 "In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed.\n\nFor example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus)." xsd:string +property_value: IAO:0000118 "genomic location" xsd:string +property_value: IAO:0000118 "genomic locus" xsd:string + +[Term] +id: GENO:0000904 +name: organismal entity +def: "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc)." [] +is_a: BFO:0000040 ! material entity +property_value: GENO:0000905 "true" xsd:boolean +property_value: IAO:0000116 "useful organizational term to collect entities that have genomes/genotypes." xsd:string + +[Term] +id: GENO:0000907 +name: gene product +def: "The molecular product resulting from transcription of a single gene (either a protein or RNA molecule)" [] +is_a: SO:0000110 ! sequence_feature + +[Term] +id: GENO:0000910 +name: reporter role +is_a: OBI:0000086 ! reagent role + +[Term] +id: GENO:0000911 +name: selectable marker role +is_a: OBI:0000086 ! reagent role + +[Term] +id: GENO:0000912 +name: selectable marker region +is_a: GENO:0000638 ! expressed transgene region + +[Term] +id: GENO:0000914 +name: reference genome +def: "A genome whose sequence is identical to that of a genome sequence considered to be the reference." [] +is_a: SO:0001026 ! genome +relationship: GENO:0000239 SO:0001505 ! has_sequence reference genome sequence + +[Term] +id: GENO:0000915 +name: obsolete_haplotype +def: "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it." [] +comment: 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. +is_a: ObsoleteClass +property_value: IAO:0000116 "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"" xsd:string +property_value: IAO:0000119 "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype." xsd:string +property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" xsd:string + +[Term] +id: GENO:0000916 +name: obsolete_haplotype block +def: "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations." [] +comment: A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.\n\nThe boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.\n\n-----------------------\n\n* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. +is_a: ObsoleteClass +property_value: IAO:0000119 "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." xsd:string +property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets." xsd:string + +[Term] +id: GENO:0000918 +name: organellar plasmy +def: "An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell." [] +comment: Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene. +is_a: GENO:0000875 ! allelic state + +[Term] +id: GENO:0000919 +name: qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification." [] +comment: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). +comment: Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes. +is_a: GENO:0000713 ! qualified sequence feature or collection +property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." xsd:string + +[Term] +id: GENO:0000920 +name: qualified sequence feature set +def: "A set of qualified seqeunce features." [] +comment: 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'. +is_a: GENO:0000713 ! qualified sequence feature or collection +relationship: BFO:0000051 GENO:0000919 ! has part qualified sequence feature +relationship: GENO:0000726 GENO:0000659 ! has_sequence_feature sequence feature set + +[Term] +id: GENO:0000921 +name: biological sequence or set +def: "A biolocical sequence, or set of such sequences." [] +is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000118 "biological sequence or collection" xsd:string + +[Term] +id: GENO:0000922 +name: biological sequence set +def: "A set of biological sequences." [] +comment: 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. \n\nA set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence. +is_a: GENO:0000921 ! biological sequence or set + +[Term] +id: GENO:0000923 +name: obsolete_functional copy number complement +def: "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome." [] +comment: As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). +comment: The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. +is_a: ObsoleteClass +property_value: IAO:0000116 "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"" xsd:string +property_value: IAO:0000118 "functional feature complement" xsd:string +property_value: IAO:0000118 "genetic dosage" xsd:string +property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." xsd:string + +[Term] +id: GENO:0000924 +name: obsolete_intrinsic sequence feature attribute +def: "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form." [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000925 +name: obsolete_extrinsic sequence feature attribute +def: "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)" [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000926 +name: allelic cellular distribution +def: "A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism)." [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: GENO:0000927 +name: constitutional +def: "A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin." [] +is_a: GENO:0000926 ! allelic cellular distribution + +[Term] +id: GENO:0000928 +name: clonal +def: "A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin." [] +is_a: GENO:0000926 ! allelic cellular distribution + +[Term] +id: GENO:0000929 +name: multifactorial inheritance +def: "An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors." [] +comment: Diseases inherited in this manner are termed 'complex diseases'. +xref: http://purl.obolibrary.org/obo/HP_0001426 +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000118 "complex inherritance" xsd:string +property_value: IAO:0000118 "multi-factorial inheritance" xsd:string +property_value: IAO:0000118 "multi-genic inheritance" xsd:string +property_value: IAO:0000118 "multi-locus inheritance" xsd:string +property_value: IAO:0000118 "multigenic inheritance" xsd:string + +[Term] +id: GENO:0000930 +name: digenic inheritance +def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes." [] +xref: http://purl.obolibrary.org/obo/HP_0010984 +is_a: GENO:0000929 ! multifactorial inheritance + +[Term] +id: GENO:0000931 +name: oligogenic inheritance +def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes." [] +comment: It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform. +xref: http://purl.obolibrary.org/obo/HP_0010983 +is_a: GENO:0000929 ! multifactorial inheritance + +[Term] +id: GENO:0000932 +name: polygenic inheritance +def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes." [] +comment: Typically used for traits/conditions governed by more than three gene loci. +xref: http://purl.obolibrary.org/obo/HP_0010982 +is_a: GENO:0000929 ! multifactorial inheritance + +[Term] +id: GENO:0000933 +name: monogenic inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors." [] +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000118 "single-gene inheritance" xsd:string + +[Term] +id: GENO:0000934 +name: autosomal inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome." [] +is_a: GENO:0000933 ! monogenic inheritance + +[Term] +id: GENO:0000935 +name: allosomal inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome." [] +xref: http://purl.obolibrary.org/obo/HP_0010985 +is_a: GENO:0000933 ! monogenic inheritance +property_value: IAO:0000118 "gonosomal inheritance" xsd:string + +[Term] +id: GENO:0000936 +name: X-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome." [] +xref: http://purl.obolibrary.org/obo/HP_0001417 +is_a: GENO:0000935 ! allosomal inheritance + +[Term] +id: GENO:0000937 +name: complete X-linked dominant inheritance +def: "An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." [] +is_a: GENO:0000146 ! X-linked dominant inheritance + +[Term] +id: GENO:0000938 +name: incomplete X-linked dominant inheritance +def: "An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." [] +is_a: GENO:0000146 ! X-linked dominant inheritance +property_value: IAO:0000118 "semi-dominant X-linked inheritance" xsd:string + +[Term] +id: GENO:0000939 +name: co-dominant X-linked inheritance +def: "An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." [] +is_a: GENO:0000146 ! X-linked dominant inheritance + +[Term] +id: GENO:0000941 +name: Y-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome." [] +xref: http://purl.obolibrary.org/obo/HP_0001450 +is_a: GENO:0000935 ! allosomal inheritance +property_value: IAO:0000118 "holandric inheritance" xsd:string + +[Term] +id: GENO:0000942 +name: Z-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome." [] +is_a: GENO:0000935 ! allosomal inheritance + +[Term] +id: GENO:0000943 +name: Z-linked dominant inheritance +def: "A Z-linked inheritance pattern wherein the trait manifests in heterozygotes." [] +is_a: GENO:0000942 ! Z-linked inheritance + +[Term] +id: GENO:0000944 +name: complete Z-linked dominant inheritance +def: "A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." [] +is_a: GENO:0000943 ! Z-linked dominant inheritance + +[Term] +id: GENO:0000945 +name: incomplete Z-linked dominant inheritance +def: "A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." [] +is_a: GENO:0000943 ! Z-linked dominant inheritance +property_value: IAO:0000118 "semi-dominant Z-linked inheritance" xsd:string + +[Term] +id: GENO:0000946 +name: co-dominant Z-linked inheritance +def: "An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." [] +is_a: GENO:0000943 ! Z-linked dominant inheritance + +[Term] +id: GENO:0000947 +name: Z-linked reccessive inheritance +def: "A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals." [] +is_a: GENO:0000942 ! Z-linked inheritance + +[Term] +id: GENO:0000948 +name: W-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome." [] +is_a: GENO:0000935 ! allosomal inheritance + +[Term] +id: GENO:0000949 +name: mitochondrial inheritance +def: "An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome." [] +comment: Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy). +xref: http://purl.obolibrary.org/obo/HP_0001427 +is_a: GENO:0000141 ! inheritance pattern + +[Term] +id: GENO:0000952 +name: sex-limited autosomal dominant inheritance +def: "An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females)." [] +xref: http://purl.obolibrary.org/obo/HP_0001470 +is_a: GENO:0000147 ! autosomal dominant inheritance + +[Term] +id: GENO:0000953 +name: sex-limited autosomal recessive inheritance +def: "An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females)." [] +xref: http://purl.obolibrary.org/obo/HP_0031362 +is_a: GENO:0000148 ! autosomal recessive inheritance + +[Term] +id: GENO:0000954 +name: allele set +def: "A set of discrete alleles within a particular genome." [] +comment: 'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An "Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'. +is_a: GENO:0000660 ! genomic feature set + +[Term] +id: GENO:0000955 +name: obsolete_variant copy number complement +def: "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s)." [] +comment: In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. +is_a: GENO:0000956 ! obsolete_copy number complement +property_value: IAO:0000118 "copy number variation" xsd:string +property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level." xsd:string + +[Term] +id: GENO:0000956 +name: obsolete_copy number complement +def: "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger." [] +comment: 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. +is_a: ObsoleteClass +property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." xsd:string + +[Term] +id: GENO:0000960 +name: genomic sequence +def: "A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)." [] +comment: A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. +is_a: GENO:0000702 ! biological sequence +relationship: GENO:0000251 GENO:0000481 ! is_sequence_of genomic feature + +[Term] +id: GENO:0000961 +name: copy number complement +def: "A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome." [] +comment: The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result.\n\nA 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. \n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. +comment: The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence. +is_a: GENO:0000872 ! genomic sequence set +property_value: IAO:0000116 "The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome.\n\nWe represent the notion of copy number at the \"sequence level\" (as opposed to the \"sequence feature level\") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The \"sequence level\" representation here supports this use case. By contrast, a \"feature level\" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity)." xsd:string + +[Term] +id: GENO:0000962 +name: variant copy number complement +def: "A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s)." [] +comment: 'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome. +is_a: GENO:0000961 ! copy number complement +property_value: IAO:0000116 "Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a \"sequence feature level\" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred).\n\nFor example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains." xsd:string + +[Term] +id: GENO:0000963 +name: functional copy complement +def: "A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence.\n\n'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nAs we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele. +is_a: GENO:0000872 ! genomic sequence set +property_value: IAO:0000118 "functional genetic dosage" xsd:string + +[Term] +id: GENO:0000964 +name: mosaic +comment: A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type. +is_a: GENO:0000928 ! clonal + +[Term] +id: GENO:0000965 +name: sequence interval +def: "A pair of integers representing start and end position of a location on a sequence coordinate system." [] +is_a: IAO:0000030 ! information content entity + +[Term] +id: GO:0003674 +name: molecular function +is_a: BFO:0000034 ! function + +[Term] +id: GO:0032502 +name: developmental process +def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete]" [] +is_a: GENO:0000351 ! biological process + +[Term] +id: HP:0000118 +name: human phenotypic abnormality +comment: pulling in HP 'phenotypic abnormality' root here +is_a: UPHENO:0001001 ! Phenotype + +[Term] +id: HsapDv:0000000 +name: human life cycle stage +is_a: GENO:0000351 ! biological process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology." xsd:string +property_value: IAO:0000119 "A spatiotemporal region encompassing some part of the life cycle of an organism." xsd:string + +[Term] +id: IAO:0000027 +name: data item +is_a: IAO:0000030 ! information content entity + +[Term] +id: IAO:0000030 +name: information content entity +def: "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity" [] +is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000111 "information content entity" xsd:string +property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000119 "OBI_0000142" xsd:string + +[Term] +id: IAO:0000078 +name: curation status specification +def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string +property_value: IAO:0000118 "ontology metadata" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: IAO:8000000 +name: ontology module +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000116 "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000118 "ontology file" xsd:string +property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:03Z + +[Term] +id: IAO:8000001 +name: base ontology module +def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 +created_by: cjm +creation_date: 2018-05-20T20:55:30Z + +[Term] +id: IAO:8000002 +name: editors ontology module +def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "source ontology module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:47Z + +[Term] +id: IAO:8000003 +name: main release ontology module +def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:56:13Z + +[Term] +id: IAO:8000004 +name: bridge ontology module +def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies +created_by: cjm +creation_date: 2018-05-20T20:56:23Z + +[Term] +id: IAO:8000005 +name: import ontology module +def: "A subset ontology module that is intended to be imported from another ontology." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000118 "import file" xsd:string +property_value: seeAlso http://robot.obolibrary.org/extract +created_by: cjm +creation_date: 2018-05-20T20:56:47Z + +[Term] +id: IAO:8000006 +name: subset ontology module +def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "ontology slim" xsd:string +property_value: IAO:0000118 "subset ontology" xsd:string +property_value: seeAlso http://robot.obolibrary.org/filter +property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide +created_by: cjm +creation_date: 2018-05-20T20:58:11Z + +[Term] +id: IAO:8000007 +name: curation subset ontology module +def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:38Z + +[Term] +id: IAO:8000008 +name: analysis subset ontology module +def: "An ontology module that is intended for usage in analysis or discovery applications." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:49Z + +[Term] +id: IAO:8000009 +name: single layer subset ontology module +def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "ribbon subset" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:19Z + +[Term] +id: IAO:8000010 +name: exclusion subset ontology module +def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "antislim" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:57Z + +[Term] +id: IAO:8000011 +name: external import ontology module +def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] +is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000118 "external import" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:00:14Z + +[Term] +id: IAO:8000012 +name: species subset ontology module +def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "taxon subset" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +created_by: cjm +creation_date: 2018-05-20T21:14:16Z + +[Term] +id: IAO:8000013 +name: reasoned ontology module +def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso http://robot.obolibrary.org/reason +created_by: cjm +creation_date: 2018-05-20T21:20:33Z + +[Term] +id: IAO:8000014 +name: generated ontology module +def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:21:12Z + +[Term] +id: IAO:8000015 +name: template generated ontology module +def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] +is_a: IAO:8000014 ! generated ontology module +property_value: seeAlso http://robot.obolibrary.org/template +property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 +property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ +created_by: cjm +creation_date: 2018-05-20T21:21:21Z + +[Term] +id: IAO:8000016 +name: taxonomic bridge ontology module +is_a: IAO:8000004 ! bridge ontology module +created_by: cjm +creation_date: 2018-05-20T21:28:15Z + +[Term] +id: IAO:8000017 +name: ontology module subsetted by expressivity +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-22T04:15:54Z + +[Term] +id: IAO:8000018 +name: obo basic subset ontology module +def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: seeAlso "6.2" +created_by: cjm +creation_date: 2018-05-22T04:16:10Z + +[Term] +id: IAO:8000019 +name: ontology module subsetted by OWL profile +is_a: IAO:8000017 ! ontology module subsetted by expressivity +created_by: cjm +creation_date: 2018-05-22T04:16:28Z + +[Term] +id: IAO:8000020 +name: EL++ ontology module +is_a: IAO:8000019 ! ontology module subsetted by OWL profile +created_by: cjm +creation_date: 2018-05-22T04:16:48Z + +[Term] +id: MP:0000001 +name: mammalian phenotype +comment: where to place this depends on if we take the organismal view or the quality centric view. +is_a: UPHENO:0001001 ! Phenotype + +[Term] +id: NCBITaxon:10090 +name: Mus musculus +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:10239 +name: Viruses +comment: Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies. +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:7955 +name: Danio rerio +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:8090 +name: Oryzias latipes +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:9606 +name: Homo sapiens +is_a: OBI:0100026 ! organism + +[Term] +id: OBI:0000011 +name: planned process +def: "A processual entity that realizes a plan which is the concretization of a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO." xsd:string + +[Term] +id: OBI:0000086 +name: reagent role +is_a: BFO:0000023 ! role + +[Term] +id: OBI:0000181 +name: population +def: "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area" [] +is_a: GENO:0000113 ! taxonomic group + +[Term] +id: OBI:0000435 +name: genotyping assay +def: "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions." [] +is_a: ERO:0000007 ! technique + +[Term] +id: OBI:0001148 +name: targeted gene knock-out technique +def: "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods." [] +comment: A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. +is_a: GENO:0000166 ! targeted gene mutation technique + +[Term] +id: OBI:0001149 +name: targeted gene knock-in technique +is_a: GENO:0000166 ! targeted gene mutation technique + +[Term] +id: OBI:0100026 +name: organism +is_a: GENO:0000904 ! organismal entity +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy." xsd:string + +[Term] +id: OBI:0600043 +name: genetic modification technique +def: "the introduction. alteration or integration of genetic material into a cell or organism" [] +is_a: ERO:0000007 ! technique + +[Term] +id: PATO:0000016 +name: obsolete_color brightness +is_a: ObsoleteClass +property_value: IAO:0000116 "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html" xsd:string +property_value: IAO:0000116 "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." xsd:string +property_value: IAO:0000118 "color value" xsd:string + +[Term] +id: PATO:0000383 +name: female +is_a: PATO:0001894 ! phenotypic sex + +[Term] +id: PATO:0000384 +name: male +is_a: PATO:0001894 ! phenotypic sex + +[Term] +id: PATO:0001894 +name: phenotypic sex +is_a: BFO:0000019 ! quality + +[Term] +id: PCO:0000000 +name: collection of organisms +def: "A material entity that consists of two or more organisms, viruses, or viroids." [] +comment: A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role). +is_a: GENO:0000904 ! organismal entity +relationship: RO:0002351 OBI:0100026 ! has member organism + +[Term] +id: PCO:0000020 +name: family +def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] +is_a: PCO:0000000 ! collection of organisms + +[Term] +id: Position +name: Position +def: "Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate." [] +is_a: GENO:0000902 ! genomic feature location +property_value: IAO:0000116 "We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region)." xsd:string +property_value: IAO:0000412 "FALDO" xsd:string + +[Term] +id: Region +name: Region +def: "A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene." [] +is_a: SO:0000110 ! sequence_feature +relationship: begin Position {cardinality="1"} ! Position +relationship: end Position {cardinality="1"} ! Position +property_value: IAO:0000116 "From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence." xsd:string + +[Term] +id: ReverseStrandPosition +name: Negative strand +is_a: StrandedPosition ! Stranded position + +[Term] +id: SO:0000034 +name: morpholino_oligo +def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [] +is_a: GENO:0000533 ! gene knockdown reagent + +[Term] +id: SO:0000105 +name: chromosome arm +def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [] +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 SO:0000830 ! is part of chromosome part +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000116 "Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string + +[Term] +id: SO:0000110 +name: sequence_feature +def: "Any extent of continuous biological sequence." [] +comment: A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome. +is_a: GENO:0000701 ! sequence feature or set +relationship: GENO:0000239 GENO:0000702 {http://purl.obolibrary.org/obo/GENO_0000834="true", comment="Formalizes the first identity criteria for a sequence feature of its sequence."} ! has_sequence biological sequence +relationship: GENO:0000903 GENO:0000815 {http://purl.obolibrary.org/obo/GENO_0000834="true", comment="Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property)."} ! has_location sequence feature location +property_value: IAO:0000116 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." xsd:string + +[Term] +id: SO:0000143 +name: obsolete_assembly_component +def: "A region of known length which may be used to manufacture a longer region." [] +is_a: SO:0001410 ! obsolete_experimental_feature + +[Term] +id: SO:0000149 +name: obsolete_contig +def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [] +is_a: SO:0000143 ! obsolete_assembly_component + +[Term] +id: SO:0000159 +name: deletion +def: "The point at which one or more contiguous nucleotides were excised." [] +xref: http://en.wikipedia.org/wiki/Nucleotide_deletion +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000033 xsd:string +property_value: IAO:0000118 "deleted_sequence" xsd:string +property_value: IAO:0000118 "nucleotide deletion" xsd:string +property_value: IAO:0000118 "nucleotide_deletion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0000165 +name: enhancer +is_a: SO:0005836 ! regulatory_region + +[Term] +id: SO:0000167 +name: promoter +def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [] +is_a: SO:0005836 ! regulatory_region + +[Term] +id: SO:0000199 +name: translocation +def: "A region of nucleotide sequence that has translocated to a new position." [] +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000118 "transchr" xsd:string +property_value: IAO:0000118 "translocated sequence" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0000207 +name: simple_sequence_length_variation +is_a: SO:0000248 ! sequence_length_variation +property_value: IAO:0000118 "simple sequence length polymorphism" xsd:string +property_value: IAO:0000118 "simple sequence length variation" xsd:string +property_value: IAO:0000118 "SSLP" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0000248 +name: sequence_length_variation +is_a: SO:1000002 ! substitution +property_value: IAO:0000118 "sequence length variation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0000281 +name: engineered_foreign_gene +is_a: SO:0000704 ! gene +is_a: SO:0000804 ! engineered_region +property_value: IAO:0000116 "See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25.\n\nIncludes things like loxP sites, inducible promoters, ires elements, etc." xsd:string + +[Term] +id: SO:0000289 +name: microsatellite +def: "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [] +comment: A defined feature that includes any type of VNTR or SSLP locus. +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000119 http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29 xsd:string + +[Term] +id: SO:0000337 +name: RNAi_reagent +is_a: GENO:0000533 ! gene knockdown reagent + +[Term] +id: SO:0000340 +name: chromosome +def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [] +comment: A complete chromosome sequence. +is_a: GENO:0000481 ! genomic feature + +[Term] +id: SO:0000341 +name: chromosome band +def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [] +comment: "Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 GENO:0000614 ! is part of chromosomal region +relationship: GENO:0000207 GENO:0000618 ! has_sequence_attribute chromosomal band intensity +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band\n" xsd:string + +[Term] +id: SO:0000577 +name: centromere +is_a: SO:0000830 ! chromosome part + +[Term] +id: SO:0000637 +name: obsolete_engineered_plasmid +is_a: ObsoleteClass +property_value: IAO:0000116 "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." xsd:string + +[Term] +id: SO:0000667 +name: insertion +def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [] +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000034 xsd:string +property_value: IAO:0000118 "insertion" xsd:string +property_value: IAO:0000118 "nucleotide insertion" xsd:string +property_value: IAO:0000118 "nucleotide_insertion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0000694 +name: SNP +def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [] +is_a: SO:0001483 ! SNV +property_value: IAO:0000118 "single nucleotide polymorphism" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0000699 +name: junction +comment: A junction is a boundary between regions. A boundary has an extent of zero. +is_a: SO:0000110 ! sequence_feature + +[Term] +id: SO:0000704 +name: gene +def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [] +comment: A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion. +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000116 "Regarding the distinction between a 'gene' and a 'gene allele': \nEvery zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment)." xsd:string + +[Term] +id: SO:0000771 +name: QTL +def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [] +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000118 "quantitative trait locus" xsd:string + +[Term] +id: SO:0000783 +name: engineered +def: "An attribute to describe a region that was modified in vitro." [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: SO:0000804 +name: engineered_region +is_a: SO:0000110 ! sequence_feature +intersection_of: SO:0000110 ! sequence_feature +intersection_of: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered +relationship: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered +property_value: IAO:0000118 "construct" xsd:string + +[Term] +id: SO:0000830 +name: chromosome part +def: "An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'." [] +is_a: GENO:0000481 ! genomic feature +intersection_of: GENO:0000481 ! genomic feature +intersection_of: GENO:0000248 SO:0000340 ! is_proper_part_of chromosome +relationship: GENO:0000248 SO:0000340 ! is_proper_part_of chromosome +property_value: IAO:0000118 "chromosomal feature" xsd:string +property_value: IAO:0000118 "gross chromosomal part" xsd:string + +[Term] +id: SO:0000902 +name: transgene +def: "A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome)." [] +comment: On the relationship between 'transgenic insertions', 'transgenes', and 'alleles'\nTransgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete.\n\nIn addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. \n\nFor the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach. +comment: Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism).\n\nNote that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome. +is_a: SO:0000704 ! gene + +[Term] +id: SO:0001013 +name: MNP +def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [] +is_a: SO:1000002 ! substitution +property_value: IAO:0000118 "multiple nucleotide polymorphism" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001019 +name: copy_number_variation +def: "A variation that increases or decreases the copy number of a given region." [] +xref: http://en.wikipedia.org/wiki/Copy_number_variation +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000118 "CNP" xsd:string +property_value: IAO:0000118 "CNV" xsd:string +property_value: IAO:0000118 "copy number polymorphism" xsd:string +property_value: IAO:0000118 "copy number variation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0001026 +name: genome +def: "A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny)" [] +comment: A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'. +is_a: GENO:0000660 ! genomic feature set +property_value: IAO:0000116 "Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence." xsd:string +property_value: IAO:0000118 "'genome sequence'" xsd:string + +[Term] +id: SO:0001059 +name: sequence_alteration +def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [] +comment: 1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. \n\nAlleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part.\n\n2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. \n\nFor a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference.\n\n3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism. +is_a: GENO:0000512 ! allele +intersection_of: GENO:0000512 ! allele +intersection_of: GENO:0000784 GENO:0000481 ! completely_varies_with genomic feature +relationship: GENO:0000784 GENO:0000481 ! completely_varies_with genomic feature +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000004 xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000007 xsd:string +property_value: IAO:0000112 "A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': \n\n1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871.\n\n2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112.\n\n3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112." xsd:string +property_value: IAO:0000118 "sequence variation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0001218 +name: transgenic_insertion +def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [] +is_a: SO:0000667 ! insertion +relationship: BFO:0000051 GENO:0000093 ! has part integrated transgene +property_value: IAO:0000118 "transgenic insertion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001410 +name: obsolete_experimental_feature +def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [] +is_a: ObsoleteClass +property_value: IAO:0000231 "not currently needed to support modeling use cases. can re-introduce if becomes necessary." xsd:string + +[Term] +id: SO:0001477 +name: gene_trap_construct +def: "A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: SO:0001478 +name: promoter_trap_construct +def: "A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: SO:0001479 +name: enhancer_trap_construct +def: "A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: SO:0001483 +name: SNV +def: "SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist." [] +is_a: SO:1000002 ! substitution +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Thu Oct 08 11:37:49 PDT 2009" xsd:string +property_value: IAO:0000118 "single nucleotide variant" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0001500 +name: heritable_phenotypic_marker +def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [] +is_a: GENO:0000481 ! genomic feature + +[Term] +id: SO:0001505 +name: reference genome sequence +def: "A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced." [] +is_a: GENO:0000017 ! reference sequence +property_value: IAO:0000112 "'GRCh37.p10' (a human reference genome build)" xsd:string + +[Term] +id: SO:0001742 +name: copy_number_gain +def: "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [] +is_a: SO:0001019 ! copy_number_variation +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 01:54:09 PST 2011" xsd:string +property_value: IAO:0000118 "copy number gain" xsd:string +property_value: IAO:0000118 "gain" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001743 +name: copy_number_loss +def: "A sequence alteration whereby the copy number of a given region is less than the reference sequence." [] +is_a: SO:0001019 ! copy_number_variation +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 01:55:02 PST 2011" xsd:string +property_value: IAO:0000118 "copy number loss" xsd:string +property_value: IAO:0000118 "loss" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001744 +name: UPD +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [] +xref: http:http\\\://en.wikipedia.org/wiki/Uniparental_disomy +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:01:05 PST 2011" xsd:string +property_value: IAO:0000118 "uniparental disomy" xsd:string +property_value: IAO:0000118 "UPD" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001745 +name: maternal_uniparental_disomy +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [] +is_a: SO:0001744 ! UPD +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:03:01 PST 2011" xsd:string +property_value: IAO:0000118 "maternal uniparental disomy" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001746 +name: paternal_uniparental_disomy +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [] +is_a: SO:0001744 ! UPD +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:03:30 PST 2011" xsd:string +property_value: IAO:0000118 "paternal uniparental disomy" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001784 +name: complex_structural_alteration +def: "A structural sequence alteration where there are multiple equally plausible explanations for the change." [] +is_a: SO:0001785 ! structural_alteration +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Wed Mar 23 03:21:19 PDT 2011" xsd:string +property_value: IAO:0000118 "complex" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001785 +name: structural_alteration +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 25 02:27:41 PDT 2011" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0005836 +name: regulatory_region +is_a: GENO:0000666 ! gene part +property_value: IAO:0000116 "Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term." xsd:string +property_value: IAO:0000118 "regulatory element" xsd:string +property_value: IAO:0000118 "regulatory gene region" xsd:string + +[Term] +id: SO:1000002 +name: substitution +def: "Any change in genomic DNA caused by a single event." [] +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000005 +name: complex_substitution +def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\\"complex\\\" should be used. Usually there are multiple equally plausible explanations for the change." [] +is_a: SO:1000002 ! substitution +property_value: IAO:0000118 "complex substitution" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000008 +name: point_mutation +def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [] +xref: http://en.wikipedia.org/wiki/Point_mutation +is_a: SO:0001483 ! SNV +property_value: IAO:0000118 "point mutation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000009 +name: transition +def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [] +is_a: SO:0001483 ! SNV +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000010 +name: pyrimidine_transition +def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [] +is_a: SO:1000009 ! transition +property_value: IAO:0000118 "pyrimidine transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000011 +name: C_to_T_transition +def: "A transition of a cytidine to a thymine." [] +is_a: SO:1000010 ! pyrimidine_transition +property_value: IAO:0000118 "C to T transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000012 +name: C_to_T_transition_at_pCpG_site +def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [] +is_a: SO:1000011 ! C_to_T_transition +property_value: IAO:0000118 "C to T transition at pCpG site" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000013 +name: T_to_C_transition +is_a: SO:1000010 ! pyrimidine_transition +property_value: IAO:0000118 "T to C transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000014 +name: purine_transition +def: "A substitution of a purine, A or G, for another purine." [] +is_a: SO:1000009 ! transition +property_value: IAO:0000118 "purine transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000015 +name: A_to_G_transition +def: "A transition of an adenine to a guanine." [] +is_a: SO:1000014 ! purine_transition +property_value: IAO:0000118 "A to G transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000016 +name: G_to_A_transition +def: "A transition of a guanine to an adenine." [] +is_a: SO:1000014 ! purine_transition +property_value: IAO:0000118 "G to A transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000017 +name: transversion +def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [] +xref: http://en.wikipedia.org/wiki/Transversion +is_a: SO:0001483 ! SNV +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000018 +name: pyrimidine_to_purine_transversion +def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [] +is_a: SO:1000017 ! transversion +property_value: IAO:0000118 "pyrimidine to purine transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000019 +name: C_to_A_transversion +def: "A transversion from cytidine to adenine." [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "C to A transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000020 +name: C_to_G_transversion +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "C to G transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000021 +name: T_to_A_transversion +def: "A transversion from T to A." [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "T to A transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000022 +name: T_to_G_transversion +def: "A transversion from T to G." [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "T to G transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000023 +name: purine_to_pyrimidine_transversion +def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [] +is_a: SO:1000017 ! transversion +property_value: IAO:0000118 "purine to pyrimidine transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000024 +name: A_to_C_transversion +def: "A transversion from adenine to cytidine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "A to C transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000025 +name: A_to_T_transversion +def: "A transversion from adenine to thymine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "A to T transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000026 +name: G_to_C_transversion +def: "A transversion from guanine to cytidine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "G to C transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000027 +name: G_to_T_transversion +def: "A transversion from guanine to thymine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "G to T transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000032 +name: indel +def: "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [] +comment: Indels can have a different number of bases than the corresponding reference sequence. +xref: http://en.wikipedia.org/wiki/Indel +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000035 +name: duplication +def: "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point." [] +is_a: SO:0000667 ! insertion +property_value: IAO:0000118 "nucleotide duplication" xsd:string +property_value: IAO:0000118 "nucleotide_duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000036 +name: inversion +def: "A continuous nucleotide sequence is inverted in the same position." [] +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000118 "inversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000039 +name: direct_tandem_duplication +def: "A tandem duplication where the individual regions are in the same orientation." [] +is_a: SO:1000173 ! tandem_duplication +property_value: IAO:0000118 "direct tandem duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000040 +name: inverted_tandem_duplication +def: "A tandem duplication where the individual regions are not in the same orientation." [] +is_a: SO:1000173 ! tandem_duplication +property_value: IAO:0000118 "inverted tandem duplication" xsd:string +property_value: IAO:0000118 "mirror duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000173 +name: tandem_duplication +def: "A duplication consisting of 2 identical adjacent regions." [] +is_a: SO:1000035 ! duplication +property_value: IAO:0000118 "erverted" xsd:string +property_value: IAO:0000118 "tandem duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: StrandedPosition +name: Stranded position +comment: Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'. +is_a: Position ! Position + +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Synonym +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: SynonymType +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: UBERON:0000105 +name: life cycle stage +is_a: GENO:0000351 ! biological process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms)" xsd:string + +[Term] +id: UBERON:0001062 +name: anatomical entity +xref: http://purl.obolibrary.org/obo/CARO_0000000 +is_a: GENO:0000904 ! organismal entity +relationship: RO:0001000 OBI:0100026 ! derives from organism +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies." xsd:string + +[Term] +id: UPHENO:0001001 +name: Phenotype +comment: 1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition)\n\n2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000116 "Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework." xsd:string + +[Term] +id: WBPhenotype:0000886 +name: worm phenotype +def: "Animals exhibit variations compared to a given control." [] +is_a: UPHENO:0001001 ! Phenotype +property_value: IAO:0000116 "'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes." xsd:string +property_value: IAO:0000118 "c. elegans phenotype" xsd:string +property_value: IAO:0000118 "Variant" xsd:string + +[Term] +id: ZP:0000199 +name: abnormal(ly) malformed endocardium cell +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0000386 +name: abnormal(ly) absent dorso-rostral cluster +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0000755 +name: abnormal(ly) disrupted diencephalon development +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0005531 +name: abnormal(ly) disrupted neutrophil aggregation +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0005692 +name: abnormal(ly) absent adaxial cell +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: http://purl.org/oban/association +name: association +is_a: IAO:0000030 ! information content entity + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/20423 +name: mus musculus shh gene +comment: Equivalent to: http://www.informatics.jax.org/marker/MGI:98297 +is_a: GENO:0000057 ! mus musculus gene +property_value: IAO:0000114 GENO:0000514 + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/30269 +name: danio rerio shha gene +xref: http://zfin.org/ZDB-GENE-980526-166 +is_a: GENO:0000047 ! danio rerio gene +property_value: IAO:0000114 GENO:0000514 + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/399483 +name: danio rerio cdkn1ca gene +xref: http://zfin.org/ZDB-GENE-040123-1 +is_a: GENO:0000047 ! danio rerio gene +property_value: IAO:0000114 GENO:0000514 + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/6469 +name: homo sapiens SHH gene +comment: Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690\n\nCodes for: http://www.uniprot.org/uniprot/Q15465 +is_a: GENO:0000054 ! homo sapiens gene +property_value: IAO:0000114 GENO:0000514 + +[Typedef] +id: BFO:0000050 +name: is part of +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: GENO:0000207 +name: has_sequence_attribute +def: "A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'." [] +xref: http://purl.obolibrary.org/obo/so_has_quality +property_value: IAO:0000116 "Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants." xsd:string + +[Typedef] +id: GENO:0000211 +name: bears_concretization_of +def: "A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes" [] +comment: Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence. +property_value: IAO:0000118 "materializes" xsd:string +holds_over_chain: RO:0000053 RO:0000059 + +[Typedef] +id: GENO:0000220 +name: is_genotype_of +inverse_of: GENO:0000222 ! has_genotype + +[Typedef] +id: GENO:0000222 +name: has_genotype +def: "A relationship that holds between a biological entity and some level of genetic variation present in its genome." [] +comment: The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations. +property_value: IAO:0000116 "This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype." xsd:string + +[Typedef] +id: GENO:0000231 +name: has_proper_part +def: "An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO)" [] +xref: http://semanticscience.org/resource/SIO_000053 +property_value: IAO:0000116 "No proper part relation anymore in RO/BFO?" xsd:string +is_transitive: true +is_a: BFO:0000051 ! has part +inverse_of: GENO:0000248 ! is_proper_part_of + +[Typedef] +id: GENO:0000239 +name: has_sequence +def: "A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears." [] +comment: 'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule. +xref: VMC:state +property_value: IAO:0000118 "has_sequence_component" xsd:string +property_value: IAO:0000118 "has_state" xsd:string +range: GENO:0000702 ! biological sequence +inverse_of: GENO:0000251 ! is_sequence_of + +[Typedef] +id: GENO:0000242 +name: obsolete_specifies +def: "A relationship between an information content entity representing a specification, and the entity it specifies." [] +property_value: IAO:0000112 "A geno:intrinnsic genotype 'specifies' a SO:genome.\nA geno:karyotype 'specifies' a geno:karyotype feature collection." xsd:string +is_a: ObsoleteProperty +inverse_of: GENO:0000253 ! obsolete_is_specified_by + +[Typedef] +id: GENO:0000243 +name: obsolete_approximates_sequence +property_value: IAO:0000116 "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000244 +name: obsolete_resolves_to_sequence +property_value: IAO:0000116 "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000248 +name: is_proper_part_of +def: "An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole." [] +xref: http://semanticscience.org/resource/SIO_000093 +is_a: BFO:0000050 ! is part of + +[Typedef] +id: GENO:0000251 +name: is_sequence_of +domain: GENO:0000702 ! biological sequence + +[Typedef] +id: GENO:0000252 +name: is_subject_of +inverse_of: IAO:0000136 ! is about + +[Typedef] +id: GENO:0000253 +name: obsolete_is_specified_by +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000359 +name: obsolete_is_phenotype_of_genotype +def: "shortcut relation used to link a phenotype directly to a genotype of an organism" [] +comment: Might expand to something like:\n\nphenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype))))))) +property_value: IAO:0000118 "is_phenotype_of_organism_with_genotype" xsd:string +property_value: IAO:0000118 "is_phenotype_with_genotype" xsd:string +property_value: IAO:0000118 "phenotype_has_genotype" xsd:string +domain: UPHENO:0001001 ! Phenotype +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000368 +name: obsolete_participates_in_inheritance_process +def: "A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next." [] +property_value: IAO:0000116 "Exploratory/temporary property, as we formalize our phenotypic inheritance model." xsd:string +range: GENO:0000141 ! inheritance pattern +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000382 +name: has_variant_part +def: "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression." [] +is_transitive: true +is_a: GENO:0000654 ! has_sequence_part +inverse_of: GENO:0000383 ! is_variant_part_of + +[Typedef] +id: GENO:0000383 +name: is_variant_part_of +is_transitive: true +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000385 +name: has_reference_part +def: "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant." [] +property_value: IAO:0000118 "has_reference_sequence_part" xsd:string +is_transitive: true +is_a: GENO:0000654 ! has_sequence_part +inverse_of: GENO:0000387 ! is_reference_part_of + +[Typedef] +id: GENO:0000387 +name: is_reference_part_of +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000408 +name: is_allele_of +def: "A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size." [] +comment: To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size).\n\nWhile conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like "fgf8a is an allele of the Danio rerio fgf8a gene", and we may create data where fgf8a is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene).\n\nIt is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. \n\nThis departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\\GAL4 gene.\n\nAt the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'. +property_value: IAO:0000112 " is_allele_of the 'danio rerio fgf8a' gene locus." xsd:string +property_value: IAO:0000116 "Domain = allele \nRange = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation)." xsd:string +property_value: IAO:0000116 "Note that the allele is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product." xsd:string +property_value: IAO:0000118 "is_sequence_variant_of" xsd:string +domain: GENO:0000481 ! genomic feature +is_a: GENO:0000418 ! has_affected_feature +inverse_of: GENO:0000413 ! has_allele + +[Typedef] +id: GENO:0000410 +name: obsolete_is_genetic_variant_of +def: "A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level)." [] +comment: Domain = genomic feature instance\nRange = punned gene class IRI +property_value: IAO:0000118 "is_variant_instance_of" xsd:string +property_value: IAO:0000231 "formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus)" xsd:string +is_a: ObsoleteProperty +inverse_of: GENO:0000411 ! obsolete_has_genetic_variant + +[Typedef] +id: GENO:0000411 +name: obsolete_has_genetic_variant +def: "A relation linking a gene class to a sequence-varaint or expression-variant of the gene." [] +comment: Domain = punned gene class\nRange = genomic feature +property_value: IAO:0000118 "has_variant_instance" xsd:string +property_value: IAO:0000231 "formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by)" xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000413 +name: has_allele +def: "A relation linking a gene class to one of its sequence-variant alleles." [] +property_value: IAO:0000116 "Domain = punned gene class\nRange = allele" xsd:string +property_value: IAO:0000118 "has_sequence_variant" xsd:string +is_a: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000414 +name: targets_gene +def: "A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets." [] +comment: This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets. +is_a: GENO:0000418 ! has_affected_feature +inverse_of: GENO:0000447 ! is_gene_target_of + +[Typedef] +id: GENO:0000418 +name: has_affected_feature +def: "A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression." [] +comment: This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset. +holds_over_chain: GENO:0000382 GENO:0000418 +holds_over_chain: GENO:0000383 GENO:0000418 +inverse_of: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000443 +name: is_expression_variant_of +def: "A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents." [] +comment: This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class. +property_value: IAO:0000116 "Domain = expression variant feature.\nRange = punned gene class" xsd:string +is_a: GENO:0000418 ! has_affected_feature +inverse_of: GENO:0000449 ! has_expression_variant + +[Typedef] +id: GENO:0000445 +name: is_feature_affected_by +def: "A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature." [] +comment: This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases) +property_value: IAO:0000118 "class_to_feature_relation" xsd:string + +[Typedef] +id: GENO:0000447 +name: is_gene_target_of +def: "A relation between a gene class and a gene targeting reagent that targets it." [] +comment: Domain = punned gene class\nRange = gene knockdown reagent +property_value: IAO:0000118 "is_target_of" xsd:string +is_a: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000449 +name: has_expression_variant +def: "A relation linking a gene class to one of an expression-variant of that gene.." [] +property_value: IAO:0000116 "Domain = punned gene class\nRange = expression variant feature" xsd:string +property_value: IAO:0000118 "has_expression_variant_instance" xsd:string +is_a: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000486 +name: obsolete_is_variant_with +def: "A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression." [] +comment: This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of. +property_value: IAO:0000231 "Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property." xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000488 +name: obsolete_is_expression_variant_with +def: "A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways)." [] +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000580 +name: has_qualifier +def: "A relation used to describe a context or conditions that define and/or identify an entity." [] +property_value: IAO:0000116 "Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association.\n\nUsed in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features." xsd:string +property_value: IAO:0000118 "has_qualifying_context" xsd:string + +[Typedef] +id: GENO:0000608 +name: has_zygosity +def: "a relation to link a single locus complement to its zygosity." [] +domain: GENO:0000516 ! single locus complement +range: GENO:0000133 ! zygosity +is_a: GENO:0000207 ! has_sequence_attribute + +[Typedef] +id: GENO:0000610 +name: is_reference_allele_of +def: "A relationship between a reference locus/allele and the gene class it is an allele of." [] +domain: GENO:0000036 ! reference allele +is_a: GENO:0000408 ! is_allele_of + +[Typedef] +id: GENO:0000626 +name: has_staining_intensity +comment: Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized. +property_value: IAO:0000116 "Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed." xsd:string +property_value: IAO:0000118 "has_color_value" xsd:string +is_a: GENO:0000207 ! has_sequence_attribute + +[Typedef] +id: GENO:0000634 +name: is_targeted_by +def: "relation between an molecular agent and its molecular target" [] +property_value: IAO:0000112 "Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant." xsd:string + +[Typedef] +id: GENO:0000639 +name: sequence_derives_from +def: "Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence." [] +property_value: IAO:0000112 "1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. \n\n2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds.\n\n3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC)" xsd:string +holds_over_chain: BFO:0000051 GENO:0000639 + +[Typedef] +id: GENO:0000641 +name: is_variant_allele_of +def: "A relationship between a variant allele and the gene class it is an allele of." [] +domain: GENO:0000002 ! variant allele +is_a: GENO:0000408 ! is_allele_of + +[Typedef] +id: GENO:0000650 +name: has_sex_agnostic_part +property_value: IAO:0000116 "Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases." xsd:string +is_a: GENO:0000654 ! has_sequence_part +inverse_of: GENO:0000661 ! is_sex_agnostic_part_of + +[Typedef] +id: GENO:0000651 +name: is_mutant_allele_of +comment: A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of. +domain: GENO:0000491 ! obsolete_mutant allele +is_a: GENO:0000641 ! is_variant_allele_of + +[Typedef] +id: GENO:0000652 +name: is_polymorphic_allele_of +def: "A relationship between a polymorphic allele and the gene class it is an allele of." [] +domain: GENO:0000497 ! polymorphic allele +is_a: GENO:0000641 ! is_variant_allele_of + +[Typedef] +id: GENO:0000653 +name: is_wild_type_allele_of +def: "A relationship between a wild-type allele and the gene class it is an allele of." [] +domain: GENO:0000501 ! wild-type allele +is_a: GENO:0000408 ! is_allele_of + +[Typedef] +id: GENO:0000654 +name: has_sequence_part +def: "An organizational class to hold relations of parthood between sequences/features." [] +is_a: BFO:0000051 ! has part +inverse_of: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000655 +name: is_sequence_part_of +is_a: BFO:0000050 ! is part of + +[Typedef] +id: GENO:0000661 +name: is_sex_agnostic_part_of +def: "Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases." [] +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000683 +name: varies_with +def: "A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part)." [] +comment: This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of) +is_symmetric: true + +[Typedef] +id: GENO:0000708 +name: faldo properties +comment: organizational property to hold imports from faldo. + +[Typedef] +id: GENO:0000726 +name: has_sequence_feature +def: "A relation linking a qualified sequence feature to its component sequence feature." [] +comment: In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism. +property_value: IAO:0000118 "has_sequence_feature_component" xsd:string +range: SO:0000110 ! sequence_feature + +[Typedef] +id: GENO:0000740 +name: has_inferred_phenotype +holds_over_chain: GENO:0000382 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype."} +holds_over_chain: GENO:0000383 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration."} +holds_over_chain: GENO:0000413 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations from a (sequence-)variant locus instance to a gene class (to support cases where the phenotype association is made at the level of the variant gene locus)."} +holds_over_chain: GENO:0000449 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations from an expression-variant gene instance to a gene class (to support cases where the phenotype association is made at the level of the expression-variant gene)."} +holds_over_chain: GENO:0000661 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)"} +is_a: RO:0002200 ! has phenotype + +[Typedef] +id: GENO:0000741 +name: obsolete_has_regulatory_part +comment: Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes. +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000742 +name: obsolete_is_alteration_within +def: "A relation linking a sequence_alteration to the gene it alters." [] +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "is_within_allele_of" xsd:string +holds_over_chain: GENO:0000383 GENO:0000408 +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000743 +name: has_asserted_phenotype +is_a: RO:0002200 ! has phenotype + +[Typedef] +id: GENO:0000761 +name: is_regulatory_part_of +property_value: IAO:0000116 "Proposal for a property linking regulatory elements to larger features of which they are a part." xsd:string +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000767 +name: obsolete_has_position_component +def: "A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances." [] +property_value: IAO:0000116 "For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them." xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000783 +name: has_sequence_unit +def: "A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues)" [] +is_a: GENO:0000654 ! has_sequence_part + +[Typedef] +id: GENO:0000784 +name: completely_varies_with +def: "A relation between two seqeunces or features that are considered variant with each other along their entire extents." [] +is_symmetric: true +is_a: GENO:0000683 ! varies_with + +[Typedef] +id: GENO:0000790 +name: related_condition + +[Typedef] +id: GENO:0000791 +name: inferred_to_cause_condition +property_value: IAO:0000116 "Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene)" xsd:string +property_value: IAO:0000116 "The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains.\n\nBelow are the different kinds/paths of propagation we desire:\n1. Propagation 'down' a genotype (from larger components to smaller ones)\n2. Propagation 'up' a genotype (from smaller components to larger ones)\n3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype).\n4. From an effective genotype to its intrinsic and extrinsic components.\n5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele).\n6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this.\n\nNote that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha/shha [AB] to shha/shha [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition')" xsd:string +holds_over_chain: GENO:0000382 RO:0003303 {comment="Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype."} +holds_over_chain: GENO:0000383 RO:0003303 {comment="Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration."} +holds_over_chain: GENO:0000445 RO:0003303 {comment="Property chain to propagate inferred condition associations from a variant locus instance to a gene class (to support cases where the phenotype association is made directly at the level of the variant locus/allele)."} +holds_over_chain: GENO:0000661 RO:0003303 {comment="Property chain to propagate inferred condition associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)"} +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000793 +name: inferred_to_contribute_to_condition +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000794 +name: inferred_to_correlate_with_condition +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000840 +name: pathogenic_for_condition +xref: LOINC:LA6668-3 +is_a: RO:0003303 ! causes condition + +[Typedef] +id: GENO:0000841 +name: likely_pathogenic_for_condition +xref: LOINC:LA26332-9 +is_a: RO:0003303 ! causes condition + +[Typedef] +id: GENO:0000842 +name: non-causal_for_condition +def: "Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to." [] +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000843 +name: benign_for_condition +xref: LOINC:LA6675-8 +is_a: GENO:0000842 ! non-causal_for_condition + +[Typedef] +id: GENO:0000844 +name: likely_benign_for_condition +xref: LOINC:LA26334-5 +is_a: GENO:0000842 ! non-causal_for_condition + +[Typedef] +id: GENO:0000845 +name: has_uncertain_significance_for_condition +xref: LOINC:LA26333-7 +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000846 +name: has_qualifying_process +def: "A relation used to describe a process contextualizing the identity of an entity." [] +is_a: GENO:0000580 ! has_qualifier + +[Typedef] +id: GENO:0000847 +name: has_qualifying_environment +def: "A relation used to describe an environment contextualizing the identity of an entity." [] +is_a: GENO:0000580 ! has_qualifier + +[Typedef] +id: GENO:0000849 +name: is_candidate_variant_for +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000903 +name: has_location +def: "A relation linking a sequence feature to the location it occupies on some reference sequence." [] +property_value: IAO:0000118 "occupies" xsd:string +domain: SO:0000110 ! sequence_feature +range: GENO:0000815 ! sequence feature location + +[Typedef] +id: GENO:0000906 +name: on strand +comment: Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from. + +[Typedef] +id: GENO:0000957 +name: has_defining_location +def: "Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement." [] +comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location.\n\nFor copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. +range: GENO:0000815 ! sequence feature location + +[Typedef] +id: GENO:0000958 +name: has_defining_sequence +def: "Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement." [] +comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement. +range: GENO:0000702 ! biological sequence + +[Typedef] +id: GENO:0000959 +name: has_defining_feature +def: "Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement." [] +comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference.\n\nFor copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. +range: SO:0000110 ! sequence_feature + +[Typedef] +id: GENO:0000966 +name: has_interval +def: "Relates a sequence feature location to an interval that defines its start and end position." [] +comment: Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects. +domain: GENO:0000815 ! sequence feature location + +[Typedef] +id: GENO:0000967 +name: has_reference_sequence +def: "Relates a 'sequence feature location' to a sequence that it is anchored to." [] + +[Typedef] +id: IAO:0000136 +name: is about +def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." [] + +[Typedef] +id: IAO:0000219 +name: denotes +def: "Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" [] +property_value: IAO:0000116 "Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of." xsd:string +is_a: IAO:0000136 ! is about + +[Typedef] +id: OBI:0000293 +name: has_specified_input +def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +is_a: RO:0002233 ! has input + +[Typedef] +id: OBI:0000299 +name: has_specified_output +def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +is_a: RO:0002234 ! has output + +[Typedef] +id: RO:0000052 +name: inheres_in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] + +[Typedef] +id: RO:0000059 +name: concretizes +def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000087 +name: has_role +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0001000 +name: derives from + +[Typedef] +id: RO:0002091 +name: starts during +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002093 +name: ends during +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +is_symmetric: true + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] + +[Typedef] +id: RO:0002200 +name: has phenotype +def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] +range: UPHENO:0001001 ! Phenotype +inverse_of: RO:0002201 ! phenotype of + +[Typedef] +id: RO:0002201 +name: phenotype of +domain: UPHENO:0001001 ! Phenotype + +[Typedef] +id: RO:0002222 +name: temporally related to + +[Typedef] +id: RO:0002233 +name: has input +def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +is_a: RO:0000057 ! has participant + +[Typedef] +id: RO:0002234 +name: has output +def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." [] +is_a: RO:0000057 ! has participant +inverse_of: RO:0002353 ! output of + +[Typedef] +id: RO:0002350 +name: is member of +is_a: BFO:0000050 ! is part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000112 "Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes\n\nExample 2: a collection of information entities such as a genotype being comprised of a background component and a variant component" xsd:string +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002352 +name: input of +is_a: RO:0000056 ! participates in + +[Typedef] +id: RO:0002353 +name: output of +is_a: RO:0000056 ! participates in + +[Typedef] +id: RO:0002354 +name: obsolete_formed as result of +is_a: ObsoleteProperty + +[Typedef] +id: RO:000244 +name: molecularly controls +def: "Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b" [] + +[Typedef] +id: RO:0002522 +name: bounds sequence of +def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: GENO:0000654 ! has_sequence_part + +[Typedef] +id: RO:0002524 +name: has subsequence +def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +is_a: GENO:0000654 ! has_sequence_part +inverse_of: RO:0002525 ! is subsequence of + +[Typedef] +id: RO:0002525 +name: is subsequence of +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: RO:0002526 +name: overlaps sequence of +def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +property_value: http://purl.org/dc/terms/source http://biorxiv.org/content/early/2014/06/27/006650.abstract xsd:string +is_a: RO:0002131 ! overlaps + +[Typedef] +id: RO:0002528 +name: is upstream of sequence of +def: "inverse of downstream of sequence of" [] + +[Typedef] +id: RO:0002529 +name: is downstream of sequence of +def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] + +[Typedef] +id: RO:0003301 +name: is model of +def: "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] +comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. +property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" xsd:string +property_value: IAO:0000117 "Matthew Brush" xsd:string + +[Typedef] +id: RO:0003302 +name: causes or contributes to condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions. +property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." xsd:string +property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: RO:0003303 +name: causes condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003304 +name: contributes to condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003305 +name: contributes to severity of condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual." [] +property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003306 +name: contributes to frequency of condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population." [] +property_value: IAO:0000118 "contributes to penetrance of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003307 +name: is preventative for condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions. +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: RO:0003308 +name: correlated with condition +def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: begin +name: begin +is_a: GENO:0000708 ! faldo properties + +[Typedef] +id: end +name: end +is_a: GENO:0000708 ! faldo properties + +[Typedef] +id: http://purl.org/oban/association_has_object +name: association has object + +[Typedef] +id: http://purl.org/oban/association_has_predicate +name: association has predicate + +[Typedef] +id: http://purl.org/oban/association_has_subject +name: association has subject + +[Typedef] +id: location +name: location +is_a: GENO:0000708 ! faldo properties + +[Typedef] +id: reference +name: reference +def: "The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly." [] +is_a: GENO:0000708 ! faldo properties + diff --git a/geno-full.owl b/geno-full.owl new file mode 100644 index 0000000..6bd98bb --- /dev/null +++ b/geno-full.owl @@ -0,0 +1,9511 @@ + + + + + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. + +Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 + GENO ontology + Unspecified + + + + + + + + + + + + + + + + + + + Used to annotation axioms that define identity criteria for instances of a class. + is_identity_criteria + + + + + + + + + proabalistic_quantifier + + + + + + + + Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models. + mixin + + + + + + + + + gene symbol + + + + + + + + editor preferred term + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + editor preferred term + + + + + + + + example + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage + + + + + + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + + + + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition + + + + + + + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + editor note + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + alternative term + + + + + + + + definition source + + formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + + + + + + + + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + + + + + + is denotator type + relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from + + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + + + + + + + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + + + + + + + first order logic expression + PERSON:Alan Ruttenberg + first order logic expression + + + + + + + + antisymmetric property + part_of antisymmetric property xsd:true + use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + + + + + + OBO foundry unique label + + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + + + + + + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + has associated axiom(fol) + + + + + + + + is allocated id range + Add as annotation triples in the granting ontology + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + is allocated id range + + + + + + + + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + 2018-09-21T16:43:39Z + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + + + + + + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + https://github.com/geneontology/go-ontology/issues/15532 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + + + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + has axiom label + + + + + + + + term replaced by + + Add as annotation triples in the granting ontology + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + term replaced by + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + begin + + + + + + + + + end + + + + + + + + + location + + + + + + + + + The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly. + reference + + + + + + + + + + + is part of + + + + + + + + + + has part + + + + + + + + + + + + + + + + + + A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'. + Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants. + http://purl.obolibrary.org/obo/so_has_quality + has_sequence_attribute + + + + + + + + + + + + A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes + materializes + Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence. + bears_concretization_of + + + + + + + + + is_genotype_of + + + + + + + + + + + + + + + + + + + A relationship that holds between a biological entity and some level of genetic variation present in its genome. + This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype. + The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations. + has_genotype + + + + + + + + + + + An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO) + No proper part relation anymore in RO/BFO? + http://semanticscience.org/resource/SIO_000053 + has_proper_part + + + + + + + + + + A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears. + has_sequence_component + has_state + VMC:state + 'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule. + has_sequence + + + + + + + + + + A geno:intrinnsic genotype 'specifies' a SO:genome. +A geno:karyotype 'specifies' a geno:karyotype feature collection. + A relationship between an information content entity representing a specification, and the entity it specifies. + obsolete_specifies + + + + + + + + + Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. + obsolete_approximates_sequence + + + + + + + + + Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. + obsolete_resolves_to_sequence + + + + + + + + + An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole. + http://semanticscience.org/resource/SIO_000093 + is_proper_part_of + + + + + + + + + is_sequence_of + + + + + + + + + is_subject_of + + + + + + + + + obsolete_is_specified_by + + + + + + + + + + shortcut relation used to link a phenotype directly to a genotype of an organism + is_phenotype_of_organism_with_genotype + is_phenotype_with_genotype + phenotype_has_genotype + Might expand to something like: + +phenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype))))))) + obsolete_is_phenotype_of_genotype + + + + + + + + + + A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next. + Exploratory/temporary property, as we formalize our phenotypic inheritance model. + obsolete_participates_in_inheritance_process + + + + + + + + + + + A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression. + has_variant_part + + + + + + + + + + is_variant_part_of + + + + + + + + + + + A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant. + has_reference_sequence_part + has_reference_part + + + + + + + + + is_reference_part_of + + + + + + + + + + + <fgf8a^ti282a> is_allele_of the 'danio rerio fgf8a' gene locus. + A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size. + Domain = allele +Range = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation). + Note that the allele <fgf8a^ti282a> is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the <fgf8a^ti282a> allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product. + is_sequence_variant_of + To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size). + +While conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like "fgf8a<ti282a> is an allele of the Danio rerio fgf8a gene", and we may create data where fgf8a<ti282a> is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene). + +It is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. + +This departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\GAL4 gene. + +At the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'. + is_allele_of + + + + + + + + + + A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level). + is_variant_instance_of + formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus) + Domain = genomic feature instance +Range = punned gene class IRI + obsolete_is_genetic_variant_of + + + + + + + + + A relation linking a gene class to a sequence-varaint or expression-variant of the gene. + has_variant_instance + formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by) + Domain = punned gene class +Range = genomic feature + obsolete_has_genetic_variant + + + + + + + + + A relation linking a gene class to one of its sequence-variant alleles. + Domain = punned gene class +Range = allele + has_sequence_variant + has_allele + + + + + + + + + + A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets. + This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets. + targets_gene + + + + + + + + + + + + + + + + + A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression. + This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset. + has_affected_feature + + + + + + + + + + A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents. + Domain = expression variant feature. +Range = punned gene class + This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class. + is_expression_variant_of + + + + + + + + A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature. + class_to_feature_relation + This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases) + is_feature_affected_by + + + + + + + + + A relation between a gene class and a gene targeting reagent that targets it. + is_target_of + Domain = punned gene class +Range = gene knockdown reagent + is_gene_target_of + + + + + + + + + A relation linking a gene class to one of an expression-variant of that gene.. + Domain = punned gene class +Range = expression variant feature + has_expression_variant_instance + has_expression_variant + + + + + + + + + A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression. + Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property. + This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of. + obsolete_is_variant_with + + + + + + + + + A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways). + obsolete_is_expression_variant_with + + + + + + + + A relation used to describe a context or conditions that define and/or identify an entity. + Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association. + +Used in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features. + has_qualifying_context + has_qualifier + + + + + + + + + + + a relation to link a single locus complement to its zygosity. + has_zygosity + + + + + + + + + + A relationship between a reference locus/allele and the gene class it is an allele of. + is_reference_allele_of + + + + + + + + + Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed. + has_color_value + Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized. + has_staining_intensity + + + + + + + + Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant. + relation between an molecular agent and its molecular target + is_targeted_by + + + + + + + + + + + + + 1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. + +2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds. + +3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC) + Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence. + sequence_derives_from + + + + + + + + + + A relationship between a variant allele and the gene class it is an allele of. + is_variant_allele_of + + + + + + + + + + Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases. + has_sex_agnostic_part + + + + + + + + + + A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of. + is_mutant_allele_of + + + + + + + + + + A relationship between a polymorphic allele and the gene class it is an allele of. + is_polymorphic_allele_of + + + + + + + + + + A relationship between a wild-type allele and the gene class it is an allele of. + is_wild_type_allele_of + + + + + + + + + + An organizational class to hold relations of parthood between sequences/features. + has_sequence_part + + + + + + + + + is_sequence_part_of + + + + + + + + + Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases. + is_sex_agnostic_part_of + + + + + + + + + A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part). + This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of) + varies_with + + + + + + + + organizational property to hold imports from faldo. + faldo properties + + + + + + + + + + + + + + + + + A relation linking a qualified sequence feature to its component sequence feature. + has_sequence_feature_component + In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism. + has_sequence_feature + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_inferred_phenotype + + + + + + + + + Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype. + + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration. + + + + + + + + + + Property chain to propagate inferred phenotype associations from an intrinsic genotype component (e.g. a (sequence-)variant locus instance) to a gene class. + + + + + + + + + Property chain to propagate inferred phenotype associations from a (sequence-)variant locus instance to a gene class (to support cases where the phenotype association is made at the level of the variant gene locus). + + + + + + + + + + Property chain to propagate inferred phenotype associations from an extrinnsic genotype component (e.g. a expression-variant gene instance) to a gene class. + + + + + + + + + Property chain to propagate inferred phenotype associations from an expression-variant gene instance to a gene class (to support cases where the phenotype association is made at the level of the expression-variant gene). + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components) + + + + + + + + + Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes. + obsolete_has_regulatory_part + + + + + + + + + + + + + + A relation linking a sequence_alteration to the gene it alters. + is_within_allele_of + obsolete_is_alteration_within + + + + + + + + + has_asserted_phenotype + + + + + + + + + Proposal for a property linking regulatory elements to larger features of which they are a part. + is_regulatory_part_of + + + + + + + + + A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances. + For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them. + obsolete_has_position_component + + + + + + + + + A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues) + has_sequence_unit + + + + + + + + + + A relation between two seqeunces or features that are considered variant with each other along their entire extents. + completely_varies_with + + + + + + + + related_condition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene) + The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains. + +Below are the different kinds/paths of propagation we desire: +1. Propagation 'down' a genotype (from larger components to smaller ones) +2. Propagation 'up' a genotype (from smaller components to larger ones) +3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype). +4. From an effective genotype to its intrinsic and extrinsic components. +5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele). +6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this. + +Note that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha<tbx392>/shha<tbx392> [AB] to shha<tbx392>/shha<tbx392> [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition') + inferred_to_cause_condition + + + + + + + + + + This is a case of inter-gneotype phenotype propagation, requiring propagation down oen genotype and then up another. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to have this chain. + +This property chain propagates a phenotype asserted on a sex-qualified intrinsic genotype, down to its sex-agnostic genotype part, and then up to a parent effective genotype that has it as a variant part. I think this is OK in all cases, so we can implement this as the one case where we can have inter-genotype pheno propagation. But as noted, there will likely be no data that actually meets criteria to use this chain, so we can probably leave it out. + + + + + + + + + Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype. + + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, to the coompnent variant parts of this sex-agnostic genotype. + + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to move past the sex-agnostic genotype and down to its parts. + +The following shorter chain would also suffice here: +is_variant_part_of o inferred_to_cause_condition + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration. + + + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, through the coompnent variant parts of this sex-agnostic genotype, and to the affected gene. + + + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to propagate to genes. + +The shorter chain below would also suffice for this propagation: +has_allele o inferred_to_cause_condition + + + + + + + + + + Property chain to propagate inferred condition associations from an sequence alteration through the variant locus to a gene class. (separate chains are needed to propagate from the variant locus to the gene class, and another to propagate from a genotype, GVC, or VSLC to the gene class). + + +NOTE that i dont need this property chain if I have a property chain to infer a has_affected_locus link from a sequence alteration to a gene when the link is asserted from the variant locus to the gene: + +is_variant_part_of o has_affected_locus --> has_affected_locus + + + + + + + + + + Obsolete comment: Property chain to propagate inferred condition associations from an intrinsic genotype, GC, or VLSC to a gene class. (a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class). + +The following, shorter chain, would also suffice here: +has_allele o inferred_to_cause_condition -> inferred_to_cause_condition + Property chain to propagate inferred condition associations from an intrinsic genotype, GVC, or VLSC to an affected gene class, or from an extrinsic gneotype or component to an affected gene class. + +The following, shorter chain, would also suffice here: +has_affected_locus o inferred_to_cause_condition -> inferred_to_cause_condition + +Note that a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class in cases where the link to gene is through the variant locus rather than the seq alteration). + + + + + + + + + Property chain to propagate inferred condition associations from a variant locus instance to a gene class (to support cases where the phenotype association is made directly at the level of the variant locus/allele). + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype to a sex-agnostic intrinsic genotype. + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components) + + + + + + + + + inferred_to_contribute_to_condition + + + + + + + + + inferred_to_correlate_with_condition + + + + + + + + + LOINC:LA6668-3 + pathogenic_for_condition + + + + + + + + + LOINC:LA26332-9 + likely_pathogenic_for_condition + + + + + + + + + Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to. + non-causal_for_condition + + + + + + + + + LOINC:LA6675-8 + benign_for_condition + + + + + + + + + LOINC:LA26334-5 + likely_benign_for_condition + + + + + + + + + LOINC:LA26333-7 + has_uncertain_significance_for_condition + + + + + + + + + A relation used to describe a process contextualizing the identity of an entity. + has_qualifying_process + + + + + + + + + A relation used to describe an environment contextualizing the identity of an entity. + has_qualifying_environment + + + + + + + + + is_candidate_variant_for + + + + + + + + + + A relation linking a sequence feature to the location it occupies on some reference sequence. + occupies + has_location + + + + + + + + Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from. + on strand + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location. + +For copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. + has_defining_location + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement. + has_defining_sequence + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference. + +For copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. + has_defining_feature + + + + + + + + + Relates a sequence feature location to an interval that defines its start and end position. + Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects. + has_interval + + + + + + + + Relates a 'sequence feature location' to a sequence that it is anchored to. + has_reference_sequence + + + + + + + + is_about is a (currently) primitive relation that relates an information artifact to an entity. + is about + + + + + + + + + Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically + Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of. + denotes + + + + + + + + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + has_specified_input + + + + + + + + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + has_specified_output + + + + + + + + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + inheres_in + + + + + + + + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + bearer of + + + + + + + + + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates in + + + + + + + + a relation between a process and a continuant, in which the continuant is somehow involved in the process + has participant + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + has quality + + + + + + + + + has_role + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + derives from + + + + + + + + + starts during + + + + + + + + + ends during + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + overlaps + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + in taxon + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + has phenotype + + + + + + + + + phenotype of + + + + + + + + temporally related to + + + + + + + + + p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + has input + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + has output + + + + + + + + + + is member of + + + + + + + + + Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes + +Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component + has member is a mereological relation between a collection and an item. + has member + + + + + + + + + input of + + + + + + + + + output of + + + + + + + + + obsolete_formed as result of + + + + + + + + Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b + molecularly controls + + + + + + + + + x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + Chris Mungall + bounds sequence of + + + + + + + + + + x has subsequence y iff all of the sequence parts of x are sequence parts of y + has subsequence + + + + + + + + + is subsequence of + + + + + + + + + x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. + http://biorxiv.org/content/early/2014/06/27/006650.abstract + overlaps sequence of + + + + + + + + inverse of downstream of sequence of + is upstream of sequence of + + + + + + + + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + is downstream of sequence of + + + + + + + + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + Matthew Brush + The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + is model of + + + + + + + + + The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. + +An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition. + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. + causes or contributes to condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition. + causes condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition. + contributes to condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual. + contributes to expressivity of condition + contributes to severity of condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population. + contributes to penetrance of condition + contributes to frequency of condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. + is preventative for condition + + + + + + + + + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + correlated with condition + + + + + + + + association has object + + + + + + + + association has predicate + + + + + + + + association has subject + + + + + + + + + + + + + + + + + + + The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is. + position + + + + + + + + + Property linking a sequence or sequence feature to an integer representing its length in terms of the number of units in the sequence. + has_extent + + + + + + + + + + Shortcut relation linking a sequence feature directly to a string representing the 'state' of its sequence - i.e. the ordering of units that comprise it (e.g. 'atgcagctagctaccgtcgatcg'). + has_sequence_string + + + + + + + + ObsoleteDataProperty + + + + + + + + The 'rank' quantifier in Bgee gene-anatomy associations, that indicates the imporatnace/specificity of a gene expression in a given anatommy relative to expressionin other anatomies for the same gene. + Property to link an assertion or association with some value quantifying its relevance or ranking. + has_quantifier + + + + + + + + The starting position of a sequence feature or interval. + start_position + + + + + + + + The ending position of a sequence feature or interval. + end_position + + + + + + + + + + Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg'). + has_string + + + + + + + + Describes the number of members in some set. + has_count + In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'. + has_member_count + + + + + + + + + + + + + + Both strands + + + + + + + + + A position that is exactly known. + Exact position + + + + + + + + + Positive strand + + + + + + + + + Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate. + We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region). + FALDO + Position + + + + + + + + + + + + + + 1 + + + + + 1 + + + + + + A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene. + From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence. + Region + + + + + + + + + Negative strand + + + + + + + + + Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'. + Stranded position + + + + + + + + + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + + + + + + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + continuant + continuant + + + + + + + + + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + occurrent + occurrent + + + + + + + + + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + independent continuant + independent continuant + + + + + + + + + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + + process + process + + + + + + + + + + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocitosis and exocitosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89 + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + + disposition + disposition + + + + + + + + + + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + realizable entity + realizable entity + + + + + + + + + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + + quality + quality + + + + + + + + + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + specifically dependent continuant + specifically dependent continuant + + + + + + + + + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + role + role + + + + + + + + + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + generically dependent continuant + generically dependent continuant + + + + + + + + + the function of a hammer to drive in nails + the function of a heart pacemaker to regulate the beating of a heart through electricity + the function of amylase in saliva to break down starch into sugar + BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + + function + + + + + + + + + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + material entity + material entity + + + + + + + + + Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology. + molecular entity + + + + + + + + + nucleic acid + + + + + + + + + + + + + + + A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). + cell line + + + + + + + + + Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies. + cell + + + + + + + + + 1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions. + +2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity). + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system + + + + + + + + + A technique is a planned process used to accomplish a specific activity or task. + technique + + + + + + + + + A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo. + embryonic stem cell line + + + + + + + + + A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types. + stem cell line + + + + + + + + + Example zebrafish intrinsic genotype: + +Genotype = fgf8a<ti282a/+>; shha<tb392/tb392> (AB) +reference component (genomic background) = AB +variant component ('genomic variation complement') = fgf8a<ti282a/+>; shha<tb392/tb392> + +. . . and within this variant component, there are two 'variant single locus complements' represented: + +allele complement 1 = fgf8a<ti282a/+> +allele complement 2 = shha<tb392/tb392> + +and within each of these 'variant single locus complements' there is one or more variant gene locus member: + +in complement 1: fgf8a<ti282a> +in complement 2: shha<ttb392> + A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement) + This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). + +Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. + genotype + organismal genotype + sex-agnostic intrinsic genotype + In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances). + genomic genotype (sex-agnostic) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An allele that varies in it sequence from what is considered the reference or canonical sequence at that location. + The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles. + alternate allele + sequence-variant feature + variant feature + Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another. + +A variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence. + variant allele + + + + + + + + + + + + + + + + + + + + + + + + + + A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype. + Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases. + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation. + +In model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a<t1282a/+>(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)). + genomic variation complement + + + + + + + + + The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB) + A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). + Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it. + genomic background + OBI:genetic population background information + background genome + + + + + + + + + + + + + + + The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The "mn004Gt" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome. + +http://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722 + +http://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8 + A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene) + Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment). + +This design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not. + http://purl.obolibrary.org/obo/SO_0001023 ! allele + In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion. + +A genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene. + gene allele + + + + + + + + + + + + + + + + + + + + + + + + + + A sequence that serves as a standard against which other sequences at the same location are compared. + The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant. + reference sequence + A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence. + reference sequence + + + + + + + + + a collection more than one sequence features (ie a collection of discontinuous sequence features) + perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one) + 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. + obsolete_sequence feature collection + + + + + + + + + A sequence feature collection comprised of discontiguous sequences from a single genome + Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system. + genomic feature collection + Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. + obsolete_genomic feature collection + + + + + + + + + A single locus complement that serves as a standard against which 'variant' sequences are compared + reference allelic complement + reference single locus feature complement + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class axiom: +'single locus complement' + and (has_sequence_attribute some reference) + +SC axioms: +'has member' exactly 0 'variant allele' +'has member' only 'reference genomic feature' +'has member' some 'reference genomic feature' + obsolete_reference single locus complement + + + + + + + + + + + + + + + + + + + + + + + + + + A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13). + variant allelic complement + Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members. + +Note that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant. + variant single locus complement + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A genome that varies at one or more loci from the sequence of some reference genome. + http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here) + variant genome + + + + + + + + + + + + + + + + + + + + + + + + + + An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome. + Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population. + +In model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared. + reference allele + + + + + + + + + + A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus). + Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '. + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class def: 'genomic feature' + and (has_sequence_attribute some unspecified) + An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). + obsolete_unspecified feature + + + + + + + + + A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature. + hemizygous reference junction + Eliminating unecessary defined/organizational classes. Former logical def: + +junction + and (has_sequence_attribute some reference) + +Subclass axiom: +is_variant_with some insertion + In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. + +The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. + obsolete_reference junction + + + + + + + + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a danio rerio. + danio rerio gene + + + + + + + + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a homo sapiens. + homo sapiens gene + + + + + + + + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a mus musculus. + mus musculus gene + + + + + + + + + A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development. +http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690 + +Note that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469 + A version/allele of a gene that serves as a standard against which variant genes are compared. + reference gene + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class axiom: +'gene allele' + and (has_sequence_attribute some reference) + +SC axioms: +is_variant_with some 'gene allele' +is_reference_allele_of some gene + Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. + +In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. + obsolete_reference gene allele + + + + + + + + + obsolete_experimental insertion + + + + + + + + + + + + + + + gene trap insertion + + + + + + + + + + + + + + + A transgene that has been integrated into a chrromosome in the host genome. + An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion. + +An 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome. + integrated transgene + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny. + 1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. + +2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way. + 1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. + +2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms. + genomic material + + + + + + + + + A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion. + physical genome + A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements. + +Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome. + material genome + + + + + + + + + a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role) + Consider http://semanticscience.org/resource/SIO_001062 ! human population ("A human population refers to a collection of human beings"). + homo sapiens population + human population + + + + + + + + + + + + + + + A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical. + organism strain or breed + Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR) + strain or breed + + + + + + + + + A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon) + taxonomic group + + + + + + + + + mus musculus strain + + + + + + + + + + + + + + + + + + + + + danio rerio strain + + + + + + + + + sequence attribute that can inhere only in a collection of more than one sequence features + obsolete_sequence feature collection attribute + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes). + in cis + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes). + in trans + + + + + + + + + + + + + + + An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different). + allelic state + derived from https://en.wikipedia.org/wiki/Zygosity + http://semanticscience.org/resource/SIO_001263 + zygosity + + + + + + + + + hemizygous + + + + + + + + + heterozygous + + + + + + + + + homozygous + + + + + + + + + indeterminite zygosity + no-call zygosity + unknown zygosity + unspecified zygosity + + + + + indeterminite zygosity + MGI uses this term when zygosity is not known. + + + + + no-call zygosity + (this is how the GVF10 format/standard refers to loci without enough data to make an accurate call . . . see http://www.sequenceontology.org/resources/gvf.html#quick_gvf_examples) + + + + + + + + + The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event. + We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells). + +We can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms. + heritabililty + + + + + + + + + heritable + + + + + + + + + non-heritable + + + + + + + + + The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment. + The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family. + mode of inheritance + phenotypic inheritance pattern + http://purl.obolibrary.org/obo/HP_0000005 + http://purl.obolibrary.org/obo/NCIT_C45827 + An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, "genetic context" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. + +These genetic and environmental "interactions" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y. + inheritance pattern + + + + + + + + + disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes + Triage until decide if want to define this as grouping class that would result in multiple-inheritance. + obsolete_dominant inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant autosomal inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + pure dominant inheritance + complete autosomal dominant inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + intermediate dominant autosomal inheritance + semi-dominant autosomal inheritance + incomplete autosomal dominant inheritance + + + + + + + + + An X-linked inheritance pattern wherein the trait manifests in heterozygotes. + http://purl.obolibrary.org/obo/HP_0001423 + X-linked dominant inheritance + + + + + + + + + An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes. + vertical inheritance + http://purl.obolibrary.org/obo/HP_0000006 + autosomal dominant inheritance + + + + + + + + + An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals. + autosomal recessive inheritance + + + + + + + + + An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals. + http://purl.obolibrary.org/obo/HP_0001419 + X-linked recessive inheritance + + + + + + + + + duplicate term, use GENO:0000148 + obsolete_autosomal recessive inheritance + + + + + + + + + An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared. + Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another. + reference + + + + + + + + + unspecified life cycle stage + + + + + + + + + objective is to insert some specified sequence into the genome of a cell or virus + genetic insertion technique + + + + + + + + + mutagen treatment technique + + + + + + + + + + + + + + + a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). + This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. + targeted gene mutation technique + + + + + + + + + Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. + random genetic insertion technique + + + + + + + + + + + + + + + targeted genetic insertion technique + + + + + + + + + enhancer trapping technique + + + + + + + + + gene trapping technique + + + + + + + + + promoter trapping technique + + + + + + + + + targeted knock-in technique + + + + + + + + + random transgene insertion technique + + + + + + + + + A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome + obsolete_chromosome complement + + + + + + + + + + + + + + + + A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation + duplicate chromosome + This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome. + gained aneusomic chromosome + + + + + + + + + + + + 0 + + + + A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation. + This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as "the point at which one or more contiguous nucleotides were excised". + absent aneusomic chromosome + lost aneusomic chromosome + + + + + + + + + + + + + + + + + A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation. + Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism. + aneuploid chromosomal segment + aneusomic chromosomal subregion/segment + partial aneusomic chromosomal element + Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome." + aneusomic chromosomal part + + + + + + + + + + A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event. + duplicate partial aneuploid chromosomal element + translocated duplicate chromosomal element + translocated duplicate chromosomal segment + Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location. + gained aneusomic chromosomal segment + + + + + + + + + + + + 0 + + + + A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome. + In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement + dropped partial anneuploid chromosomal element + translocated absent chromosomal segment + truncated chromosome terminus + This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome. + +Loss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus. + lost aneusomic chromosomal segment + + + + + + + + + + + + + + + + + A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation + complete aneusomic chromosome + Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism. + +Similarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication. + aneusomic chromosome + + + + + + + + + Stub class to serve as root of hierarchy for imports of biological processes from GO-BP. + biological process + + + + + + + + + disomic zygosity + + + + + + + + + aneusomic zygosity + + + + + + + + + trisomic homozygous + + + + + + + + + trisomic heterozygous + + + + + + + + + A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a<ti282a>/fgf8a<x15>) + trans-heterozygous + compound heterozygous + + + + + + + + + A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe) + replaced with SO:engineered_region + extra-genomic sequence + obsolete_reagent sequence feature + + + + + + + + + a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a<ti282a/+>) + simple heterozygous + + + + + + + + + + + + + + + + + + + + + + + + + + A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc) + transgene part + + + + + + + + + An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level + variant + + + + + + + + + An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant. + polymorphic + + + + + + + + + An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence. + mutant + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism) + This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology. + 1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. + +2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). + +3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome. + genomic feature + + + + + + + + + + A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion). + This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material. + genetic material + + + + + + + + + + An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain. + Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines + Not required for any specific use case at this point so removed for simplicity. +Formely asserted as allele and inferred as varaint allele. +Eq class definition: +allele + and (mutation or ('has subsequence' some mutation)) + 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. + obsolete_mutant allele + + + + + + + + + + + + + + + A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain. + mutation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon) + Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element + episomal replicon + Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. + extrachromosomal replicon + + + + + + + + + expression construct feature + expression construct + + + + + + + + + An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population. + PMID: 25741868 ACMG Guidelines + Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%). + polymorphic allele + + + + + + + + + A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location. + major allele + major polymorphic allele + + + + + + + + + A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location). + minor allele + minor polymorphic allele + + + + + + + + + A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree. + ancestral allele + ancestral polymorphic allele + + + + + + + + + An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared. + wild-type allele + 'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain. + +The notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis. + wild-type allele + + + + + + + + + + wild-type gene allele + A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation. + wild-type gene + + + + + + + + + + + + + + + + + + + + + A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi. + The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position. + reagent targeted gene + + + + + + + + + A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome). + experimentally-expressed transgene + extrinsic transgene + transiently-expressed transgene + + + + + + + + + An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared. + wild-type + + + + + + + + + + + + + + + + + + + + + + + + + + One of a set of sequence features known to exist at a particular genomic location. + A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene. + +To be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene. + +[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17) +[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17) +[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17) +[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17) +[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17) +[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17) +[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483 +[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17) +[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17) +[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17) +[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17) +[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17) + variable feature + An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). + +Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence). + allele + + + + + + + + + + a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation. + aneusomic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An allele of a gene that contains some sequence alteration. + A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset. + variant gene allele + + + + + + + + + The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a<ti282a/+>. + +The collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome. + A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism. + TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label. + allelic complement + homologous allele complement + single locus feature complement + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes. + +The fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. + single locus complement + + + + + + + + + In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as: + + shha<MO1-1ng/ul>; shhb<pFLAG-mmusShhb> + +This notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct. + A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state. + We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. + +Our rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. + +Finally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." + experimental genotype + expression genotype + An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment. + +The 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations. + extrinsic genotype + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs). + Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." + An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment. + effective genotype + + + + + + + + + + + + + + + A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes). + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment. + reagent-targeted gene complement + + + + + + + + + + + + + + + The set of all transgenes trransiently expressed in a biological system in the context of a given experiment. + experimental transgene complement + transiently-expressed transgene complement + + + + + + + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes). + A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism). + See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself. + expression allele + Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism). + +The identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system. + expression-variant gene + + + + + + + + + gene targeting reagent + sequence targeting reagent + gene knockdown reagent + + + + + + + + + A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent. + targeted gene segment + reagent-targeted gene subregion + + + + + + + + + + + + + + + + + + + + + + A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference. + As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh<tbx292>, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above. + Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). +Note however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO. + 1. Scope of 'Genetic State': +'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs. + +2. Genotype Subtypes: +In GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. + +Two more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features. + +3. The Genotype Partonomy: +'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a<ti282a/ti282a>; fgf3<t24149/+>[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements: + + - GVC: fgf8a<ti282a/ti282a>; fgf3<t24149/+> (total intrinsic variation in the genome) + - Genomic Background: AB (the reference against which the GVC is variant) + - VSLC1: fgf8a<ti282a/ti282a> (homozygous complement of gene alleles at one known variant locus) + - VSLC2: fgf3<t24149/+> (heterozygous complement of gene alleles at another known variant locus) + - Allele 1: fgf8a<ti282a> (variant version of the fgf8a gene, present in two copies) + - Allele 2: fgf3<t24149> (variant version of the fgf3 gene, present in one copy) + - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy) + - Sequence Alteration1: <ti282a> (the specific mutation within the fgf8a gene that makes it variant) + - Sequence Alteration2: <t24149> (the specific mutation within the fgf3 gene that makes it variant) + +A graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md + +One reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data. + genotype + + + + + + + + + ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl +This ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes. + zebrafish phenotype + + + + + + + + + an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. + homoplasmic + + + + + + + + + an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. + heteroplasmic + + + + + + + + + hemizygous X-linked + + + + + + + + + hemizygous Y-linked + + + + + + + + + hemizygous insertion-linked + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). + Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it. + background genotype + genomic background + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. + New term request for SO. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosomal region + + + + + + + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosome sub-band + + + + + + + + + chromosomal band brightness + chromosomal band intensity + + + + + + + + + gpos + + + + + + + + + gneg + + + + + + + + + gvar + + + + + + + + + gpos100 + + + + + + + + + gpos75 + + + + + + + + + gpos50 + + + + + + + + + gpos25 + + + + + + + + + A chromosome arm that is the shorter of the two arms of a given chromosome. + p-arm + stalk + short chromosome arm + + + + + + + + + A chromosome arm that is the longer of the two arms of a given chromosome. + q-arm + long chromosome arm + + + + + + + + + gpos66 + + + + + + + + + gpos33 + + + + + + + + + + A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed. + regulatory transgene region + + + + + + + + + A transgene part whose sequence is expressed in a gene product through transcription and/or translation. + coding transgene feature + expressed transgene region + + + + + + + + + reporter region + + + + + + + + + + + + + + + + + + + + + + + + + + + A transgene whose product is used as a selectable marker. + selectable marker transgene + + + + + + + + + A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell. + Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28) + Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). + +A base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation). + karyotype + + + + + + + + + + + + + + + A genomic genotype where the genomic background specifies a male or female sex chromosome complement. + This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). + +In the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former. + intrinsic genotype (sex-specific) + sex-qualified genotype + sex-qualified intrinsic genotype + We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances. + +Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. + genomic genotype (sex-qualified) + + + + + + + + + A genomic genotype here the genomic background specifies a male sex chromosome complement. + male intrinsic genotype + + + + + + + + + A genomic genotype here the genomic background specifies a female sex chromosome complement. + female intrinsic genotype + + + + + + + + + A background genotype whose sequence or identity is not known or specified. + unspecified background genotype + unspecified genomic background + + + + + + + + + + + + + + + + + + + + + 1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus + +2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele. + +3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y} + A set of sequence features. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature). + +The notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3]. + +[1] https://www.snpedia.com/index.php/APOE-%CE%B54 +[2] https://www.snpedia.com/index.php/APOE-%CE%B52 +[3] https://www.snpedia.com/index.php/Gs270 + sequence feature set + + + + + + + + + + + + + + + + A set of genomic features (i.e. sequence features that are of genomic origin). + In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member. + genomic locus complement + A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature. + +The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. + genomic feature set + + + + + + + + + + + + + + + + + + + + + + + + + + A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc). + defined gene part + SO:0000831 (gene member region) + gene part + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A transgene that codes for a product used as a reporter of gene expression or activity. + reporter transgene + + + + + + + + + A junction between bases, a deletion variant, a terminus at the end of a chromosome. + A genomic feature that has an extent of zero. + Former logical def: +'genomic feature' + and (has_extent value 0) + obsolete_null feature + + + + + + + + + + + + + + + + + + + + An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found. + aberrant extrachromosomal replicon + exogenous extrachromosomal replicon + transgenic extrachromosomal replicon + Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. + novel extrachromosomal replicon + + + + + + + + + + + + + + + + A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome. + This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature. + Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles. + novel replicon + + + + + + + + + An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome. + novel + + + + + + + + + A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide). + terminus + + + + + + + + + + + + + + + + + A sequence feature or a set of such features. + sequence feature or collection + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location. + sequence feature or set + + + + + + + + + + + + + + + + + A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides). + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + biomacromolecular sequence + state + VMC:State + 'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome. + biological sequence + + + + + + + + + + + true + + + + + state + In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele. + + + + + + + + + A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification. + qualified sequence feature or collection + + + + + + + + + + + + + + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes). + A qualified sequence feature that carries sequence derived from the genome of a cell or organism. + qualified genomic feature + + + + + + + + + + + true + This axiom is an initial attempt to formalize the identity criteria of an extrinnsic context that separates qualified sequence features from sequence features (i.e. the context of its material bearer). As we further develop our efforts here this will get refined and more precise. + + + + + + + + + + + true + Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position). + + + + + + + + + + + + + + + + + + + + + + A set of qualified sequence features that carry genomic sequence. + Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member. + A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele. + +A complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome. + qualified genomic feature set + + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. + Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome. + 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. + +2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. + intrinsic genotype + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + DNA sequence + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + RNA sequence + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + amino acid sequence + + + + + + + + + obsolete_biological sequence or collection + + + + + + + + + obsolete_biological sequence collection + + + + + + + + + + A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature. + As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell). + location-qualified sequence feature + + + + + + + + + A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct) + expression-qualified sequence feature + + + + + + + + + A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence. + This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature. + genomic coordinates + remodeling notion of sequence feature position around the idea of a 'genomic locus' + obsolete_genomic position + + + + + + + + + phenotypic inheritance process + + + + + + + + + A sequence attribute inhering in a feature whose identity is not specified. + obsolete_unspecified + + + + + + + + + An attribute describing a type of variation inhering in a sequence feature or collection. + allele attribute + variation attribute + + + + + + + + + + + + + + + + + + + + + + + + + + An intrinsic genotype that specifies variation from a defined reference genome. + variant genomic genotype + + + + + + + + + An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities. + eliminating classes that are not necessary or add uneeded complexity. + obsolete_sequence information entity + + + + + + + + + + + + + + 1 + + + + + + biological sequence residue + monomeric residue + biological sequence unit + + + + + + + + + deoxyribonucleic acid residue + DNA residue + + + + + + + + + ribonucleic acid residue + RNA residue + + + + + + + + + amino acid residue + + + + + + + + + An attribute, quality, or state of a sequence feature or collection. + http://purl.obolibrary.org/obo/SO_0000400 + Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity. + sequence feature attribute + + + + + + + + + + The location of a sequence feature as defined by its start and end position on some reference coordinate system. + 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). + +2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there. + sequence feature location + + + + + + + + + + A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature) + modification-qualified sequence feature + + + + + + + + + + + + + + + + + + + + + + + + + + + 1. The zebrafish "fgf8a<ti282a>/fgf8a<+>" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state). + +2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308. + + ##fileformat=VCFv4.2 + ##FORMAT=<ID=GT, Description="Genotype, 0=REF, 1=ALT"> + #CHROM POS REF ALT FILTER FORMAT SAMP001 + 20 2300608 C T PASS GT 0/1 + 20 2301308 T G PASS GT 1/1 + (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html) + +3. Some allelic genotype formats encode the genotype as a single string - e.g. "GRCh38 Chr12:258635(A;T)" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12. + A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes. + single locus genotype + An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location. + +This contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background. + allelic genotype + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each. + genotype-phenotype association + + + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + + + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + true + + + + + + + + + + + + + + + knockdown reagent targeted gene complement + + + + + + + + + + A sequence alteration within the coding sequence of a gene. + Not required at this poitn, so marked exploratory and obsoleted. +Asserted under sequence_alteration. + obsolete_coding sequence alteration + + + + + + + + + A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome. + P-element construct + + + + + + + + + An engineered region that is used to transfer foreign genetic material into a host cell. + engineered_genetic_vector + Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. + +Constructs are typically packaged as part of delivery systems such as plasmids or viral vectors. + engineered genetic construct + + + + + + + + + A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct. + non-integrated transgene + extra-chromosomal transgene + + + + + + + + + A collection of more than one sequence feature. + http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection + obsolete_sequence feature collection + + + + + + + + + + + + + + + A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block. + Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block. + +Instead, we can create an 'allele set' class as the haplotype parent? + Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype. + A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. + +As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': + +1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. + +2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). "Star alleles" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/). + +3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. + +Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. + haplotype + + + + + + + + + A set of genomic sequences (a biological sequence that is of genomic origin). + copy number complement + A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. + genomic sequence set + + + + + + + + + A relation used to describe an environment contextualizing the identity of an entity. + microsatellite alteration + + + + + + + + + A relation used to describe a process contextualizing the identity of an entity. + repeat region alteration + + + + + + + + + A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism + allelic state + + + + + + + + + allelic dosage + an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome. + gene dosage + Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute. + Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. + +Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. + obsolete_genetic dosage + + + + + + + + + A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent. + genetic origin + variant origin + allele origin + + + + + + + + + Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg. + maternally inherited + maternal allele origin + + + + + + + + + Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm. + paternally inherited + paternal allele origin + + + + + + + + + Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis. + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. + +De novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder. + de novo allele origin + + + + + + + + + Describes an allele whose origin is not known. + unknown allele origin + + + + + + + + + Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body. + acquired + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells. + +These acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations. + somatic allele origin + + + + + + + + + a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells). + germ-line + replaced by GENO:0000900 ! 'germline' + obsolete_gametic + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement') + +Alt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome. + "Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes." +From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/ +https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/ + diplotype + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes. + allelic phase + + + + + + + + + + + + + + + + + + + + + oryzias latipes strain + + + + + + + + + Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg). + hereditary + parental origin + parentally inherited + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells. + germline allele origin + + + + + + + + + An inheritance pattern that is not determined or not known. + unknown inheritance + undetermined inheritance + + + + + + + + + The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”. + One of a set of sequence features or haplotypes that exist at a particular genetic locus. <see ClinGen Allele Model> + The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. + http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/ + No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. + ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) + As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. + +In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) + obsolete_canonical allele + + + + + + + + + An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence. + The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. + http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ + No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. + +Former axiom: denotes some 'obsolete_canonical allele' + ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) + The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. + obsolete_contextual allele + + + + + + + + + A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not. + heteroplasmic mitochondrial inheritance + + + + + + + + + A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited. + homoplasmic mitochondrial inheritance + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + An generically dependent continuant that carries biological sequence that is part of or derived from a genome. + An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities. + genomic entity + + + + + + + + + A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations. + Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as +"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations." Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location. + +Current definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele. + Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424. + A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. + haplotype block + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. + 'Genomic Genotype' vs 'Genome' in GENO: +A genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome. + complete genotype + 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. + +2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. + genomic genotype + + + + + + + + + A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells) + decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin + Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. + obsolete_allele cellular context + + + + + + + + + The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system + In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. + +We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences. + In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. + +For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus). + genomic location + genomic locus + VMC:Location + 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. + +2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. + +3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there. + genomic feature location + + + + + + + + + + + + + + + + + + + + + + + + true + A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc). + useful organizational term to collect entities that have genomes/genotypes. + organismal entity + + + + + + + + + The molecular product resulting from transcription of a single gene (either a protein or RNA molecule) + gene product + + + + + + + + + reporter role + + + + + + + + + selectable marker role + + + + + + + + + selectable marker region + + + + + + + + + + + + + + + A genome whose sequence is identical to that of a genome sequence considered to be the reference. + reference genome + + + + + + + + + A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it. + Former comment: "Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project." + Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype. + Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. + +Former SC axioms: +- is_allele_of some 'haplotype block' +- 'has part' some sequence_alteration + 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene). + +2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. + +GENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. + +3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': + +a. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. +b. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. +c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. + +The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. + obsolete_haplotype + + + + + + + + + A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations. + Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block. + Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. + A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. + +The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. + +----------------------- + +* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. + obsolete_haplotype block + + + + + + + + + An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell. + Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene. + organellar plasmy + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes). + A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification. + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes. + qualified sequence feature + + + + + + + + + + + + + + + + + + + + + A set of qualified seqeunce features. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'. + qualified sequence feature set + + + + + + + + + A biolocical sequence, or set of such sequences. + biological sequence or collection + biological sequence or set + + + + + + + + + A set of biological sequences. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. + +A set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence. + biological sequence set + + + + + + + + + A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome. + Formerly considered modeling this as an informational entity, defined as "An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome." + functional feature complement + genetic dosage + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963. + As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). + The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. + obsolete_functional copy number complement + + + + + + + + + A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form. + obsolete_intrinsic sequence feature attribute + + + + + + + + + A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.) + obsolete_extrinsic sequence feature attribute + + + + + + + + + A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism). + allelic cellular distribution + + + + + + + + + A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin. + constitutional + + + + + + + + + A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin. + clonal + + + + + + + + + An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors. + complex inherritance + multi-factorial inheritance + multi-genic inheritance + multi-locus inheritance + multigenic inheritance + http://purl.obolibrary.org/obo/HP_0001426 + Diseases inherited in this manner are termed 'complex diseases'. + multifactorial inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes. + http://purl.obolibrary.org/obo/HP_0010984 + digenic inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes. + http://purl.obolibrary.org/obo/HP_0010983 + It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform. + oligogenic inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes. + http://purl.obolibrary.org/obo/HP_0010982 + Typically used for traits/conditions governed by more than three gene loci. + polygenic inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors. + single-gene inheritance + monogenic inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome. + autosomal inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome. + gonosomal inheritance + http://purl.obolibrary.org/obo/HP_0010985 + allosomal inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome. + http://purl.obolibrary.org/obo/HP_0001417 + X-linked inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + complete X-linked dominant inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + semi-dominant X-linked inheritance + incomplete X-linked dominant inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant X-linked inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome. + holandric inheritance + http://purl.obolibrary.org/obo/HP_0001450 + Y-linked inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome. + Z-linked inheritance + + + + + + + + + A Z-linked inheritance pattern wherein the trait manifests in heterozygotes. + Z-linked dominant inheritance + + + + + + + + + A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + complete Z-linked dominant inheritance + + + + + + + + + A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + semi-dominant Z-linked inheritance + incomplete Z-linked dominant inheritance + + + + + + + + + An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant Z-linked inheritance + + + + + + + + + A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals. + Z-linked reccessive inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome. + W-linked inheritance + + + + + + + + + An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome. + http://purl.obolibrary.org/obo/HP_0001427 + Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy). + mitochondrial inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females). + http://purl.obolibrary.org/obo/HP_0001470 + sex-limited autosomal dominant inheritance + + + + + + + + + An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females). + http://purl.obolibrary.org/obo/HP_0031362 + sex-limited autosomal recessive inheritance + + + + + + + + + A set of discrete alleles within a particular genome. + 'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An "Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'. + allele set + + + + + + + + + A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s). + copy number variation + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. + In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). + +Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. + obsolete_variant copy number complement + + + + + + + + + A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger. + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961. + 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. + +2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. + +3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. + obsolete_copy number complement + + + + + + + + + + + + + + + + + + + + + A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism). + A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. + genomic sequence + + + + + + + + + A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome. + The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome. + +We represent the notion of copy number at the "sequence level" (as opposed to the "sequence feature level") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The "sequence level" representation here supports this use case. By contrast, a "feature level" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity). + The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result. + +A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. + +The fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. + The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence. + copy number complement + + + + + + + + + A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s). + Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a "sequence feature level" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred). + +For example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains. + 'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome. + variant copy number complement + + + + + + + + + A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome. + functional genetic dosage + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence. + +'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. + +As we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele. + functional copy complement + + + + + + + + + A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type. + mosaic + + + + + + + + + A pair of integers representing start and end position of a location on a sequence coordinate system. + sequence interval + + + + + + + + + molecular function + + + + + + + + + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete] + developmental process + + + + + + + + + pulling in HP 'phenotypic abnormality' root here + human phenotypic abnormality + + + + + + + + + Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology. + A spatiotemporal region encompassing some part of the life cycle of an organism. + human life cycle stage + + + + + + + + + data item + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + information content entity + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + ontology metadata + data about an ontology part + data about an ontology part + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification + + + + + + + + + + + + + + + + + + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + + + + + + + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + cjm + 2018-05-20T20:55:03Z + ontology module + + + + + + + + + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + cjm + 2018-05-20T20:55:30Z + base ontology module + + + + + + + + + + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + cjm + 2018-05-20T20:55:47Z + editors ontology module + + + + + + + + + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + cjm + 2018-05-20T20:56:13Z + main release ontology module + + + + + + + + + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + cjm + 2018-05-20T20:56:23Z + bridge ontology module + + + + + + + + + + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + cjm + 2018-05-20T20:56:47Z + import ontology module + + + + + + + + + + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + cjm + 2018-05-20T20:58:11Z + subset ontology module + + + + + + + + + + + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + cjm + 2018-05-20T20:58:38Z + curation subset ontology module + + + + + + + + + An ontology module that is intended for usage in analysis or discovery applications. + cjm + 2018-05-20T20:58:49Z + analysis subset ontology module + + + + + + + + + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + cjm + 2018-05-20T20:59:19Z + single layer subset ontology module + + + + + + + + + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + cjm + 2018-05-20T20:59:57Z + exclusion subset ontology module + + + + + + + + + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + cjm + 2018-05-20T21:00:14Z + external import ontology module + + + + + + + + + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + cjm + 2018-05-20T21:14:16Z + species subset ontology module + + + + + + + + + + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + cjm + 2018-05-20T21:20:33Z + reasoned ontology module + + + + + + + + + + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + cjm + 2018-05-20T21:21:12Z + generated ontology module + + + + + + + + + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + cjm + 2018-05-20T21:21:21Z + template generated ontology module + + + + + + + + + + + + cjm + 2018-05-20T21:28:15Z + taxonomic bridge ontology module + + + + + + + + + cjm + 2018-05-22T04:15:54Z + ontology module subsetted by expressivity + + + + + + + + + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + cjm + 2018-05-22T04:16:10Z + obo basic subset ontology module + + + + + + + + + + cjm + 2018-05-22T04:16:28Z + ontology module subsetted by OWL profile + + + + + + + + + cjm + 2018-05-22T04:16:48Z + EL++ ontology module + + + + + + + + + where to place this depends on if we take the organismal view or the quality centric view. + mammalian phenotype + + + + + + + + + Mus musculus + + + + + + + + + Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies. + Viruses + + + + + + + + + Danio rerio + + + + + + + + + Oryzias latipes + + + + + + + + + Homo sapiens + + + + + + + + + A processual entity that realizes a plan which is the concretization of a plan specification. + Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO. + planned process + + + + + + + + + reagent role + + + + + + + + + a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area + population + + + + + + + + + An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. + genotyping assay + + + + + + + + + A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. + A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. + targeted gene knock-out technique + + + + + + + + + targeted gene knock-in technique + + + + + + + + + Stub class to serve as root of hierarchy for imports from NCBI Taxonomy. + organism + + + + + + + + + + + + + + + + + + + + + + + + + the introduction. alteration or integration of genetic material into a cell or organism + genetic modification technique + + + + + + + + + 'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html + Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute. + color value + obsolete_color brightness + + + + + + + + + female + + + + + + + + + male + + + + + + + + + phenotypic sex + + + + + + + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role). + collection of organisms + + + + + + + + + A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. + family + + + + + + + + + Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. + morpholino_oligo + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. + Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosome arm + + + + + + + + + + + + + + + + + + + + + Any extent of continuous biological sequence. + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome. + sequence_feature + + + + + + + + + + + true + Formalizes the first identity criteria for a sequence feature of its sequence. + + + + + + + + + + + true + Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property). + + + + + + + + + A region of known length which may be used to manufacture a longer region. + obsolete_assembly_component + + + + + + + + + A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. + obsolete_contig + + + + + + + + + + + + 0 + + + The point at which one or more contiguous nucleotides were excised. + deleted_sequence + nucleotide deletion + nucleotide_deletion + + SO:1000033 + SO:0000159 + SOFA + http://en.wikipedia.org/wiki/Nucleotide_deletion + deletion + + + + + + + + + enhancer + + + + + + + + + A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. + promoter + + + + + + + + + A region of nucleotide sequence that has translocated to a new position. + transchr + translocated sequence + + SO:0000199 + DBVAR + translocation + + + + + + + + + SSLP + simple sequence length polymorphism + simple sequence length variation + + SO:0000207 + simple_sequence_length_variation + + + + + + + + + sequence length variation + + SO:0000248 + sequence_length_variation + + + + + + + + + + See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25. + +Includes things like loxP sites, inducible promoters, ires elements, etc. + engineered_foreign_gene + + + + + + + + + A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. + http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29 + A defined feature that includes any type of VNTR or SSLP locus. + microsatellite + + + + + + + + + RNAi_reagent + + + + + + + + + Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. + A complete chromosome sequence. + chromosome + + + + + + + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + + "Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. + chromosome band + + + + + + + + + centromere + + + + + + + + + Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct. + obsolete_engineered_plasmid + + + + + + + + + The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. + insertion + nucleotide insertion + nucleotide_insertion + + SO:1000034 + SO:0000667 + DBVAR + SOFA + insertion + + + + + + + + + SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. + single nucleotide polymorphism + + SO:0000694 + SOFA + SNP + + + + + + + + + A junction is a boundary between regions. A boundary has an extent of zero. + junction + + + + + + + + + A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. + Regarding the distinction between a 'gene' and a 'gene allele': +Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment). + A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion. + gene + + + + + + + + + A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. + quantitative trait locus + QTL + + + + + + + + + An attribute to describe a region that was modified in vitro. + engineered + + + + + + + + + + + + + + + + + + + + + + + + + + construct + engineered_region + + + + + + + + + + + + + + + + + + + + + + + + + + An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'. + chromosomal feature + gross chromosomal part + chromosome part + + + + + + + + + A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome). + On the relationship between 'transgenic insertions', 'transgenes', and 'alleles' +Transgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete. + +In addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. + +For the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach. + Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism). + +Note that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome. + transgene + + + + + + + + + A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. + multiple nucleotide polymorphism + + SO:0001013 + MNP + + + + + + + + + A variation that increases or decreases the copy number of a given region. + CNP + CNV + copy number polymorphism + copy number variation + + SO:0001019 + SOFA + http://en.wikipedia.org/wiki/Copy_number_variation + copy_number_variation + + + + + + + + + A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny) + Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. + 'genome sequence' + A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'. + genome + + + + + + + + + + + + + + + + + + + + + + + + + + A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': + +1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871. + +2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112. + +3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112. + A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. + sequence variation + + SO:1000004 + SO:1000007 + SO:0001059 + SOFA + 1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. + +Alleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part. + +2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. + +For a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference. + +3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism. + sequence_alteration + + + + + + + + + + + + + + + An insertion that derives from another organism, via the use of recombinant DNA technology. + transgenic insertion + + SO:0001218 + transgenic_insertion + + + + + + + + + A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. + not currently needed to support modeling use cases. can re-introduce if becomes necessary. + obsolete_experimental_feature + + + + + + + + + A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. + gene_trap_construct + + + + + + + + + A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. + promoter_trap_construct + + + + + + + + + A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. + enhancer_trap_construct + + + + + + + + + SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist. + single nucleotide variant + + kareneilbeck + Thu Oct 08 11:37:49 PDT 2009 + SO:0001483 + SOFA + SNV + + + + + + + + + A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. + heritable_phenotypic_marker + + + + + + + + + 'GRCh37.p10' (a human reference genome build) + A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced. + reference genome sequence + + + + + + + + + A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. + copy number gain + gain + + kareneilbeck + Mon Feb 28 01:54:09 PST 2011 + SO:0001742 + DBVAR + copy_number_gain + + + + + + + + + A sequence alteration whereby the copy number of a given region is less than the reference sequence. + copy number loss + loss + + kareneilbeck + Mon Feb 28 01:55:02 PST 2011 + SO:0001743 + DBVAR + copy_number_loss + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. + UPD + uniparental disomy + + kareneilbeck + Mon Feb 28 02:01:05 PST 2011 + SO:0001744 + DBVAR + http:http\://en.wikipedia.org/wiki/Uniparental_disomy + UPD + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. + maternal uniparental disomy + + kareneilbeck + Mon Feb 28 02:03:01 PST 2011 + SO:0001745 + maternal_uniparental_disomy + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. + paternal uniparental disomy + + kareneilbeck + Mon Feb 28 02:03:30 PST 2011 + SO:0001746 + paternal_uniparental_disomy + + + + + + + + + A structural sequence alteration where there are multiple equally plausible explanations for the change. + complex + + kareneilbeck + Wed Mar 23 03:21:19 PDT 2011 + SO:0001784 + DBVAR + complex_structural_alteration + + + + + + + + + + kareneilbeck + Fri Mar 25 02:27:41 PDT 2011 + SO:0001785 + DBVAR + structural_alteration + + + + + + + + + Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term. + regulatory element + regulatory gene region + regulatory_region + + + + + + + + + Any change in genomic DNA caused by a single event. + + SO:1000002 + SOFA + substitution + + + + + + + + + When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change. + complex substitution + + SO:1000005 + SOFA + complex_substitution + + + + + + + + + A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. + point mutation + + SO:1000008 + SOFA + http://en.wikipedia.org/wiki/Point_mutation + point_mutation + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. + + SO:1000009 + transition + + + + + + + + + A substitution of a pyrimidine, C or T, for another pyrimidine. + pyrimidine transition + + SO:1000010 + pyrimidine_transition + + + + + + + + + A transition of a cytidine to a thymine. + C to T transition + + SO:1000011 + C_to_T_transition + + + + + + + + + The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine. + C to T transition at pCpG site + + SO:1000012 + C_to_T_transition_at_pCpG_site + + + + + + + + + T to C transition + + SO:1000013 + T_to_C_transition + + + + + + + + + A substitution of a purine, A or G, for another purine. + purine transition + + SO:1000014 + purine_transition + + + + + + + + + A transition of an adenine to a guanine. + A to G transition + + SO:1000015 + A_to_G_transition + + + + + + + + + A transition of a guanine to an adenine. + G to A transition + + SO:1000016 + G_to_A_transition + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. + + SO:1000017 + http://en.wikipedia.org/wiki/Transversion + transversion + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. + pyrimidine to purine transversion + + SO:1000018 + pyrimidine_to_purine_transversion + + + + + + + + + A transversion from cytidine to adenine. + C to A transversion + + SO:1000019 + C_to_A_transversion + + + + + + + + + C to G transversion + + SO:1000020 + C_to_G_transversion + + + + + + + + + A transversion from T to A. + T to A transversion + + SO:1000021 + T_to_A_transversion + + + + + + + + + A transversion from T to G. + T to G transversion + + SO:1000022 + T_to_G_transversion + + + + + + + + + Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. + purine to pyrimidine transversion + + SO:1000023 + purine_to_pyrimidine_transversion + + + + + + + + + A transversion from adenine to cytidine. + A to C transversion + + SO:1000024 + A_to_C_transversion + + + + + + + + + A transversion from adenine to thymine. + A to T transversion + + SO:1000025 + A_to_T_transversion + + + + + + + + + A transversion from guanine to cytidine. + G to C transversion + + SO:1000026 + G_to_C_transversion + + + + + + + + + A transversion from guanine to thymine. + G to T transversion + + SO:1000027 + G_to_T_transversion + + + + + + + + + A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. + + SO:1000032 + http://en.wikipedia.org/wiki/Indel + Indels can have a different number of bases than the corresponding reference sequence. + indel + + + + + + + + + One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point. + nucleotide duplication + nucleotide_duplication + + SO:1000035 + duplication + + + + + + + + + A continuous nucleotide sequence is inverted in the same position. + inversion + + SO:1000036 + DBVAR + SOFA + inversion + + + + + + + + + A tandem duplication where the individual regions are in the same orientation. + direct tandem duplication + + SO:1000039 + direct_tandem_duplication + + + + + + + + + A tandem duplication where the individual regions are not in the same orientation. + inverted tandem duplication + mirror duplication + + SO:1000040 + inverted_tandem_duplication + + + + + + + + + A duplication consisting of 2 identical adjacent regions. + erverted + tandem duplication + + SO:1000173 + DBVAR + tandem_duplication + + + + + + + + + Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms) + life cycle stage + + + + + + + + + + + + + + + Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies. + http://purl.obolibrary.org/obo/CARO_0000000 + anatomical entity + + + + + + + + + Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework. + 1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition) + +2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment + Phenotype + + + + + + + + + Animals exhibit variations compared to a given control. + 'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes. + Variant + c. elegans phenotype + worm phenotype + + + + + + + + + abnormal(ly) malformed endocardium cell + + + + + + + + + abnormal(ly) absent dorso-rostral cluster + + + + + + + + + abnormal(ly) disrupted diencephalon development + + + + + + + + + abnormal(ly) disrupted neutrophil aggregation + + + + + + + + + abnormal(ly) absent adaxial cell + + + + + + + + + association + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Equivalent to: http://www.informatics.jax.org/marker/MGI:98297 + mus musculus shh gene + + + + + + + + + + http://zfin.org/ZDB-GENE-980526-166 + danio rerio shha gene + + + + + + + + + + http://zfin.org/ZDB-GENE-040123-1 + danio rerio cdkn1ca gene + + + + + + + + + + Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690 + +Codes for: http://www.uniprot.org/uniprot/Q15465 + homo sapiens SHH gene + + + + + + + + + + + + + + exploratory term + + + + + + + + + exemplar term + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + core + + + + + + + + + placeholder removed + + + + + + + + + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + + + + + + + + + Initially created such that integrated transgene infers as child of sequence_alteration. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/geno.json b/geno.json new file mode 100644 index 0000000..266763c --- /dev/null +++ b/geno.json @@ -0,0 +1,11682 @@ +{ + "graphs" : [ { + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/SO_0000165", + "type" : "CLASS", + "lbl" : "enhancer" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000167", + "meta" : { + "definition" : { + "val" : "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "promoter" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001013", + "meta" : { + "definition" : { + "val" : "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001013" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multiple nucleotide polymorphism" + } ] + }, + "type" : "CLASS", + "lbl" : "MNP" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000281", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25.\n\nIncludes things like loxP sites, inducible promoters, ires elements, etc." + } ] + }, + "type" : "CLASS", + "lbl" : "engineered_foreign_gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000060", + "meta" : { + "definition" : { + "val" : "A version/allele of a gene that serves as a standard against which variant genes are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development.\nhttp://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690\n\nNote that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference gene" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reference gene allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000057", + "meta" : { + "definition" : { + "val" : "A gene that originates from the genome of a mus musculus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "mus musculus gene" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10090", + "type" : "CLASS", + "lbl" : "Mus musculus" + }, { + "id" : "http://purl.obolibrary.org/obo/ERO_0000007", + "meta" : { + "definition" : { + "val" : "A technique is a planned process used to accomplish a specific activity or task.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "technique" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000159", + "meta" : { + "definition" : { + "val" : "The point at which one or more contiguous nucleotides were excised.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Nucleotide_deletion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000033" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide deletion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "deleted_sequence" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide_deletion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000159" + } ] + }, + "type" : "CLASS", + "lbl" : "deletion" + }, { + "id" : "http://purl.obolibrary.org/obo/PCO_0000020", + "meta" : { + "definition" : { + "val" : "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "family" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000034", + "meta" : { + "definition" : { + "val" : "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "morpholino_oligo" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001483", + "meta" : { + "definition" : { + "val" : "SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single nucleotide variant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001483" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Thu Oct 08 11:37:49 PDT 2009" + } ] + }, + "type" : "CLASS", + "lbl" : "SNV" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000173", + "type" : "CLASS", + "lbl" : "promoter trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000172", + "type" : "CLASS", + "lbl" : "gene trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000054", + "meta" : { + "definition" : { + "val" : "A gene that originates from the genome of a homo sapiens.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "homo sapiens gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000175", + "type" : "CLASS", + "lbl" : "random transgene insertion technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000174", + "type" : "CLASS", + "lbl" : "targeted knock-in technique" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "color value" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_color brightness" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000435", + "meta" : { + "definition" : { + "val" : "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "genotyping assay" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "in taxon" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000171", + "type" : "CLASS", + "lbl" : "enhancer trapping technique" + }, { + "id" : "http://www.ncbi.nlm.nih.gov/gene/6469", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690\n\nCodes for: http://www.uniprot.org/uniprot/Q15465" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000514" + } ] + }, + "type" : "CLASS", + "lbl" : "homo sapiens SHH gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000170", + "type" : "CLASS", + "lbl" : "targeted genetic insertion technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000169", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination." + } ] + }, + "type" : "CLASS", + "lbl" : "random genetic insertion technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000166", + "meta" : { + "definition" : { + "val" : "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created." + } ] + }, + "type" : "CLASS", + "lbl" : "targeted gene mutation technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000165", + "type" : "CLASS", + "lbl" : "mutagen treatment technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000047", + "meta" : { + "definition" : { + "val" : "A gene that originates from the genome of a danio rerio.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "danio rerio gene" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001478", + "meta" : { + "definition" : { + "val" : "A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "promoter_trap_construct" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0005836", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulatory element" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulatory gene region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term." + } ] + }, + "type" : "CLASS", + "lbl" : "regulatory_region" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001477", + "meta" : { + "definition" : { + "val" : "A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "gene_trap_construct" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000149", + "meta" : { + "definition" : { + "val" : "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_contig" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001479", + "meta" : { + "definition" : { + "val" : "A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "enhancer_trap_construct" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000409", + "meta" : { + "definition" : { + "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Barry Smith, Werner Ceusters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "CLASS", + "lbl" : "denotator type" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000020", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:48Z" + } ] + }, + "type" : "CLASS", + "lbl" : "EL++ ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000019", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:28Z" + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module subsetted by OWL profile" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0000383", + "type" : "CLASS", + "lbl" : "female" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0000384", + "type" : "CLASS", + "lbl" : "male" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000011", + "meta" : { + "definition" : { + "val" : "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:00:14Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "external import" + } ] + }, + "type" : "CLASS", + "lbl" : "external import ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000012", + "meta" : { + "definition" : { + "val" : "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "taxon subset" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:14:16Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + }, + "type" : "CLASS", + "lbl" : "species subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000411", + "meta" : { + "definition" : { + "val" : "relates an class defined in an ontology, to the type of it's denotator", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is denotator type" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is denotator type" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000013", + "meta" : { + "definition" : { + "val" : "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/reason" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:20:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "reasoned ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000014", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:21:12Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" + } ] + }, + "type" : "CLASS", + "lbl" : "generated ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000412", + "meta" : { + "definition" : { + "val" : "For external terms/classes, the ontology from which the term was imported", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "imported from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + }, + "type" : "PROPERTY", + "lbl" : "imported from" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0000386", + "type" : "CLASS", + "lbl" : "abnormal(ly) absent dorso-rostral cluster" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000015", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/template" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://doi.org/10.1186/s13326-017-0126-0" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:21:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "template generated ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:28:15Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "taxonomic bridge ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001026", + "meta" : { + "definition" : { + "val" : "A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "'genome sequence'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "genome" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "universal" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000017", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:15:54Z" + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module subsetted by expressivity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000018", + "meta" : { + "definition" : { + "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:10Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "obo basic subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "meta" : { + "definition" : { + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term replaced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term replaced by" + }, { + "id" : "http://purl.obolibrary.org/obo/PCO_0000000", + "meta" : { + "definition" : { + "val" : "A material entity that consists of two or more organisms, viruses, or viroids.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)." + } ] + }, + "type" : "CLASS", + "lbl" : "collection of organisms" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000010", + "meta" : { + "definition" : { + "val" : "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "antislim" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:59:57Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "exclusion subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "type" : "PROPERTY", + "lbl" : "has_role" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has quality" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000008", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended for usage in analysis or discovery applications.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:49Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "analysis subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000009", + "meta" : { + "definition" : { + "val" : "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ribbon subset" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:59:19Z" + } ] + }, + "type" : "CLASS", + "lbl" : "single layer subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand expression to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "expand expression to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:03Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology file" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001019", + "meta" : { + "definition" : { + "val" : "A variation that increases or decreases the copy number of a given region.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number polymorphism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Copy_number_variation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001019" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number variation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "CNP" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "CNV" + } ] + }, + "type" : "CLASS", + "lbl" : "copy_number_variation" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000425", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand assertion to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "expand assertion to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000001", + "meta" : { + "definition" : { + "val" : "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:30Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "base ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000002", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:47Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "source ontology module" + } ] + }, + "type" : "CLASS", + "lbl" : "editors ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000003", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:13Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" + } ] + }, + "type" : "CLASS", + "lbl" : "main release ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "meta" : { + "definition" : { + "val" : "Terms with this status should eventually replaced with a term from another ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "to be replaced with external ontology term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000004", + "meta" : { + "definition" : { + "val" : "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:23Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "bridge ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "meta" : { + "definition" : { + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "defined class" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0100026", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy." + } ] + }, + "type" : "CLASS", + "lbl" : "organism" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "meta" : { + "definition" : { + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "named class expression" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000289", + "meta" : { + "definition" : { + "val" : "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A defined feature that includes any type of VNTR or SSLP locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29" + } ] + }, + "type" : "CLASS", + "lbl" : "microsatellite" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000005", + "meta" : { + "definition" : { + "val" : "A subset ontology module that is intended to be imported from another ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "import file" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add axioms that indicate this is the output of a module extraction process." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/extract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:47Z" + } ] + }, + "type" : "CLASS", + "lbl" : "import ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000006", + "meta" : { + "definition" : { + "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/filter" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:11Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "subset ontology" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology slim" + } ] + }, + "type" : "CLASS", + "lbl" : "subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000007", + "meta" : { + "definition" : { + "val" : "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:38Z" + } ] + }, + "type" : "CLASS", + "lbl" : "curation subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002131", + "meta" : { + "definition" : { + "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "overlaps" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0001894", + "type" : "CLASS", + "lbl" : "phenotypic sex" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006011", + "meta" : { + "definition" : { + "val" : "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "VFB" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "#40" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-21T16:43:39Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "may be identical to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006012", + "meta" : { + "definition" : { + "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "GO ontology" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/15532" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/32" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall, Jie Zheng" + } ] + }, + "type" : "PROPERTY", + "lbl" : "scheduled for obsoletion on or after" + }, { + "id" : "http://purl.org/oban/association", + "type" : "CLASS", + "lbl" : "association" + }, { + "id" : "http://purl.obolibrary.org/obo/CHEBI_23367", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology." + } ] + }, + "type" : "CLASS", + "lbl" : "molecular entity" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000199", + "meta" : { + "definition" : { + "val" : "A region of nucleotide sequence that has translocated to a new position.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000199" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "transchr" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "translocated sequence" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + } ] + }, + "type" : "CLASS", + "lbl" : "translocation" + }, { + "id" : "http://biohackathon.org/resource/faldo#BothStrandsPosition", + "type" : "CLASS", + "lbl" : "Both strands" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0032502", + "meta" : { + "definition" : { + "val" : "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete]", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "developmental process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000092", + "type" : "CLASS", + "lbl" : "gene trap insertion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000091", + "type" : "CLASS", + "lbl" : "obsolete_experimental insertion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000093", + "meta" : { + "definition" : { + "val" : "A transgene that has been integrated into a chrromosome in the host genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion.\n\nAn 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome." + } ] + }, + "type" : "CLASS", + "lbl" : "integrated transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_000244", + "meta" : { + "definition" : { + "val" : "Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "molecularly controls" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "meta" : { + "definition" : { + "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + } ] + }, + "type" : "PROPERTY", + "lbl" : "concretizes" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has participant" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000600", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "elucidation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Barry Smith" + } ] + }, + "type" : "PROPERTY", + "lbl" : "elucidation" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000601", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(nl)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom associated with a term expressed using natural language" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has associated axiom(nl)" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000602", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom expressed in first order logic using CLIF syntax" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(fol)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has associated axiom(fol)" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000603", + "meta" : { + "definition" : { + "val" : "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\"", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is allocated id range" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is allocated id range" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "type" : "PROPERTY", + "lbl" : "input of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "inheres_in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "type" : "PROPERTY", + "lbl" : "output of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has input" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "type" : "PROPERTY", + "lbl" : "obsolete_formed as result of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has output" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "participates in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "type" : "PROPERTY", + "lbl" : "is member of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "meta" : { + "definition" : { + "val" : "has member is a mereological relation between a collection and an item.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes\n\nExample 2: a collection of information entities such as a genotype being comprised of a background component and a variant component" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has member" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "bearer of" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000105", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms)" + } ] + }, + "type" : "CLASS", + "lbl" : "life cycle stage" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "type" : "PROPERTY", + "lbl" : "temporally related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003307", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is preventative for condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003306", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to penetrance of condition" + } ] + }, + "type" : "PROPERTY", + "lbl" : "contributes to frequency of condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003308", + "meta" : { + "definition" : { + "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "correlated with condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003303", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "causes condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003302", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." + } ] + }, + "type" : "PROPERTY", + "lbl" : "causes or contributes to condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to expressivity of condition" + } ] + }, + "type" : "PROPERTY", + "lbl" : "contributes to severity of condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003304", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "contributes to condition" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_8090", + "type" : "CLASS", + "lbl" : "Oryzias latipes" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001059", + "meta" : { + "definition" : { + "val" : "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001059" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence variation" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. \n\nAlleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part.\n\n2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. \n\nFor a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference.\n\n3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': \n\n1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871.\n\n2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112.\n\n3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000007" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + } ] + }, + "type" : "CLASS", + "lbl" : "sequence_alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "term imported" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "term split" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "type" : "PROPERTY", + "lbl" : "derives from" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "meta" : { + "definition" : { + "val" : "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Brush" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is model of" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0005531", + "type" : "CLASS", + "lbl" : "abnormal(ly) disrupted neutrophil aggregation" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "meta" : { + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "editor note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "meta" : { + "definition" : { + "val" : "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term editor" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term editor" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000281" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has curation status" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has curation status" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000598", + "meta" : { + "definition" : { + "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID policy for" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000599", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID prefix" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "meta" : { + "definition" : { + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "meta" : { + "definition" : { + "val" : "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + }, + "type" : "PROPERTY", + "lbl" : "example of usage" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000596", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID digit count" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The 'tracker item' can associate a tracker with a specific ontology term." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term tracker item" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term tracker item" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000234", + "meta" : { + "definition" : { + "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The 'term requester' can credit the person, organization or project who request the ontology term." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "ontology term requester" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000113", + "meta" : { + "definition" : { + "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "in branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000277" + } ] + }, + "type" : "PROPERTY", + "lbl" : "in branch" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000597", + "meta" : { + "definition" : { + "val" : "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID range allocated to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "meta" : { + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has obsolescence reason" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has obsolescence reason" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "meta" : { + "definition" : { + "val" : "An administrative note of use for a curator but of no use for a user", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curator note" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "curator note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "meta" : { + "definition" : { + "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + } ] + }, + "type" : "PROPERTY", + "lbl" : "editor preferred term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "alternative term" + } ] + }, + "type" : "PROPERTY", + "lbl" : "alternative term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "meta" : { + "definition" : { + "val" : "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition source" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition source" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "type" : "PROPERTY", + "lbl" : "phenotype of" + }, { + "id" : "http://biohackathon.org/resource/faldo#end", + "type" : "PROPERTY", + "lbl" : "end" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "metadata complete" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "pending final vetting" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "metadata incomplete" + }, { + "id" : "http://www.ncbi.nlm.nih.gov/gene/20423", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Equivalent to: http://www.informatics.jax.org/marker/MGI:98297" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000514" + } ] + }, + "type" : "CLASS", + "lbl" : "mus musculus shh gene" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "type" : "INDIVIDUAL", + "lbl" : "example to be eventually removed" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "uncurated" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "meta" : { + "definition" : { + "val" : "term created to ease viewing/sort terms for development purpose, and will not be included in a release", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "organizational term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "ready for release" + }, { + "id" : "http://www.ncbi.nlm.nih.gov/gene/30269", + "meta" : { + "xrefs" : [ { + "val" : "http://zfin.org/ZDB-GENE-980526-166" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000514" + } ] + }, + "type" : "CLASS", + "lbl" : "danio rerio shha gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000919", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000918", + "meta" : { + "definition" : { + "val" : "An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene." + } ] + }, + "type" : "CLASS", + "lbl" : "organellar plasmy" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000915", + "meta" : { + "definition" : { + "val" : "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_haplotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000914", + "meta" : { + "definition" : { + "val" : "A genome whose sequence is identical to that of a genome sequence considered to be the reference.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "reference genome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000917", + "meta" : { + "definition" : { + "val" : "Describes the number of members in some set.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_count" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_member_count" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000136", + "meta" : { + "definition" : { + "val" : "is_about is a (currently) primitive relation that relates an information artifact to an entity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is about" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000916", + "meta" : { + "definition" : { + "val" : "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.\n\nThe boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.\n\n-----------------------\n\n* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_haplotype block" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000911", + "type" : "CLASS", + "lbl" : "selectable marker role" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000910", + "type" : "CLASS", + "lbl" : "reporter role" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000912", + "type" : "CLASS", + "lbl" : "selectable marker region" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000293", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_specified_input" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000907", + "meta" : { + "definition" : { + "val" : "The molecular product resulting from transcription of a single gene (either a protein or RNA molecule)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "gene product" + }, { + "id" : "http://biohackathon.org/resource/faldo#reference", + "meta" : { + "definition" : { + "val" : "The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "reference" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000909", + "type" : "PROPERTY", + "lbl" : "gene symbol" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000299", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_specified_output" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0001148", + "meta" : { + "definition" : { + "val" : "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a \"targeted\" insertion." + } ] + }, + "type" : "CLASS", + "lbl" : "targeted gene knock-out technique" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0001149", + "type" : "CLASS", + "lbl" : "targeted gene knock-in technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000904", + "meta" : { + "definition" : { + "val" : "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "useful organizational term to collect entities that have genomes/genotypes." + }, { + "pred" : "http://purl.obolibrary.org/obo/GENO_0000905", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "organismal entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000903", + "meta" : { + "definition" : { + "val" : "A relation linking a sequence feature to the location it occupies on some reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occupies" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000906", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from." + } ] + }, + "type" : "PROPERTY", + "lbl" : "on strand" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000027", + "type" : "CLASS", + "lbl" : "data item" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000905", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models." + } ] + }, + "type" : "PROPERTY", + "lbl" : "mixin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000902", + "meta" : { + "definition" : { + "val" : "The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "VMC:Location" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed.\n\nFor example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future.\n\nWe don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic location" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. \n\t\n2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus.\n\n3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic locus" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic feature location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000901", + "meta" : { + "definition" : { + "val" : "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_allele cellular context" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "requires discussion" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "first order logic expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "first order logic expression" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000427", + "meta" : { + "definition" : { + "val" : "use boolean value xsd:true to indicate that the property is an antisymmetric property", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "antisymmetric property" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part_of antisymmetric property xsd:true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "antisymmetric property" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "type" : "PROPERTY", + "lbl" : "is subsequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "meta" : { + "definition" : { + "val" : "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + }, + "type" : "PROPERTY", + "lbl" : "overlaps sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000931", + "meta" : { + "definition" : { + "val" : "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010983" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform." + } ] + }, + "type" : "CLASS", + "lbl" : "oligogenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "meta" : { + "definition" : { + "val" : "inverse of downstream of sequence of", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is upstream of sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000930", + "meta" : { + "definition" : { + "val" : "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010984" + } ] + }, + "type" : "CLASS", + "lbl" : "digenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "meta" : { + "definition" : { + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "bounds sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "meta" : { + "definition" : { + "val" : "x has subsequence y iff all of the sequence parts of x are sequence parts of y", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has subsequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000937", + "meta" : { + "definition" : { + "val" : "An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "complete X-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000936", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001417" + } ] + }, + "type" : "CLASS", + "lbl" : "X-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000815", + "meta" : { + "definition" : { + "val" : "The location of a sequence feature as defined by its start and end position on some reference coordinate system.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms).\n\n2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000818", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "modification-qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000939", + "meta" : { + "definition" : { + "val" : "An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "co-dominant X-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000938", + "meta" : { + "definition" : { + "val" : "An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "semi-dominant X-linked inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "incomplete X-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000933", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single-gene inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "monogenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "meta" : { + "definition" : { + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is downstream of sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000932", + "meta" : { + "definition" : { + "val" : "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010982" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Typically used for traits/conditions governed by more than three gene loci." + } ] + }, + "type" : "CLASS", + "lbl" : "polygenic inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000935", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0010985" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gonosomal inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "allosomal inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000934", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "autosomal inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000929", + "meta" : { + "definition" : { + "val" : "An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001426" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complex inherritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-factorial inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multigenic inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-locus inheritance" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Diseases inherited in this manner are termed 'complex diseases'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-genic inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "multifactorial inheritance" + }, { + "id" : "http://biohackathon.org/resource/faldo#ReverseStrandPosition", + "type" : "CLASS", + "lbl" : "Negative strand" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0010000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has axiom id" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has axiom label" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000920", + "meta" : { + "definition" : { + "val" : "A set of qualified seqeunce features.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified sequence feature set" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000902", + "meta" : { + "definition" : { + "val" : "A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism).\n\nNote that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "On the relationship between 'transgenic insertions', 'transgenes', and 'alleles'\nTransgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete.\n\nIn addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. \n\nFor the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach." + } ] + }, + "type" : "CLASS", + "lbl" : "transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000926", + "meta" : { + "definition" : { + "val" : "A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "allelic cellular distribution" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000925", + "meta" : { + "definition" : { + "val" : "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_extrinsic sequence feature attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000928", + "meta" : { + "definition" : { + "val" : "A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "clonal" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000927", + "meta" : { + "definition" : { + "val" : "A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "constitutional" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000922", + "meta" : { + "definition" : { + "val" : "A set of biological sequences.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. \n\nA set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000921", + "meta" : { + "definition" : { + "val" : "A biolocical sequence, or set of such sequences.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "biological sequence or collection" + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence or set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000924", + "meta" : { + "definition" : { + "val" : "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_intrinsic sequence feature attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000923", + "meta" : { + "definition" : { + "val" : "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genetic dosage" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "functional feature complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_functional copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000953", + "meta" : { + "definition" : { + "val" : "An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0031362" + } ] + }, + "type" : "CLASS", + "lbl" : "sex-limited autosomal recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000952", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001470" + } ] + }, + "type" : "CLASS", + "lbl" : "sex-limited autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/HsapDv_0000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A spatiotemporal region encompassing some part of the life cycle of an organism." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology." + } ] + }, + "type" : "CLASS", + "lbl" : "human life cycle stage" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000959", + "meta" : { + "definition" : { + "val" : "Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference.\n\nFor copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_defining_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000958", + "meta" : { + "definition" : { + "val" : "Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_defining_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000719", + "meta" : { + "definition" : { + "val" : "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons." + } ] + }, + "type" : "CLASS", + "lbl" : "intrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000839", + "type" : "CLASS", + "lbl" : "knockdown reagent targeted gene complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000834", + "meta" : { + "definition" : { + "val" : "Used to annotation axioms that define identity criteria for instances of a class.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_identity_criteria" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000955", + "meta" : { + "definition" : { + "val" : "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number variation" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_variant copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000713", + "meta" : { + "definition" : { + "val" : "A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "qualified sequence feature or collection" + }, { + "id" : "http://biohackathon.org/resource/faldo#ExactPosition", + "meta" : { + "definition" : { + "val" : "A position that is exactly known.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Exact position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000712", + "type" : "PROPERTY", + "lbl" : "ObsoleteDataProperty" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000954", + "meta" : { + "definition" : { + "val" : "A set of discrete alleles within a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An \"Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'." + } ] + }, + "type" : "CLASS", + "lbl" : "allele set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000833", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each." + } ] + }, + "type" : "CLASS", + "lbl" : "genotype-phenotype association" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000957", + "meta" : { + "definition" : { + "val" : "Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their \"identity\" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location.\n\nFor copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_defining_location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000715", + "meta" : { + "definition" : { + "val" : "A set of qualified sequence features that carry genomic sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele.\n\nA complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified genomic feature set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000956", + "meta" : { + "definition" : { + "val" : "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000714", + "meta" : { + "definition" : { + "val" : "A qualified sequence feature that carries sequence derived from the genome of a cell or organism.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." + } ] + }, + "type" : "CLASS", + "lbl" : "qualified genomic feature" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000219", + "meta" : { + "definition" : { + "val" : "Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of." + } ] + }, + "type" : "PROPERTY", + "lbl" : "denotes" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7955", + "type" : "CLASS", + "lbl" : "Danio rerio" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000011", + "meta" : { + "definition" : { + "val" : "A processual entity that realizes a plan which is the concretization of a plan specification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO." + } ] + }, + "type" : "CLASS", + "lbl" : "planned process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000942", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Z-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000941", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001450" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "holandric inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "Y-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000804", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "construct" + } ] + }, + "type" : "CLASS", + "lbl" : "engineered_region" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "type" : "INDIVIDUAL", + "lbl" : "placeholder removed" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which is unique across the OBO Foundry.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "OBO foundry unique label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBO Foundry " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." + } ] + }, + "type" : "PROPERTY", + "lbl" : "OBO foundry unique label" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000948", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "W-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "terms merged" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000947", + "meta" : { + "definition" : { + "val" : "A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Z-linked reccessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000224", + "meta" : { + "definition" : { + "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "core" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000708", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "organizational property to hold imports from faldo." + } ] + }, + "type" : "PROPERTY", + "lbl" : "faldo properties" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "meta" : { + "definition" : { + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "failed exploratory term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "meta" : { + "definition" : { + "val" : "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obsolescence reason specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolescence reason specification" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0000199", + "type" : "CLASS", + "lbl" : "abnormal(ly) malformed endocardium cell" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000949", + "meta" : { + "definition" : { + "val" : "An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy)." + } ] + }, + "type" : "CLASS", + "lbl" : "mitochondrial inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000823", + "meta" : { + "definition" : { + "val" : "A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location.\n\nThis contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single locus genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "1. The zebrafish \"fgf8a/fgf8a<+>\" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state).\n\n2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308.\n\n ##fileformat=VCFv4.2\n ##FORMAT=\n #CHROM POS REF ALT FILTER FORMAT SAMP001\n 20 2300608 C T PASS GT\t 0/1\t\n 20 2301308 T G PASS GT\t 1/1\n (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html)\n\n3. Some allelic genotype formats encode the genotype as a single string - e.g. \"GRCh38 Chr12:258635(A;T)\" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12." + } ] + }, + "type" : "CLASS", + "lbl" : "allelic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000702", + "meta" : { + "definition" : { + "val" : "A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "VMC:State" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "biomacromolecular sequence" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "state" + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000944", + "meta" : { + "definition" : { + "val" : "A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "complete Z-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000943", + "meta" : { + "definition" : { + "val" : "A Z-linked inheritance pattern wherein the trait manifests in heterozygotes.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "Z-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000701", + "meta" : { + "definition" : { + "val" : "A sequence feature or a set of such features.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence feature or collection" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature or set" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000102", + "meta" : { + "definition" : { + "val" : "data about an ontology part is a data item about a part of an ontology, for example a term", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology metadata" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "CLASS", + "lbl" : "data about an ontology part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000946", + "meta" : { + "definition" : { + "val" : "An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "co-dominant Z-linked inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000703", + "meta" : { + "definition" : { + "val" : "Shortcut relation linking a sequence feature directly to a string representing the 'state' of its sequence - i.e. the ordering of units that comprise it (e.g. 'atgcagctagctaccgtcgatcg').", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_string" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000945", + "meta" : { + "definition" : { + "val" : "A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "semi-dominant Z-linked inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "incomplete Z-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000016", + "meta" : { + "definition" : { + "val" : "A transition of a guanine to an adenine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "G to A transition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000016" + } ] + }, + "type" : "CLASS", + "lbl" : "G_to_A_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000015", + "meta" : { + "definition" : { + "val" : "A transition of an adenine to a guanine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : 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"pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "T to C transition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000013" + } ] + }, + "type" : "CLASS", + "lbl" : "T_to_C_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0003674", + "type" : "CLASS", + "lbl" : "molecular function" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000019", + "meta" : { + "definition" : { + "val" : "A transversion from cytidine to adenine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "C to A transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "C_to_A_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000018", + "meta" : { + "definition" : { + "val" : "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000018" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "pyrimidine to purine transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "pyrimidine_to_purine_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000017", + "meta" : { + "definition" : { + "val" : "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000610", + "meta" : { + "definition" : { + "val" : "A relationship between a reference locus/allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_reference_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies." + } ] + }, + "type" : "CLASS", + "lbl" : "cell" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000611", + "meta" : { + "definition" : { + "val" : "A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "background genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic background" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000850", + "meta" : { + "definition" : { + "val" : "A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "P-element construct" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000618", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "chromosomal band brightness" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal band intensity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000619", + "type" : "CLASS", + "lbl" : "gpos" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000614", + "meta" : { + "definition" : { + "val" : "An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "New term request for SO." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal region" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000023", + "meta" : { + "definition" : { + "val" : "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000023" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "purine to pyrimidine transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "purine_to_pyrimidine_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000856", + "meta" : { + "definition" : { + "val" : "An engineered region that is used to transfer foreign genetic material into a host cell.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "engineered_genetic_vector" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. \n\nConstructs are typically packaged as part of delivery systems such as plasmids or viral vectors." + } ] + }, + "type" : "CLASS", + "lbl" : "engineered genetic construct" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000022", + "meta" : { + "definition" : { + "val" : "A transversion from T to G.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "T to G transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000022" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "T_to_G_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000616", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome sub-band" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000737", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "expression-qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000021", + "meta" : { + "definition" : { + "val" : "A transversion from T to A.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000021" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "T to A transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "T_to_A_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000830", + "meta" : { + "definition" : { + "val" : "An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "chromosomal feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gross chromosomal part" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome part" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000078", + "meta" : { + "definition" : { + "val" : "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curation status specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000266" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "CLASS", + "lbl" : "curation status specification" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000020", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "C to G transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "C_to_G_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000736", + "meta" : { + "definition" : { + "val" : "A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "location-qualified sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000005", + "meta" : { + "definition" : { + "val" : "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\\"complex\\\" should be used. Usually there are multiple equally plausible explanations for the change.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complex substitution" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000005" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "complex_substitution" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000002", + "meta" : { + "definition" : { + "val" : "Any change in genomic DNA caused by a single event.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "substitution" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000009", + "meta" : { + "definition" : { + "val" : "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000009" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "transition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000008", + "meta" : { + "definition" : { + "val" : "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "point mutation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Point_mutation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000008" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "point_mutation" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000962", + "meta" : { + "definition" : { + "val" : "A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a \"sequence feature level\" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred).\n\nFor example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome." + } ] + }, + "type" : "CLASS", + "lbl" : "variant copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000720", + "type" : "CLASS", + "lbl" : "DNA sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000841", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA26332-9" + } ] + }, + "type" : "PROPERTY", + "lbl" : "likely_pathogenic_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000840", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA6668-3" + } ] + }, + "type" : "PROPERTY", + "lbl" : "pathogenic_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000961", + "meta" : { + "definition" : { + "val" : "A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result.\n\nA 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. \n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome.\n\nWe represent the notion of copy number at the \"sequence level\" (as opposed to the \"sequence feature level\") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The \"sequence level\" representation here supports this use case. By contrast, a \"feature level\" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "copy number complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000964", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type." + } ] + }, + "type" : "CLASS", + "lbl" : "mosaic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000843", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA6675-8" + } ] + }, + "type" : "PROPERTY", + "lbl" : "benign_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000722", + "type" : "CLASS", + "lbl" : "amino acid sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000721", + "type" : "CLASS", + "lbl" : "RNA sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000963", + "meta" : { + "definition" : { + "val" : "A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "functional genetic dosage" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence.\n\n'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nAs we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele." + } ] + }, + "type" : "CLASS", + "lbl" : "functional copy complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000842", + "meta" : { + "definition" : { + "val" : "Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "non-causal_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000704", + "meta" : { + "definition" : { + "val" : "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Regarding the distinction between a 'gene' and a 'gene allele': \nEvery zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment)." + } ] + }, + "type" : "CLASS", + "lbl" : "gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000960", + "meta" : { + "definition" : { + "val" : "A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000849", + "type" : "PROPERTY", + "lbl" : "is_candidate_variant_for" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000848", + "meta" : { + "definition" : { + "val" : "A sequence alteration within the coding sequence of a gene.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_coding sequence alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000606", + "type" : "CLASS", + "lbl" : "hemizygous insertion-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000608", + "meta" : { + "definition" : { + "val" : "a relation to link a single locus complement to its zygosity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000845", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA26333-7" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_uncertain_significance_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000012", + "meta" : { + "definition" : { + "val" : "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000012" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "C to T transition at pCpG site" + } ] + }, + "type" : "CLASS", + "lbl" : "C_to_T_transition_at_pCpG_site" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000966", + "meta" : { + "definition" : { + "val" : "Relates a sequence feature location to an interval that defines its start and end position.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_interval" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000724", + "type" : "CLASS", + "lbl" : "obsolete_biological sequence or collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000603", + "meta" : { + "definition" : { + "val" : "an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "heteroplasmic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000602", + "meta" : { + "definition" : { + "val" : "an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "homoplasmic" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000011", + "meta" : { + "definition" : { + "val" : "A transition of a cytidine to a thymine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "C to T transition" + } ] + }, + "type" : "CLASS", + "lbl" : "C_to_T_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000965", + "meta" : { + "definition" : { + "val" : "A pair of integers representing start and end position of a location on a sequence coordinate system.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "sequence interval" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000844", + "meta" : { + "xrefs" : [ { + "val" : "LOINC:LA26334-5" + } ] + }, + "type" : "PROPERTY", + "lbl" : "likely_benign_for_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000010", + "meta" : { + "definition" : { + "val" : "A substitution of a pyrimidine, C or T, for another pyrimidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "pyrimidine transition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000010" + } ] + }, + "type" : "CLASS", + "lbl" : "pyrimidine_transition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000726", + "meta" : { + "definition" : { + "val" : "A relation linking a qualified sequence feature to its component sequence feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_sequence_feature_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000847", + "meta" : { + "definition" : { + "val" : "A relation used to describe an environment contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_qualifying_environment" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000605", + "type" : "CLASS", + "lbl" : "hemizygous Y-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000967", + "meta" : { + "definition" : { + "val" : "Relates a 'sequence feature location' to a sequence that it is anchored to.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_reference_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000725", + "type" : "CLASS", + "lbl" : "obsolete_biological sequence collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000604", + "type" : "CLASS", + "lbl" : "hemizygous X-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000846", + "meta" : { + "definition" : { + "val" : "A relation used to describe a process contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_qualifying_process" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000036", + "meta" : { + "definition" : { + "val" : "A continuous nucleotide sequence is inverted in the same position.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000036" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inversion" + } ] + }, + "type" : "CLASS", + "lbl" : "inversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000035", + "meta" : { + "definition" : { + "val" : "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide_duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000035" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide duplication" + } ] + }, + "type" : "CLASS", + "lbl" : "duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000039", + "meta" : { + "definition" : { + "val" : "A tandem duplication where the individual regions are in the same orientation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "direct tandem duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000039" + } ] + }, + "type" : "CLASS", + "lbl" : "direct_tandem_duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000874", + "meta" : { + "definition" : { + "val" : "A relation used to describe a process contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "repeat region alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000632", + "type" : "CLASS", + "lbl" : "gpos66" + }, { + "id" : "http://biohackathon.org/resource/faldo#ForwardStrandPosition", + "type" : "CLASS", + "lbl" : "Positive strand" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000511", + "meta" : { + "definition" : { + "val" : "An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "wild-type" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000873", + "meta" : { + "definition" : { + "val" : "A relation used to describe an environment contextualizing the identity of an entity.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "microsatellite alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000634", + "meta" : { + "definition" : { + "val" : "relation between an molecular agent and its molecular target", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_targeted_by" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000513", + "meta" : { + "definition" : { + "val" : "a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "aneusomic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000876", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allelic dosage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gene dosage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_genetic dosage" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000875", + "meta" : { + "definition" : { + "val" : "A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "allelic state" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000512", + "meta" : { + "definition" : { + "val" : "One of a set of sequence features known to exist at a particular genomic location.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations).\n\nAlleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variable feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene.\n\nTo be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene.\n\t\n[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17)\n[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17)\n[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17)\n[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17)\n[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17)\n[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17)\n[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483\n[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17)\n[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17)\n[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17)\n[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17)\n[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)" + } ] + }, + "type" : "CLASS", + "lbl" : "allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000633", + "type" : "CLASS", + "lbl" : "gpos33" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000870", + "meta" : { + "definition" : { + "val" : "A collection of more than one sequence feature.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence feature collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000872", + "meta" : { + "definition" : { + "val" : "A set of genomic sequences (a biological sequence that is of genomic origin).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number complement" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic sequence set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000871", + "meta" : { + "definition" : { + "val" : "A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. \n\nAs highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\n1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \n\n2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). \"Star alleles\" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/).\n\n3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. \n\nEach of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block.\n\nInstead, we can create an 'allele set' class as the haplotype parent?" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype." + } ] + }, + "type" : "CLASS", + "lbl" : "haplotype" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000040", + "meta" : { + "definition" : { + "val" : "A tandem duplication where the individual regions are not in the same orientation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inverted tandem duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "mirror duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000040" + } ] + }, + "type" : "CLASS", + "lbl" : "inverted_tandem_duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000639", + "meta" : { + "definition" : { + "val" : "Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. \n\n2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds.\n\n3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "sequence_derives_from" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000878", + "meta" : { + "definition" : { + "val" : "Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "maternally inherited" + } ] + }, + "type" : "CLASS", + "lbl" : "maternal allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000515", + "meta" : { + "definition" : { + "val" : "An allele of a gene that contains some sequence alteration.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset." + } ] + }, + "type" : "CLASS", + "lbl" : "variant gene allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000877", + "meta" : { + "definition" : { + "val" : "A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genetic origin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variant origin" + } ] + }, + "type" : "CLASS", + "lbl" : "allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000514", + "type" : "INDIVIDUAL", + "lbl" : "exemplar term" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000638", + "meta" : { + "definition" : { + "val" : "A transgene part whose sequence is expressed in a gene product through transcription and/or translation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "coding transgene feature" + } ] + }, + "type" : "CLASS", + "lbl" : "expressed transgene region" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000879", + "meta" : { + "definition" : { + "val" : "Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "paternally inherited" + } ] + }, + "type" : "CLASS", + "lbl" : "paternal allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000516", + "meta" : { + "definition" : { + "val" : "A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allelic complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "homologous allele complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single locus feature complement" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes.\n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a.\n\nThe collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome." + } ] + }, + "type" : "CLASS", + "lbl" : "single locus complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000637", + "meta" : { + "definition" : { + "val" : "A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "regulatory transgene region" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000027", + "meta" : { + "definition" : { + "val" : "A transversion from guanine to thymine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000027" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "G to T transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "G_to_T_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000026", + "meta" : { + "definition" : { + "val" : "A transversion from guanine to cytidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000026" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "G to C transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "G_to_C_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000025", + "meta" : { + "definition" : { + "val" : "A transversion from adenine to thymine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "A to T transversion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000025" + } ] + }, + "type" : "CLASS", + "lbl" : "A_to_T_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000024", + "meta" : { + "definition" : { + "val" : "A transversion from adenine to cytidine.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000024" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "A to C transversion" + } ] + }, + "type" : "CLASS", + "lbl" : "A_to_C_transversion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000742", + "meta" : { + "definition" : { + "val" : "A relation linking a sequence_alteration to the gene it alters.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_within_allele_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_alteration_within" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000500", + "meta" : { + "definition" : { + "val" : "A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral allele" + } ] + }, + "type" : "CLASS", + "lbl" : "ancestral polymorphic allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000621", + "type" : "CLASS", + "lbl" : "gvar" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000741", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_has_regulatory_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000620", + "type" : "CLASS", + "lbl" : "gneg" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000623", + "type" : "CLASS", + "lbl" : "gpos75" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000502", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "wild-type gene allele" + } ] + }, + "type" : "CLASS", + "lbl" : "wild-type gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000501", + "meta" : { + "definition" : { + "val" : "An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain.\n\nThe notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "wild-type allele" + } ] + }, + "type" : "CLASS", + "lbl" : "wild-type allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000622", + "type" : "CLASS", + "lbl" : "gpos100" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000743", + "type" : "PROPERTY", + "lbl" : "has_asserted_phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000740", + "type" : "PROPERTY", + "lbl" : "has_inferred_phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000861", + "meta" : { + "definition" : { + "val" : "A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "non-integrated transgene" + } ] + }, + "type" : "CLASS", + "lbl" : "extra-chromosomal transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000629", + "meta" : { + "definition" : { + "val" : "A chromosome arm that is the longer of the two arms of a given chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "q-arm" + } ] + }, + "type" : "CLASS", + "lbl" : "long chromosome arm" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000628", + "meta" : { + "definition" : { + "val" : "A chromosome arm that is the shorter of the two arms of a given chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "stalk" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "p-arm" + } ] + }, + "type" : "CLASS", + "lbl" : "short chromosome arm" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000625", + "type" : "CLASS", + "lbl" : "gpos25" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000504", + "meta" : { + "definition" : { + "val" : "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position." + } ] + }, + "type" : "CLASS", + "lbl" : "reagent targeted gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000867", + "type" : "PROPERTY", + "lbl" : "proabalistic_quantifier" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000624", + "type" : "CLASS", + "lbl" : "gpos50" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000866", + "meta" : { + "definition" : { + "val" : "Property to link an assertion or association with some value quantifying its relevance or ranking.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The 'rank' quantifier in Bgee gene-anatomy associations, that indicates the imporatnace/specificity of a gene expression in a given anatommy relative to expressionin other anatomies for the same gene." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_quantifier" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000506", + "meta" : { + "definition" : { + "val" : "A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "extrinsic transgene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "experimentally-expressed transgene" + } ] + }, + "type" : "CLASS", + "lbl" : "transiently-expressed transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000032", + "meta" : { + "definition" : { + "val" : "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Indels can have a different number of bases than the corresponding reference sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http://en.wikipedia.org/wiki/Indel" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000032" + } ] + }, + "type" : "CLASS", + "lbl" : "indel" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000626", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_color_value" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_staining_intensity" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000181", + "meta" : { + "definition" : { + "val" : "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "population" + }, { + "id" : "http://biohackathon.org/resource/faldo#Region", + "meta" : { + "definition" : { + "val" : "A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "Region" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000780", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "deoxyribonucleic acid residue" + } ] + }, + "type" : "CLASS", + "lbl" : "DNA residue" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000896", + "meta" : { + "definition" : { + "val" : "Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg').", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_string" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000533", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gene targeting reagent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence targeting reagent" + } ] + }, + "type" : "CLASS", + "lbl" : "gene knockdown reagent" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000654", + "meta" : { + "definition" : { + "val" : "An organizational class to hold relations of parthood between sequences/features.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000411", + "meta" : { + "definition" : { + "val" : "A relation linking a gene class to a sequence-varaint or expression-variant of the gene.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Domain = punned gene class\nRange = genomic feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_variant_instance" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_has_genetic_variant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000653", + "meta" : { + "definition" : { + "val" : "A relationship between a wild-type allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_wild_type_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000895", + "meta" : { + "definition" : { + "val" : "The ending position of a sequence feature or interval.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "end_position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000414", + "meta" : { + "definition" : { + "val" : "A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets." + } ] + }, + "type" : "PROPERTY", + "lbl" : "targets_gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000898", + "meta" : { + "definition" : { + "val" : "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as \n\"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.\" Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location.\n\nCurrent definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424." + } ] + }, + "type" : "CLASS", + "lbl" : "haplotype block" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000777", + "meta" : { + "definition" : { + "val" : "An intrinsic genotype that specifies variation from a defined reference genome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "variant genomic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000030", + "meta" : { + "definition" : { + "val" : "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000142" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples of information content entites include journal articles, data, graphical layouts, and graphs." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Chris Stoeckert" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "information content entity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." + } ] + }, + "type" : "CLASS", + "lbl" : "information content entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000534", + "meta" : { + "definition" : { + "val" : "A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "targeted gene segment" + } ] + }, + "type" : "CLASS", + "lbl" : "reagent-targeted gene subregion" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000897", + "meta" : { + "definition" : { + "val" : "An generically dependent continuant that carries biological sequence that is part of or derived from a genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/GENO_0000905", + "val" : "true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000655", + "type" : "PROPERTY", + "lbl" : "is_sequence_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000413", + "meta" : { + "definition" : { + "val" : "A relation linking a gene class to one of its sequence-variant alleles.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = punned gene class\nRange = allele" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_sequence_variant" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000892", + "meta" : { + "definition" : { + "val" : "A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "heteroplasmic mitochondrial inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000650", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sex_agnostic_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000770", + "type" : "CLASS", + "lbl" : "phenotypic inheritance process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000891", + "meta" : { + "definition" : { + "val" : "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/source", + "val" : "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.\n\nFormer axiom: denotes some 'obsolete_canonical allele'" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_contextual allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000410", + "meta" : { + "definition" : { + "val" : "A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_variant_instance_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Domain = genomic feature instance\nRange = punned gene class IRI" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_genetic_variant_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000652", + "meta" : { + "definition" : { + "val" : "A relationship between a polymorphic allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_polymorphic_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000894", + "meta" : { + "definition" : { + "val" : "The starting position of a sequence feature or interval.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "start_position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000773", + "meta" : { + "definition" : { + "val" : "An attribute describing a type of variation inhering in a sequence feature or collection.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allele attribute" + } ] + }, + "type" : "CLASS", + "lbl" : "variation attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000893", + "meta" : { + "definition" : { + "val" : "A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "homoplasmic mitochondrial inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0005692", + "type" : "CLASS", + "lbl" : "abnormal(ly) absent adaxial cell" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000651", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_mutant_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000772", + "meta" : { + "definition" : { + "val" : "A sequence attribute inhering in a feature whose identity is not specified.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_unspecified" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000637", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_engineered_plasmid" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000779", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "biological sequence residue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "monomeric residue" + } ] + }, + "type" : "CLASS", + "lbl" : "biological sequence unit" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000415", + "meta" : { + "definition" : { + "val" : "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "replaced with SO:engineered_region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "extra-genomic sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reagent sequence feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000778", + "meta" : { + "definition" : { + "val" : "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "eliminating classes that are not necessary or add uneeded complexity." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence information entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000536", + "meta" : { + "definition" : { + "val" : "A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Scope of 'Genetic State': \n'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs.\n\n2. Genotype Subtypes:\nIn GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. \n\nTwo more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features.\n\n3. The Genotype Partonomy: \n'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype \"fgf8a; fgf3[AB]\", described at zfin.org/ZDB-FISH-150901-9362, include the following elements:\n\n - GVC: fgf8a; fgf3 (total intrinsic variation in the genome)\n - Genomic Background: AB (the reference against which the GVC is variant)\n - VSLC1: fgf8a (homozygous complement of gene alleles at one known variant locus)\n - VSLC2: fgf3 (heterozygous complement of gene alleles at another known variant locus)\n - Allele 1: fgf8a (variant version of the fgf8a gene, present in two copies)\n - Allele 2: fgf3 (variant version of the fgf3 gene, present in one copy)\n - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy)\n - Sequence Alteration1: (the specific mutation within the fgf8a gene that makes it variant)\n - Sequence Alteration2: (the specific mutation within the fgf3 gene that makes it variant)\n\nA graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md\n\nOne reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to \"propagate phenotypes\" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). \nNote however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above." + } ] + }, + "type" : "CLASS", + "lbl" : "genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000899", + "meta" : { + "definition" : { + "val" : "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "'Genomic Genotype' vs 'Genome' in GENO: \nA genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complete genotype" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000418", + "meta" : { + "definition" : { + "val" : "A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_affected_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000659", + "meta" : { + "definition" : { + "val" : "A set of sequence features.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus\n\n2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele.\n\n3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature).\n\nThe notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3].\n\n[1] https://www.snpedia.com/index.php/APOE-%CE%B54\n[2] https://www.snpedia.com/index.php/APOE-%CE%B52\n[3] https://www.snpedia.com/index.php/Gs270" + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature set" + }, { + "id" : "http://biohackathon.org/resource/faldo#StrandedPosition", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'." + } ] + }, + "type" : "CLASS", + "lbl" : "Stranded position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000890", + "meta" : { + "definition" : { + "val" : "One of a set of sequence features or haplotypes that exist at a particular genetic locus. ", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand.\n\nIn the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references)" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_canonical allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000885", + "meta" : { + "definition" : { + "val" : "An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement')\n\nAlt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "\"Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes.\"\nFrom https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/" + } ] + }, + "type" : "CLASS", + "lbl" : "diplotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000642", + "meta" : { + "definition" : { + "val" : "A transgene whose product is used as a selectable marker.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "selectable marker transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000524", + "meta" : { + "definition" : { + "val" : "A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment.\n\nThe 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "experimental genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "expression genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. \n\nOur rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. \n\nFinally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as:\n\n shha; shhb\n\nThis notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct." + } ] + }, + "type" : "CLASS", + "lbl" : "extrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000645", + "meta" : { + "definition" : { + "val" : "A genomic genotype where the genomic background specifies a male or female sex chromosome complement.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sex-qualified genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "intrinsic genotype (sex-specific)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances.\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nIn the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sex-qualified intrinsic genotype" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic genotype (sex-qualified)" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000887", + "type" : "CLASS", + "lbl" : "oryzias latipes strain" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000402", + "meta" : { + "definition" : { + "val" : "A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a/fgf8a)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "trans-heterozygous" + } ] + }, + "type" : "CLASS", + "lbl" : "compound heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000644", + "meta" : { + "definition" : { + "val" : "A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). \n\nA base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation)." + } ] + }, + "type" : "CLASS", + "lbl" : "karyotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000886", + "meta" : { + "definition" : { + "val" : "A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "allelic phase" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000881", + "meta" : { + "definition" : { + "val" : "Describes an allele whose origin is not known.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "unknown allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000880", + "meta" : { + "definition" : { + "val" : "Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. \n\t\t\nDe novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" + } ] + }, + "type" : "CLASS", + "lbl" : "de novo allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000883", + "meta" : { + "definition" : { + "val" : "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "replaced by GENO:0000900 ! 'germline'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "germ-line" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_gametic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000641", + "meta" : { + "definition" : { + "val" : "A relationship between a variant allele and the gene class it is an allele of.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_variant_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000882", + "meta" : { + "definition" : { + "val" : "Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells.\n\t\t\nThese acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "acquired" + } ] + }, + "type" : "CLASS", + "lbl" : "somatic allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000761", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Proposal for a property linking regulatory elements to larger features of which they are a part." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_regulatory_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000640", + "type" : "CLASS", + "lbl" : "reporter region" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_1000173", + "meta" : { + "definition" : { + "val" : "A duplication consisting of 2 identical adjacent regions.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tandem duplication" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:1000173" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "erverted" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + } ] + }, + "type" : "CLASS", + "lbl" : "tandem_duplication" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000529", + "meta" : { + "definition" : { + "val" : "A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism).\n\nThe identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "expression allele" + } ] + }, + "type" : "CLASS", + "lbl" : "expression-variant gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000408", + "meta" : { + "definition" : { + "val" : "A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_sequence_variant_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size).\n\nWhile conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like \"fgf8a is an allele of the Danio rerio fgf8a gene\", and we may create data where fgf8a is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene).\n\nIt is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. \n\nThis departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\\GAL4 gene.\n\nAt the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = allele \nRange = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that the allele is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " is_allele_of the 'danio rerio fgf8a' gene locus." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000768", + "meta" : { + "definition" : { + "val" : "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "remodeling notion of sequence feature position around the idea of a 'genomic locus'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic coordinates" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_genomic position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000647", + "meta" : { + "definition" : { + "val" : "A genomic genotype here the genomic background specifies a female sex chromosome complement.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "female intrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000889", + "meta" : { + "definition" : { + "val" : "An inheritance pattern that is not determined or not known.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unknown inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "undetermined inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000646", + "meta" : { + "definition" : { + "val" : "A genomic genotype here the genomic background specifies a male sex chromosome complement.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "male intrinsic genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000525", + "meta" : { + "definition" : { + "val" : "A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" + } ] + }, + "type" : "CLASS", + "lbl" : "effective genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000888", + "meta" : { + "definition" : { + "val" : "Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parental origin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parentally inherited" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "hereditary" + } ] + }, + "type" : "CLASS", + "lbl" : "germline allele origin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000767", + "meta" : { + "definition" : { + "val" : "A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_has_position_component" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000649", + "meta" : { + "definition" : { + "val" : "A background genotype whose sequence or identity is not known or specified.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unspecified background genotype" + } ] + }, + "type" : "CLASS", + "lbl" : "unspecified genomic background" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000528", + "meta" : { + "definition" : { + "val" : "The set of all transgenes trransiently expressed in a biological system in the context of a given experiment.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "experimental transgene complement" + } ] + }, + "type" : "CLASS", + "lbl" : "transiently-expressed transgene complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000527", + "meta" : { + "definition" : { + "val" : "A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment." + } ] + }, + "type" : "CLASS", + "lbl" : "reagent-targeted gene complement" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000783", + "meta" : { + "definition" : { + "val" : "An attribute to describe a region that was modified in vitro.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "engineered" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000086", + "type" : "CLASS", + "lbl" : "reagent role" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000681", + "meta" : { + "definition" : { + "val" : "An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "transgenic extrachromosomal replicon" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "exogenous extrachromosomal replicon" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "aberrant extrachromosomal replicon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'." + } ] + }, + "type" : "CLASS", + "lbl" : "novel extrachromosomal replicon" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000680", + "meta" : { + "definition" : { + "val" : "A genomic feature that has an extent of zero.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Former logical def: \n'genomic feature'\n and (has_extent value 0)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A junction between bases, a deletion variant, a terminus at the end of a chromosome." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_null feature" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", + "type" : "CLASS", + "lbl" : "Homo sapiens" + }, { + "id" : "http://purl.obolibrary.org/obo/MP_0000001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "where to place this depends on if we take the organismal view or the quality centric view." + } ] + }, + "type" : "CLASS", + "lbl" : "mammalian phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000678", + "meta" : { + "definition" : { + "val" : "Property linking a sequence or sequence feature to an integer representing its length in terms of the number of units in the sequence.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_extent" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000793", + "type" : "PROPERTY", + "lbl" : "inferred_to_contribute_to_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000794", + "type" : "PROPERTY", + "lbl" : "inferred_to_correlate_with_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001746", + "meta" : { + "definition" : { + "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001746" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "paternal uniparental disomy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 02:03:30 PST 2011" + } ] + }, + "type" : "CLASS", + "lbl" : "paternal_uniparental_disomy" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001745", + "meta" : { + "definition" : { + "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 02:03:01 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001745" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "maternal uniparental disomy" + } ] + }, + "type" : "CLASS", + "lbl" : "maternal_uniparental_disomy" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001505", + "meta" : { + "definition" : { + "val" : "A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'GRCh37.p10' (a human reference genome build)" + } ] + }, + "type" : "CLASS", + "lbl" : "reference genome sequence" + }, { + "id" : "http://www.ncbi.nlm.nih.gov/gene/399483", + "meta" : { + "xrefs" : [ { + "val" : "http://zfin.org/ZDB-GENE-040123-1" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000514" + } ] + }, + "type" : "CLASS", + "lbl" : "danio rerio cdkn1ca gene" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001742", + "meta" : { + "definition" : { + "val" : "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 01:54:09 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number gain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001742" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "gain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + } ] + }, + "type" : "CLASS", + "lbl" : "copy_number_gain" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001500", + "meta" : { + "definition" : { + "val" : "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "heritable_phenotypic_marker" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001744", + "meta" : { + "definition" : { + "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "uniparental disomy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "UPD" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_xref", + "val" : "http:http\\://en.wikipedia.org/wiki/Uniparental_disomy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 02:01:05 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001744" + } ] + }, + "type" : "CLASS", + "lbl" : "UPD" + }, { + "id" : "http://purl.obolibrary.org/obo/WBPhenotype_0000886", + "meta" : { + "definition" : { + "val" : "Animals exhibit variations compared to a given control.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "c. elegans phenotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "Variant" + } ] + }, + "type" : "CLASS", + "lbl" : "worm phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001743", + "meta" : { + "definition" : { + "val" : "A sequence alteration whereby the copy number of a given region is less than the reference sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001743" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Mon Feb 28 01:55:02 PST 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "loss" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "copy number loss" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + } ] + }, + "type" : "CLASS", + "lbl" : "copy_number_loss" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#Subset", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000771", + "meta" : { + "definition" : { + "val" : "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quantitative trait locus" + } ] + }, + "type" : "CLASS", + "lbl" : "QTL" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000791", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains.\n\nBelow are the different kinds/paths of propagation we desire:\n1. Propagation 'down' a genotype (from larger components to smaller ones)\n2. Propagation 'up' a genotype (from smaller components to larger ones)\n3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype).\n4. From an effective genotype to its intrinsic and extrinsic components.\n5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele).\n6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this.\n\nNote that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha/shha [AB] to shha/shha [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition')" + } ] + }, + "type" : "PROPERTY", + "lbl" : "inferred_to_cause_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000790", + "type" : "PROPERTY", + "lbl" : "related_condition" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000788", + "meta" : { + "definition" : { + "val" : "An attribute, quality, or state of a sequence feature or collection.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0000400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence feature attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000667", + "meta" : { + "definition" : { + "val" : "A transgene that codes for a product used as a reporter of gene expression or activity.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "reporter transgene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000666", + "meta" : { + "definition" : { + "val" : "A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "SO:0000831 (gene member region)" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "defined gene part" + } ] + }, + "type" : "CLASS", + "lbl" : "gene part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000661", + "meta" : { + "definition" : { + "val" : "Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is_sex_agnostic_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000782", + "type" : "CLASS", + "lbl" : "amino acid residue" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000781", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ribonucleic acid residue" + } ] + }, + "type" : "CLASS", + "lbl" : "RNA residue" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000660", + "meta" : { + "definition" : { + "val" : "A set of genomic features (i.e. sequence features that are of genomic origin).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature.\n\nThe notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic locus complement" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic feature set" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000784", + "meta" : { + "definition" : { + "val" : "A relation between two seqeunces or features that are considered variant with each other along their entire extents.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "completely_varies_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000783", + "meta" : { + "definition" : { + "val" : "A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues)", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_unit" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001410", + "meta" : { + "definition" : { + "val" : "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "not currently needed to support modeling use cases. can re-introduce if becomes necessary." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_experimental_feature" + }, { + "id" : "http://biohackathon.org/resource/faldo#location", + "type" : "PROPERTY", + "lbl" : "location" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000580", + "meta" : { + "definition" : { + "val" : "A relation used to describe a context or conditions that define and/or identify an entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_qualifying_context" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association.\n\nUsed in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_qualifier" + }, { + "id" : "http://purl.obolibrary.org/obo/HP_0000118", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "pulling in HP 'phenotypic abnormality' root here" + } ] + }, + "type" : "CLASS", + "lbl" : "human phenotypic abnormality" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000460", + "meta" : { + "definition" : { + "val" : "A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc)", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "transgene part" + }, { + "id" : "http://purl.org/oban/association_has_subject", + "type" : "PROPERTY", + "lbl" : "association has subject" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000458", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a)" + } ] + }, + "type" : "CLASS", + "lbl" : "simple heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "type" : "PROPERTY", + "lbl" : "is part of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000575", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl\nThis ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes." + } ] + }, + "type" : "CLASS", + "lbl" : "zebrafish phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000211", + "meta" : { + "definition" : { + "val" : "A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "materializes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence." + } ] + }, + "type" : "PROPERTY", + "lbl" : "bears_concretization_of" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "type" : "PROPERTY", + "lbl" : "has part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000339", + "meta" : { + "definition" : { + "val" : "A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as \"the point at which one or more contiguous nucleotides were excised\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "absent aneusomic chromosome" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "lost aneusomic chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000338", + "meta" : { + "definition" : { + "val" : "A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "duplicate chromosome" + } ] + }, + "type" : "CLASS", + "lbl" : "gained aneusomic chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000445", + "meta" : { + "definition" : { + "val" : "A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "class_to_feature_relation" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_feature_affected_by" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000324", + "meta" : { + "definition" : { + "val" : "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_chromosome complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000447", + "meta" : { + "definition" : { + "val" : "A relation between a gene class and a gene targeting reagent that targets it.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Domain = punned gene class\nRange = gene knockdown reagent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_target_of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_gene_target_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000688", + "meta" : { + "definition" : { + "val" : "A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "terminus" + }, { + "id" : "http://biohackathon.org/resource/faldo#position", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is." + } ] + }, + "type" : "PROPERTY", + "lbl" : "position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000683", + "meta" : { + "definition" : { + "val" : "A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "varies_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000443", + "meta" : { + "definition" : { + "val" : "A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = expression variant feature.\nRange = punned gene class" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_expression_variant_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000685", + "meta" : { + "definition" : { + "val" : "An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "novel" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000684", + "meta" : { + "definition" : { + "val" : "A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles." + } ] + }, + "type" : "CLASS", + "lbl" : "novel replicon" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000667", + "meta" : { + "definition" : { + "val" : "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_alt_id", + "val" : "SO:1000034" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "nucleotide_insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000667" + } ] + }, + "type" : "CLASS", + "lbl" : "insertion" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an epidemic" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a human being" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a hurricane" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a flame" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a sea wave" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a tornado" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an aggregate of human beings." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the undetached arm of a human being" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a forest fire" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an energy wave" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a puff of smoke" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a photon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "material entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000449", + "meta" : { + "definition" : { + "val" : "A relation linking a gene class to one of an expression-variant of that gene..", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Domain = punned gene class\nRange = expression variant feature" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_expression_variant_instance" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_expression_variant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000207", + "meta" : { + "definition" : { + "val" : "A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/so_has_quality" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sequence_attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000341", + "meta" : { + "definition" : { + "val" : "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "\"Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band\n" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome band" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000340", + "meta" : { + "definition" : { + "val" : "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A complete chromosome sequence." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000481", + "meta" : { + "definition" : { + "val" : "A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. \n\n2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). \n\n3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic feature" + }, { + "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10239", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies." + } ] + }, + "type" : "CLASS", + "lbl" : "Viruses" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000480", + "meta" : { + "definition" : { + "val" : "An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "mutant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000482", + "meta" : { + "definition" : { + "val" : "A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "genetic material" + }, { + "id" : "http://purl.obolibrary.org/obo/ERO_0002003", + "meta" : { + "definition" : { + "val" : "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "stem cell line" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000477", + "meta" : { + "definition" : { + "val" : "An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "polymorphic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000359", + "meta" : { + "definition" : { + "val" : "shortcut relation used to link a phenotype directly to a genotype of an organism", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "phenotype_has_genotype" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Might expand to something like:\n\nphenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype)))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_phenotype_of_organism_with_genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is_phenotype_with_genotype" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_phenotype_of_genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/CHEBI_33696", + "type" : "CLASS", + "lbl" : "nucleic acid" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000111", + "meta" : { + "definition" : { + "val" : "a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider http://semanticscience.org/resource/SIO_001062 ! human population (\"A human population refers to a collection of human beings\")." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "homo sapiens population" + } ] + }, + "type" : "CLASS", + "lbl" : "human population" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000231", + "meta" : { + "definition" : { + "val" : "An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO)", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://semanticscience.org/resource/SIO_000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "No proper part relation anymore in RO/BFO?" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_proper_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000113", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon)" + } ] + }, + "type" : "CLASS", + "lbl" : "taxonomic group" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000476", + "meta" : { + "definition" : { + "val" : "An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "variant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000112", + "meta" : { + "definition" : { + "val" : "A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "organism strain or breed" + } ] + }, + "type" : "CLASS", + "lbl" : "strain or breed" + }, { + "id" : "http://purl.obolibrary.org/obo/ERO_0002002", + "meta" : { + "definition" : { + "val" : "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "embryonic stem cell line" + }, { + "id" : "http://purl.obolibrary.org/obo/UPHENO_0001001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition)\n\n2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework." + } ] + }, + "type" : "CLASS", + "lbl" : "Phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000337", + "type" : "CLASS", + "lbl" : "RNAi_reagent" + }, { + "id" : "http://biohackathon.org/resource/faldo#begin", + "type" : "PROPERTY", + "lbl" : "begin" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000119", + "type" : "CLASS", + "lbl" : "danio rerio strain" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001785", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001785" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Fri Mar 25 02:27:41 PDT 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + } ] + }, + "type" : "CLASS", + "lbl" : "structural_alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000239", + "meta" : { + "definition" : { + "val" : "A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "VMC:state" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_sequence_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_state" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000118", + "type" : "CLASS", + "lbl" : "mus musculus strain" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000699", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A junction is a boundary between regions. A boundary has an extent of zero." + } ] + }, + "type" : "CLASS", + "lbl" : "junction" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0600043", + "meta" : { + "definition" : { + "val" : "the introduction. alteration or integration of genetic material into a cell or organism", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "genetic modification technique" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000577", + "type" : "CLASS", + "lbl" : "centromere" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001784", + "meta" : { + "definition" : { + "val" : "A structural sequence alteration where there are multiple equally plausible explanations for the change.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "DBVAR" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001784" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Wed Mar 23 03:21:19 PDT 2011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_created_by", + "val" : "kareneilbeck" + } ] + }, + "type" : "CLASS", + "lbl" : "complex_structural_alteration" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000694", + "meta" : { + "definition" : { + "val" : "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "single nucleotide polymorphism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000694" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_subset", + "val" : "SOFA" + } ] + }, + "type" : "CLASS", + "lbl" : "SNP" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000351", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of biological processes from GO-BP." + } ] + }, + "type" : "CLASS", + "lbl" : "biological process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000346", + "meta" : { + "definition" : { + "val" : "A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "complete aneusomic chromosome" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism.\n\nSimilarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication." + } ] + }, + "type" : "CLASS", + "lbl" : "aneusomic chromosome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000345", + "meta" : { + "definition" : { + "val" : "A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome.\n\nLoss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "dropped partial anneuploid chromosomal element" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "translocated absent chromosomal segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "truncated chromosome terminus" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement" + } ] + }, + "type" : "CLASS", + "lbl" : "lost aneusomic chromosomal segment" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000106", + "meta" : { + "definition" : { + "val" : "A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic material" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000220", + "type" : "PROPERTY", + "lbl" : "is_genotype_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000344", + "meta" : { + "definition" : { + "val" : "A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "translocated duplicate chromosomal segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "translocated duplicate chromosomal element" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "duplicate partial aneuploid chromosomal element" + } ] + }, + "type" : "CLASS", + "lbl" : "gained aneusomic chromosomal segment" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000222", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and some level of genetic variation present in its genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_genotype" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000343", + "meta" : { + "definition" : { + "val" : "A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "aneuploid chromosomal segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "aneusomic chromosomal subregion/segment" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Aneusomic chromosomal parts are examples of \"partial aneuploidy\" as described in http://en.wikipedia.org/wiki/Aneuploidy: \"The terms \"partial monosomy\" and \"partial trisomy\" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome.\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "partial aneusomic chromosomal element" + } ] + }, + "type" : "CLASS", + "lbl" : "aneusomic chromosomal part" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000207", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "simple sequence length polymorphism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "SSLP" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "simple sequence length variation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000207" + } ] + }, + "type" : "CLASS", + "lbl" : "simple_sequence_length_variation" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000108", + "meta" : { + "definition" : { + "val" : "A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "physical genome" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements.\n\nNote that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome." + } ] + }, + "type" : "CLASS", + "lbl" : "material genome" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mass of this piece of gold." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the length of the circumference of your waist" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of your nose" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the color of a tomato" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the ambient temperature of this portion of air" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of your nostril" + } ] + }, + "type" : "CLASS", + "lbl" : "quality" + }, { + "id" : "http://purl.org/oban/association_has_predicate", + "type" : "PROPERTY", + "lbl" : "association has predicate" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "type" : "PROPERTY", + "lbl" : "starts during" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "type" : "PROPERTY", + "lbl" : "ends during" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "meta" : { + "definition" : { + "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the life of an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the flight of a bird" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of cell-division, \\ a beating of the heart" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of sleeping" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of meiosis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "your process of aging." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the course of a disease" + } ] + }, + "type" : "CLASS", + "lbl" : "process" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an atom of element X has the disposition to decay to an atom of element Y" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the cell wall is disposed to filter chemicals in endocitosis and exocitosis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "children are innately disposed to categorize objects in certain ways." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "certain people have a predisposition to colon cancer" + } ] + }, + "type" : "CLASS", + "lbl" : "disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of your blood to coagulate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of being a doctor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of your reproductive organs" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of this piece of metal to conduct electricity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of this boundary to delineate where Utah and Colorado meet" + } ] + }, + "type" : "CLASS", + "lbl" : "realizable entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000382", + "meta" : { + "definition" : { + "val" : "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has_variant_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000140", + "type" : "CLASS", + "lbl" : "non-heritable" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000142", + "meta" : { + "definition" : { + "val" : "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000141", + "meta" : { + "definition" : { + "val" : "The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/NCIT_C45827" + }, { + "val" : "http://purl.obolibrary.org/obo/HP_0000005" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, \"genetic context\" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. \n\nThese genetic and environmental \"interactions\" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "mode of inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "phenotypic inheritance pattern" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family." + } ] + }, + "type" : "CLASS", + "lbl" : "inheritance pattern" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000383", + "type" : "PROPERTY", + "lbl" : "is_variant_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000137", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "no-call zygosity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indeterminite zygosity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unknown zygosity" + } ] + }, + "type" : "CLASS", + "lbl" : "unspecified zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000499", + "meta" : { + "definition" : { + "val" : "A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "minor allele" + } ] + }, + "type" : "CLASS", + "lbl" : "minor polymorphic allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000136", + "type" : "CLASS", + "lbl" : "homozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000139", + "type" : "CLASS", + "lbl" : "heritable" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000017", + "meta" : { + "definition" : { + "val" : "A sequence that serves as a standard against which other sequences at the same location are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference sequence" + } ] + }, + "type" : "CLASS", + "lbl" : "reference sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000138", + "meta" : { + "definition" : { + "val" : "The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells).\n\nWe can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms." + } ] + }, + "type" : "CLASS", + "lbl" : "heritabililty" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000133", + "meta" : { + "definition" : { + "val" : "An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://semanticscience.org/resource/SIO_001263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "allelic state" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "derived from https://en.wikipedia.org/wiki/Zygosity" + } ] + }, + "type" : "CLASS", + "lbl" : "zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000495", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "expression construct feature" + } ] + }, + "type" : "CLASS", + "lbl" : "expression construct" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000132", + "meta" : { + "definition" : { + "val" : "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "in trans" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000253", + "type" : "PROPERTY", + "lbl" : "obsolete_is_specified_by" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000498", + "meta" : { + "definition" : { + "val" : "A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "major allele" + } ] + }, + "type" : "CLASS", + "lbl" : "major polymorphic allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000014", + "meta" : { + "definition" : { + "val" : "A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene)", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0001023 ! allele" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The \"mn004Gt\" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome.\n\nhttp://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722\n\nhttp://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion.\n\nA genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment).\n\nThis design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not." + } ] + }, + "type" : "CLASS", + "lbl" : "gene allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000135", + "type" : "CLASS", + "lbl" : "heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000497", + "meta" : { + "definition" : { + "val" : "An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "PMID: 25741868 ACMG Guidelines" + } ] + }, + "type" : "CLASS", + "lbl" : "polymorphic allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000134", + "type" : "CLASS", + "lbl" : "hemizygous" + }, { + "id" : "http://purl.org/oban/association_has_object", + "type" : "PROPERTY", + "lbl" : "association has object" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000019", + "meta" : { + "definition" : { + "val" : "a collection more than one sequence features (ie a collection of discontinuous sequence features)", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one)" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence feature collection" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000110", + "meta" : { + "definition" : { + "val" : "Any extent of continuous biological sequence.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence_feature" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", + "meta" : { + "definition" : { + "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an atom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a heart" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the interior of your mouth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a chair" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a spatial region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a leg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an orchestra." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the bottom right portion of a human torso" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a molecule" + } ] + }, + "type" : "CLASS", + "lbl" : "independent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000492", + "meta" : { + "definition" : { + "val" : "A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "mutation" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000491", + "meta" : { + "definition" : { + "val" : "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required for any specific use case at this point so removed for simplicity. \nFormely asserted as allele and inferred as varaint allele. \nEq class definition:\nallele\n and (mutation or ('has subsequence' some mutation))" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_mutant allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000010", + "meta" : { + "definition" : { + "val" : "A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "OBI:genetic population background information" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic background" + } ] + }, + "type" : "CLASS", + "lbl" : "background genome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000131", + "meta" : { + "definition" : { + "val" : "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "in cis" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000494", + "meta" : { + "definition" : { + "val" : "A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "episomal replicon" + } ] + }, + "type" : "CLASS", + "lbl" : "extrachromosomal replicon" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000252", + "type" : "PROPERTY", + "lbl" : "is_subject_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000251", + "type" : "PROPERTY", + "lbl" : "is_sequence_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000368", + "meta" : { + "definition" : { + "val" : "A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Exploratory/temporary property, as we formalize our phenotypic inheritance model." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_participates_in_inheritance_process" + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "meta" : { + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/CARO_0000000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies." + } ] + }, + "type" : "CLASS", + "lbl" : "anatomical entity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000125", + "meta" : { + "definition" : { + "val" : "sequence attribute that can inhere only in a collection of more than one sequence features", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_sequence feature collection attribute" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000488", + "meta" : { + "definition" : { + "val" : "A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways).", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_expression_variant_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000248", + "meta" : { + "definition" : { + "val" : "An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://semanticscience.org/resource/SIO_000093" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_proper_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/CLO_0000031", + "meta" : { + "definition" : { + "val" : "A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "cell line" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000243", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_approximates_sequence" + }, { + "id" : "http://biohackathon.org/resource/faldo#Position", + "meta" : { + "definition" : { + "val" : "Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "FALDO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region)." + } ] + }, + "type" : "CLASS", + "lbl" : "Position" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000000", + "meta" : { + "definition" : { + "val" : "A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sex-agnostic intrinsic genotype" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "organismal genotype" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Example zebrafish intrinsic genotype:\n\nGenotype = fgf8a; shha (AB)\nreference component (genomic background) = AB \nvariant component ('genomic variation complement') = fgf8a; shha\n\n. . . and within this variant component, there are two 'variant single locus complements' represented:\n\nallele complement 1 = fgf8a\nallele complement 2 = shha\n\nand within each of these 'variant single locus complements' there is one or more variant gene locus member:\n\nin complement 1: fgf8a\nin complement 2: shha" + } ] + }, + "type" : "CLASS", + "lbl" : "genomic genotype (sex-agnostic)" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000242", + "meta" : { + "definition" : { + "val" : "A relationship between an information content entity representing a specification, and the entity it specifies.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A geno:intrinnsic genotype 'specifies' a SO:genome.\nA geno:karyotype 'specifies' a geno:karyotype feature collection." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_specifies" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000484", + "type" : "INDIVIDUAL", + "lbl" : "exploratory term" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000002", + "meta" : { + "definition" : { + "val" : "An allele that varies in it sequence from what is considered the reference or canonical sequence at that location.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variant feature" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another.\n\nA variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "alternate allele" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence-variant feature" + } ] + }, + "type" : "CLASS", + "lbl" : "variant allele" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000486", + "meta" : { + "definition" : { + "val" : "A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property." + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_is_variant_with" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000244", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete_resolves_to_sequence" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Julius Caesar" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Verdi’s Requiem" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the Second World War" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "your body mass index" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" + } ] + }, + "type" : "CLASS", + "lbl" : "entity" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000002", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" + } ] + }, + "type" : "CLASS", + "lbl" : "continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." + } ] + }, + "type" : "CLASS", + "lbl" : "occurrent" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000009", + "meta" : { + "definition" : { + "val" : "A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation.\n\nIn model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene))." + } ] + }, + "type" : "CLASS", + "lbl" : "genomic variation complement" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000105", + "meta" : { + "definition" : { + "val" : "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term." + } ] + }, + "type" : "CLASS", + "lbl" : "chromosome arm" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000143", + "meta" : { + "definition" : { + "val" : "A region of known length which may be used to manufacture a longer region.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "obsolete_assembly_component" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000164", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "objective is to insert some specified sequence into the genome of a cell or virus" + } ] + }, + "type" : "CLASS", + "lbl" : "genetic insertion technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000042", + "meta" : { + "definition" : { + "val" : "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "hemizygous reference junction" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction.\n\nThe junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reference junction" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000160", + "type" : "CLASS", + "lbl" : "unspecified life cycle stage" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000037", + "meta" : { + "definition" : { + "val" : "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class def: 'genomic feature'\n and (has_sequence_attribute some unspecified)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele)." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_unspecified feature" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000033", + "meta" : { + "definition" : { + "val" : "A genome that varies at one or more loci from the sequence of some reference genome.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here)" + } ] + }, + "type" : "CLASS", + "lbl" : "variant genome" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000036", + "meta" : { + "definition" : { + "val" : "An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.\n\nIn model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared." + } ] + }, + "type" : "CLASS", + "lbl" : "reference allele" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of a hammer to drive in nails" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of amylase in saliva to break down starch into sugar" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" + } ] + }, + "type" : "CLASS", + "lbl" : "function" + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions.\n\n2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity)." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class \"system\". The relation \"environed_by\" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised." + } ] + }, + "type" : "CLASS", + "lbl" : "environmental system" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000031", + "meta" : { + "definition" : { + "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." + } ] + }, + "type" : "CLASS", + "lbl" : "generically dependent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000393", + "type" : "CLASS", + "lbl" : "trisomic homozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000030", + "meta" : { + "definition" : { + "val" : "A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "variant allelic complement" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members.\n\nNote that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant." + } ] + }, + "type" : "CLASS", + "lbl" : "variant single locus complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000392", + "type" : "CLASS", + "lbl" : "aneusomic zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000150", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "duplicate term, use GENO:0000148" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_autosomal recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000394", + "type" : "CLASS", + "lbl" : "trisomic heterozygous" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000152", + "meta" : { + "definition" : { + "val" : "An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another." + } ] + }, + "type" : "CLASS", + "lbl" : "reference" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000391", + "type" : "CLASS", + "lbl" : "disomic zygosity" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000148", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "autosomal recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000147", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0000006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "vertical inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000029", + "meta" : { + "definition" : { + "val" : "A single locus complement that serves as a standard against which 'variant' sequences are compared", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference allelic complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "reference single locus feature complement" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", + "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'single locus complement'\n and (has_sequence_attribute some reference)\n\nSC axioms:\n'has member' exactly 0 'variant allele'\n'has member' only 'reference genomic feature'\n'has member' some 'reference genomic feature'" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_reference single locus complement" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000149", + "meta" : { + "definition" : { + "val" : "An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001419" + } ] + }, + "type" : "CLASS", + "lbl" : "X-linked recessive inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000144", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "pure dominant inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "complete autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000022", + "meta" : { + "definition" : { + "val" : "A sequence feature collection comprised of discontiguous sequences from a single genome", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "genomic feature collection" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system." + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete_genomic feature collection" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000143", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "co-dominant autosomal inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000385", + "meta" : { + "definition" : { + "val" : "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_reference_sequence_part" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_reference_part" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000146", + "meta" : { + "definition" : { + "val" : "An X-linked inheritance pattern wherein the trait manifests in heterozygotes.", + "xrefs" : [ ] + }, + "xrefs" : [ { + "val" : "http://purl.obolibrary.org/obo/HP_0001423" + } ] + }, + "type" : "CLASS", + "lbl" : "X-linked dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000145", + "meta" : { + "definition" : { + "val" : "An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "intermediate dominant autosomal inheritance" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "semi-dominant autosomal inheritance" + } ] + }, + "type" : "CLASS", + "lbl" : "incomplete autosomal dominant inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000387", + "type" : "PROPERTY", + "lbl" : "is_reference_part_of" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0001218", + "meta" : { + "definition" : { + "val" : "An insertion that derives from another organism, via the use of recombinant DNA technology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0001218" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "transgenic insertion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "transgenic_insertion" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000023", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a boundary to demarcate two neighboring administrative territories" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a stone in marking a property boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a building in serving as a military target" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of subject in a clinical trial" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the priest role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the student role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." + } ] + }, + "type" : "CLASS", + "lbl" : "role" + }, { + "id" : "http://purl.obolibrary.org/obo/ZP_0000755", + "type" : "CLASS", + "lbl" : "abnormal(ly) disrupted diencephalon development" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000020", + "meta" : { + "definition" : { + "val" : "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "of one-sided specifically dependent continuants: the mass of this tomato" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of being a doctor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of this fish to decay" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the pink color of a medium rare piece of grilled filet mignon at its center" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the smell of this portion of mozzarella" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of this heart: to pump blood" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of this hole." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mutual dependence of proton donors and acceptors in chemical reactions [79" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" + } ] + }, + "type" : "CLASS", + "lbl" : "specifically dependent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/SO_0000248", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_id", + "val" : "SO:0000248" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "sequence length variation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/so.owl" + } ] + }, + "type" : "CLASS", + "lbl" : 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"http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000481", + "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000903", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000902" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000777", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000899" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000219", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000033" + } ] + } ], + "domainRangeAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002200", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002201", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000251", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" + } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000368", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000141" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000610", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000036" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000653", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000501" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000359", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000641", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000652", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000497" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000651", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000491" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000959", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000903", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000815" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000958", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000408", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000481" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000608", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000516" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000133" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000966", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000815" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000239", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000726", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000957", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GENO_0000815" ] + } ], + "propertyChainAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000449", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000639", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/GENO_0000639" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000418", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/GENO_0000418" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000211", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000053", "http://purl.obolibrary.org/obo/RO_0000059" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000449", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000445", "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000418", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000418" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000445", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000413", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000661", "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/RO_0003303" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000740", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000382", "http://purl.obolibrary.org/obo/GENO_0000743" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000742", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000383", "http://purl.obolibrary.org/obo/GENO_0000408" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000791", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/GENO_0000445", "http://purl.obolibrary.org/obo/RO_0003303" ] + } ] + } ] +} \ No newline at end of file diff --git a/geno.obo b/geno.obo new file mode 100644 index 0000000..6225fe0 --- /dev/null +++ b/geno.obo @@ -0,0 +1,4218 @@ +format-version: 1.2 +data-version: releases/2019-09-09 +ontology: geno +property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string +property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string +property_value: http://purl.org/dc/terms/license "Unspecified" xsd:string + +[Term] +id: BFO:0000001 +name: entity +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +is_a: BFO:0000001 ! entity +property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] +is_a: BFO:0000002 ! continuant +property_value: IAO:0000112 "a chair" xsd:string +property_value: IAO:0000112 "a heart" xsd:string +property_value: IAO:0000112 "a leg" xsd:string +property_value: IAO:0000112 "a molecule" xsd:string +property_value: IAO:0000112 "a spatial region" xsd:string +property_value: IAO:0000112 "an atom" xsd:string +property_value: IAO:0000112 "an orchestra." xsd:string +property_value: IAO:0000112 "an organism" xsd:string +property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string +property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] +is_a: BFO:0000003 ! occurrent +property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string +property_value: IAO:0000112 "a process of meiosis" xsd:string +property_value: IAO:0000112 "a process of sleeping" xsd:string +property_value: IAO:0000112 "the course of a disease" xsd:string +property_value: IAO:0000112 "the flight of a bird" xsd:string +property_value: IAO:0000112 "the life of an organism" xsd:string +property_value: IAO:0000112 "your process of aging." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role +property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string +property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string +property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string +property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocitosis and exocitosis" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89" xsd:string +property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000017 +name: realizable entity +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality +property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string +property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string +property_value: IAO:0000112 "the function of your reproductive organs" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string +property_value: IAO:0000112 "the color of a tomato" xsd:string +property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string +property_value: IAO:0000112 "the mass of this piece of gold." xsd:string +property_value: IAO:0000112 "the shape of your nose" xsd:string +property_value: IAO:0000112 "the shape of your nostril" xsd:string +property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] +is_a: BFO:0000002 ! continuant +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string +property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000023 +name: role +is_a: BFO:0000017 ! realizable entity +property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string +property_value: IAO:0000112 "the priest role" xsd:string +property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string +property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string +property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string +property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string +property_value: IAO:0000112 "the student role" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string +property_value: IAO:0000600 "b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] +is_a: BFO:0000002 ! continuant +property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition +property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string +property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string +property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string +property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +is_a: BFO:0000004 ! independent continuant +property_value: IAO:0000112 "a flame" xsd:string +property_value: IAO:0000112 "a forest fire" xsd:string +property_value: IAO:0000112 "a human being" xsd:string +property_value: IAO:0000112 "a hurricane" xsd:string +property_value: IAO:0000112 "a photon" xsd:string +property_value: IAO:0000112 "a puff of smoke" xsd:string +property_value: IAO:0000112 "a sea wave" xsd:string +property_value: IAO:0000112 "a tornado" xsd:string +property_value: IAO:0000112 "an aggregate of human beings." xsd:string +property_value: IAO:0000112 "an energy wave" xsd:string +property_value: IAO:0000112 "an epidemic" xsd:string +property_value: IAO:0000112 "the undetached arm of a human being" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BothStrandsPosition +name: Both strands +is_a: StrandedPosition ! Stranded position + +[Term] +id: CHEBI:23367 +name: molecular entity +is_a: BFO:0000040 ! material entity +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology." xsd:string + +[Term] +id: CHEBI:33696 +name: nucleic acid +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CL:0000000 +name: cell +comment: Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies. +is_a: UBERON:0001062 ! anatomical entity + +[Term] +id: CLO:0000031 +name: cell line +def: "A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture)." [] +is_a: GENO:0000904 ! organismal entity +relationship: RO:0001000 OBI:0100026 ! derives from organism + +[Term] +id: DbXref +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Definition +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: ENVO:01000254 +name: environmental system +comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. +is_a: BFO:0000040 ! material entity +property_value: IAO:0000116 "1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions.\n\n2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity)." xsd:string + +[Term] +id: ERO:0000007 +name: technique +def: "A technique is a planned process used to accomplish a specific activity or task." [] +is_a: OBI:0000011 ! planned process + +[Term] +id: ERO:0002002 +name: embryonic stem cell line +def: "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo." [] +is_a: ERO:0002003 ! stem cell line + +[Term] +id: ERO:0002003 +name: stem cell line +def: "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types." [] +is_a: CLO:0000031 ! cell line + +[Term] +id: ExactPosition +name: Exact position +def: "A position that is exactly known." [] +is_a: Position ! Position + +[Term] +id: ForwardStrandPosition +name: Positive strand +is_a: StrandedPosition ! Stranded position + +[Term] +id: GENO:0000000 +name: genomic genotype (sex-agnostic) +def: "A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement)" [] +comment: In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances). +is_a: GENO:0000899 ! genomic genotype +property_value: IAO:0000112 "Example zebrafish intrinsic genotype:\n\nGenotype = fgf8a; shha (AB)\nreference component (genomic background) = AB \nvariant component ('genomic variation complement') = fgf8a; shha\n\n. . . and within this variant component, there are two 'variant single locus complements' represented:\n\nallele complement 1 = fgf8a\nallele complement 2 = shha\n\nand within each of these 'variant single locus complements' there is one or more variant gene locus member:\n\nin complement 1: fgf8a\nin complement 2: shha" xsd:string +property_value: IAO:0000116 "This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype." xsd:string +property_value: IAO:0000118 "genotype" xsd:string +property_value: IAO:0000118 "organismal genotype" xsd:string +property_value: IAO:0000118 "sex-agnostic intrinsic genotype" xsd:string + +[Term] +id: GENO:0000002 +name: variant allele +def: "An allele that varies in it sequence from what is considered the reference or canonical sequence at that location." [] +comment: Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another.\n\nA variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence. +is_a: GENO:0000512 ! allele +intersection_of: GENO:0000512 ! allele +intersection_of: GENO:0000683 GENO:0000036 ! varies_with reference allele +relationship: GENO:0000683 GENO:0000036 ! varies_with reference allele +property_value: IAO:0000116 "The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles." xsd:string +property_value: IAO:0000118 "alternate allele" xsd:string +property_value: IAO:0000118 "sequence-variant feature" xsd:string +property_value: IAO:0000118 "variant feature" xsd:string + +[Term] +id: GENO:0000009 +name: genomic variation complement +def: "A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation.\n\nIn model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)). +is_a: GENO:0000660 ! genomic feature set +intersection_of: GENO:0000660 ! genomic feature set +intersection_of: GENO:0000382 GENO:0000030 ! has_variant_part variant single locus complement +relationship: GENO:0000382 GENO:0000030 ! has_variant_part variant single locus complement +property_value: IAO:0000116 "Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases." xsd:string + +[Term] +id: GENO:0000010 +name: background genome +def: "A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations)." [] +xref: OBI:genetic population background information +is_a: GENO:0000914 ! reference genome +property_value: IAO:0000112 "The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB)" xsd:string +property_value: IAO:0000116 "Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it." xsd:string +property_value: IAO:0000118 "genomic background" xsd:string + +[Term] +id: GENO:0000014 +name: gene allele +def: "A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene)" [] +comment: In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion.\n\nA genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene. +xref: http://purl.obolibrary.org/obo/SO_0001023 ! allele +is_a: GENO:0000512 ! allele +relationship: GENO:0000408 SO:0000704 ! is_allele_of gene +property_value: IAO:0000112 "The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The \"mn004Gt\" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome.\n\nhttp://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722\n\nhttp://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8" xsd:string +property_value: IAO:0000116 "Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment).\n\nThis design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not." xsd:string + +[Term] +id: GENO:0000017 +name: reference sequence +def: "A sequence that serves as a standard against which other sequences at the same location are compared." [] +comment: A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence. +is_a: GENO:0000702 ! biological sequence +intersection_of: GENO:0000702 ! biological sequence +intersection_of: RO:0000087 GENO:0000152 ! has_role reference +relationship: RO:0000087 GENO:0000152 ! has_role reference +property_value: IAO:0000116 "The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant." xsd:string +property_value: IAO:0000118 "reference sequence" xsd:string + +[Term] +id: GENO:0000019 +name: obsolete_sequence feature collection +def: "a collection more than one sequence features (ie a collection of discontinuous sequence features)" [] +comment: 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. +xref: perhaps not same as SO:sequence collection\, as here we explicitly include features that can have an extent of zero (and SO\:sequence collection is a collection of regions that have an extent of at least one) +is_a: ObsoleteClass + +[Term] +id: GENO:0000022 +name: obsolete_genomic feature collection +def: "A sequence feature collection comprised of discontiguous sequences from a single genome" [] +comment: Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. +is_a: ObsoleteClass +property_value: IAO:0000116 "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system." xsd:string +property_value: IAO:0000118 "genomic feature collection" xsd:string + +[Term] +id: GENO:0000029 +name: obsolete_reference single locus complement +def: "A single locus complement that serves as a standard against which 'variant' sequences are compared" [] +is_a: ObsoleteClass +property_value: IAO:0000118 "reference allelic complement" xsd:string +property_value: IAO:0000118 "reference single locus feature complement" xsd:string +property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'single locus complement'\n and (has_sequence_attribute some reference)\n\nSC axioms:\n'has member' exactly 0 'variant allele'\n'has member' only 'reference genomic feature'\n'has member' some 'reference genomic feature'" xsd:string + +[Term] +id: GENO:0000030 +name: variant single locus complement +def: "A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13)." [] +comment: Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members.\n\nNote that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant. +is_a: GENO:0000516 ! single locus complement +intersection_of: GENO:0000516 ! single locus complement +intersection_of: GENO:0000382 GENO:0000002 ! has_variant_part variant allele +relationship: GENO:0000382 GENO:0000002 ! has_variant_part variant allele +property_value: IAO:0000118 "variant allelic complement" xsd:string + +[Term] +id: GENO:0000033 +name: variant genome +def: "A genome that varies at one or more loci from the sequence of some reference genome." [] +xref: http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here) +is_a: SO:0001026 ! genome +intersection_of: SO:0001026 ! genome +intersection_of: GENO:0000683 GENO:0000914 ! varies_with reference genome +relationship: GENO:0000382 SO:0001059 ! has_variant_part sequence_alteration +relationship: GENO:0000683 GENO:0000914 ! varies_with reference genome + +[Term] +id: GENO:0000036 +name: reference allele +def: "An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome." [] +comment: Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.\n\nIn model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared. +is_a: GENO:0000512 ! allele +intersection_of: GENO:0000512 ! allele +intersection_of: RO:0000087 GENO:0000152 ! has_role reference +relationship: RO:0000087 GENO:0000152 ! has_role reference + +[Term] +id: GENO:0000037 +name: obsolete_unspecified feature +def: "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus)." [] +comment: An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). +is_a: ObsoleteClass +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '." xsd:string +property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class def: 'genomic feature'\n and (has_sequence_attribute some unspecified)" xsd:string + +[Term] +id: GENO:0000042 +name: obsolete_reference junction +def: "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature." [] +comment: In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction.\n\nThe junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. +is_a: ObsoleteClass +property_value: IAO:0000118 "hemizygous reference junction" xsd:string +property_value: IAO:0000231 "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" xsd:string + +[Term] +id: GENO:0000047 +name: danio rerio gene +def: "A gene that originates from the genome of a danio rerio." [] +is_a: SO:0000704 ! gene +intersection_of: SO:0000704 ! gene +intersection_of: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio +relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio + +[Term] +id: GENO:0000054 +name: homo sapiens gene +def: "A gene that originates from the genome of a homo sapiens." [] +is_a: SO:0000704 ! gene +intersection_of: SO:0000704 ! gene +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens + +[Term] +id: GENO:0000057 +name: mus musculus gene +def: "A gene that originates from the genome of a mus musculus." [] +is_a: SO:0000704 ! gene +intersection_of: SO:0000704 ! gene +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus + +[Term] +id: GENO:0000060 +name: obsolete_reference gene allele +def: "A version/allele of a gene that serves as a standard against which variant genes are compared." [] +comment: Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. +is_a: ObsoleteClass +property_value: IAO:0000112 "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development.\nhttp://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690\n\nNote that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469" xsd:string +property_value: IAO:0000118 "reference gene" xsd:string +property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" xsd:string + +[Term] +id: GENO:0000091 +name: obsolete_experimental insertion +is_a: ObsoleteClass + +[Term] +id: GENO:0000092 +name: gene trap insertion +is_a: SO:0000667 ! insertion +relationship: RO:0002353 GENO:0000172 ! output of gene trapping technique + +[Term] +id: GENO:0000093 +name: integrated transgene +def: "A transgene that has been integrated into a chrromosome in the host genome." [] +comment: An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion.\n\nAn 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome. +is_a: SO:0000902 ! transgene +relationship: BFO:0000050 SO:0001218 ! is part of transgenic_insertion + +[Term] +id: GENO:0000106 +name: genomic material +def: "A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny." [] +comment: 1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms. +is_a: GENO:0000482 ! genetic material +relationship: BFO:0000050 GENO:0000108 ! is part of material genome +relationship: RO:0000091 GENO:0000139 ! has disposition heritable +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way." xsd:string + +[Term] +id: GENO:0000108 +name: material genome +def: "A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion." [] +comment: A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements.\n\nNote that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome. +is_a: BFO:0000040 ! material entity +property_value: IAO:0000118 "physical genome" xsd:string + +[Term] +id: GENO:0000111 +name: human population +def: "a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)" [] +is_a: OBI:0000181 ! population +property_value: IAO:0000116 "Consider http://semanticscience.org/resource/SIO_001062 ! human population (\"A human population refers to a collection of human beings\")." xsd:string +property_value: IAO:0000118 "homo sapiens population" xsd:string + +[Term] +id: GENO:0000112 +name: strain or breed +def: "A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical." [] +comment: Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR) +is_a: GENO:0000113 ! taxonomic group +relationship: RO:0002162 OBI:0100026 ! in taxon organism +property_value: IAO:0000118 "organism strain or breed" xsd:string + +[Term] +id: GENO:0000113 +name: taxonomic group +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000116 "A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon)" xsd:string + +[Term] +id: GENO:0000118 +name: mus musculus strain +is_a: GENO:0000112 ! strain or breed + +[Term] +id: GENO:0000119 +name: danio rerio strain +is_a: GENO:0000112 ! strain or breed +relationship: RO:0002351 NCBITaxon:7955 ! has member Danio rerio +relationship: RO:0002351 NCBITaxon:7955 ! has member Danio rerio + +[Term] +id: GENO:0000125 +name: obsolete_sequence feature collection attribute +def: "sequence attribute that can inhere only in a collection of more than one sequence features" [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000131 +name: in cis +def: "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes)." [] +is_a: GENO:0000886 ! allelic phase + +[Term] +id: GENO:0000132 +name: in trans +def: "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes)." [] +is_a: GENO:0000886 ! allelic phase + +[Term] +id: GENO:0000133 +name: zygosity +def: "An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different)." [] +xref: http://semanticscience.org/resource/SIO_001263 +is_a: GENO:0000875 ! allelic state +relationship: RO:0000052 GENO:0000516 ! inheres_in single locus complement +property_value: IAO:0000118 "allelic state" xsd:string +property_value: IAO:0000119 "derived from https://en.wikipedia.org/wiki/Zygosity" xsd:string + +[Term] +id: GENO:0000134 +name: hemizygous +is_a: GENO:0000391 ! disomic zygosity + +[Term] +id: GENO:0000135 +name: heterozygous +is_a: GENO:0000391 ! disomic zygosity + +[Term] +id: GENO:0000136 +name: homozygous +is_a: GENO:0000391 ! disomic zygosity + +[Term] +id: GENO:0000137 +name: unspecified zygosity +is_a: GENO:0000133 ! zygosity +property_value: IAO:0000118 "indeterminite zygosity" xsd:string {comment="MGI uses this term when zygosity is not known."} +property_value: IAO:0000118 "no-call zygosity" xsd:string {comment="(this is how the GVF10 format/standard refers to loci without enough data to make an accurate call . . . see http://www.sequenceontology.org/resources/gvf.html#quick_gvf_examples)"} +property_value: IAO:0000118 "unknown zygosity" xsd:string + +[Term] +id: GENO:0000138 +name: heritabililty +def: "The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event." [] +comment: We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells).\n\nWe can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms. +is_a: BFO:0000016 ! disposition + +[Term] +id: GENO:0000139 +name: heritable +is_a: GENO:0000138 ! heritabililty + +[Term] +id: GENO:0000140 +name: non-heritable +is_a: GENO:0000138 ! heritabililty + +[Term] +id: GENO:0000141 +name: inheritance pattern +def: "The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment." [] +comment: An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, "genetic context" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. \n\nThese genetic and environmental "interactions" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y. +xref: http://purl.obolibrary.org/obo/HP_0000005 +xref: http://purl.obolibrary.org/obo/NCIT_C45827 +is_a: BFO:0000016 ! disposition +property_value: IAO:0000116 "The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family." xsd:string +property_value: IAO:0000118 "mode of inheritance" xsd:string +property_value: IAO:0000118 "phenotypic inheritance pattern" xsd:string + +[Term] +id: GENO:0000142 +name: obsolete_dominant inheritance +def: "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes" [] +is_a: ObsoleteClass +property_value: IAO:0000231 "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." xsd:string + +[Term] +id: GENO:0000143 +name: co-dominant autosomal inheritance +def: "An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." [] +is_a: GENO:0000147 ! autosomal dominant inheritance + +[Term] +id: GENO:0000144 +name: complete autosomal dominant inheritance +def: "An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." [] +is_a: GENO:0000147 ! autosomal dominant inheritance +property_value: IAO:0000118 "pure dominant inheritance" xsd:string + +[Term] +id: GENO:0000145 +name: incomplete autosomal dominant inheritance +def: "An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." [] +is_a: GENO:0000147 ! autosomal dominant inheritance +property_value: IAO:0000118 "intermediate dominant autosomal inheritance" xsd:string +property_value: IAO:0000118 "semi-dominant autosomal inheritance" xsd:string + +[Term] +id: GENO:0000146 +name: X-linked dominant inheritance +def: "An X-linked inheritance pattern wherein the trait manifests in heterozygotes." [] +xref: http://purl.obolibrary.org/obo/HP_0001423 +is_a: GENO:0000936 ! X-linked inheritance + +[Term] +id: GENO:0000147 +name: autosomal dominant inheritance +def: "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes." [] +xref: http://purl.obolibrary.org/obo/HP_0000006 +is_a: GENO:0000934 ! autosomal inheritance +property_value: IAO:0000118 "vertical inheritance" xsd:string + +[Term] +id: GENO:0000148 +name: autosomal recessive inheritance +def: "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals." [] +is_a: GENO:0000934 ! autosomal inheritance + +[Term] +id: GENO:0000149 +name: X-linked recessive inheritance +def: "An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals." [] +xref: http://purl.obolibrary.org/obo/HP_0001419 +is_a: GENO:0000936 ! X-linked inheritance + +[Term] +id: GENO:0000150 +name: obsolete_autosomal recessive inheritance +is_a: ObsoleteClass +property_value: IAO:0000231 "duplicate term, use GENO:0000148" xsd:string + +[Term] +id: GENO:0000152 +name: reference +def: "An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared." [] +comment: Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another. +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000160 +name: unspecified life cycle stage +is_a: UBERON:0000105 ! life cycle stage + +[Term] +id: GENO:0000164 +name: genetic insertion technique +comment: objective is to insert some specified sequence into the genome of a cell or virus +is_a: OBI:0600043 ! genetic modification technique + +[Term] +id: GENO:0000165 +name: mutagen treatment technique +is_a: OBI:0600043 ! genetic modification technique + +[Term] +id: GENO:0000166 +name: targeted gene mutation technique +def: "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping)." [] +comment: This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. +is_a: OBI:0600043 ! genetic modification technique +relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele + +[Term] +id: GENO:0000169 +name: random genetic insertion technique +comment: Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. +is_a: GENO:0000164 ! genetic insertion technique + +[Term] +id: GENO:0000170 +name: targeted genetic insertion technique +is_a: GENO:0000164 ! genetic insertion technique +relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele + +[Term] +id: GENO:0000171 +name: enhancer trapping technique +is_a: GENO:0000170 ! targeted genetic insertion technique + +[Term] +id: GENO:0000172 +name: gene trapping technique +is_a: GENO:0000170 ! targeted genetic insertion technique + +[Term] +id: GENO:0000173 +name: promoter trapping technique +is_a: GENO:0000170 ! targeted genetic insertion technique + +[Term] +id: GENO:0000174 +name: targeted knock-in technique +is_a: GENO:0000170 ! targeted genetic insertion technique + +[Term] +id: GENO:0000175 +name: random transgene insertion technique +is_a: GENO:0000169 ! random genetic insertion technique + +[Term] +id: GENO:0000324 +name: obsolete_chromosome complement +def: "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome" [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000338 +name: gained aneusomic chromosome +def: "A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation" [] +comment: This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome. +is_a: GENO:0000346 ! aneusomic chromosome +relationship: GENO:0000207 GENO:0000685 ! has_sequence_attribute novel +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "duplicate chromosome" xsd:string + +[Term] +id: GENO:0000339 +name: lost aneusomic chromosome +def: "A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation." [] +is_a: GENO:0000346 ! aneusomic chromosome +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as \"the point at which one or more contiguous nucleotides were excised\"." xsd:string +property_value: IAO:0000118 "absent aneusomic chromosome" xsd:string + +[Term] +id: GENO:0000343 +name: aneusomic chromosomal part +def: "A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation." [] +comment: Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome." +is_a: SO:0000830 ! chromosome part +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000207 GENO:0000513 ! has_sequence_attribute aneusomic +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism." xsd:string +property_value: IAO:0000118 "aneuploid chromosomal segment" xsd:string +property_value: IAO:0000118 "aneusomic chromosomal subregion/segment" xsd:string +property_value: IAO:0000118 "partial aneusomic chromosomal element" xsd:string + +[Term] +id: GENO:0000344 +name: gained aneusomic chromosomal segment +def: "A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event." [] +comment: Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location. +is_a: GENO:0000343 ! aneusomic chromosomal part +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "duplicate partial aneuploid chromosomal element" xsd:string +property_value: IAO:0000118 "translocated duplicate chromosomal element" xsd:string +property_value: IAO:0000118 "translocated duplicate chromosomal segment" xsd:string + +[Term] +id: GENO:0000345 +name: lost aneusomic chromosomal segment +def: "A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome." [] +comment: This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome.\n\nLoss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus. +is_a: GENO:0000343 ! aneusomic chromosomal part +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement" xsd:string +property_value: IAO:0000118 "dropped partial anneuploid chromosomal element" xsd:string +property_value: IAO:0000118 "translocated absent chromosomal segment" xsd:string +property_value: IAO:0000118 "truncated chromosome terminus" xsd:string + +[Term] +id: GENO:0000346 +name: aneusomic chromosome +def: "A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation" [] +comment: Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism.\n\nSimilarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication. +is_a: SO:0000340 ! chromosome +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000207 GENO:0000513 ! has_sequence_attribute aneusomic +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "complete aneusomic chromosome" xsd:string + +[Term] +id: GENO:0000351 +name: biological process +is_a: BFO:0000015 ! process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of biological processes from GO-BP." xsd:string + +[Term] +id: GENO:0000391 +name: disomic zygosity +is_a: GENO:0000133 ! zygosity + +[Term] +id: GENO:0000392 +name: aneusomic zygosity +is_a: GENO:0000133 ! zygosity + +[Term] +id: GENO:0000393 +name: trisomic homozygous +is_a: GENO:0000392 ! aneusomic zygosity + +[Term] +id: GENO:0000394 +name: trisomic heterozygous +is_a: GENO:0000392 ! aneusomic zygosity + +[Term] +id: GENO:0000402 +name: compound heterozygous +def: "A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a/fgf8a)" [] +is_a: GENO:0000135 ! heterozygous +property_value: IAO:0000118 "trans-heterozygous" xsd:string + +[Term] +id: GENO:0000415 +name: obsolete_reagent sequence feature +def: "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)" [] +is_a: ObsoleteClass +property_value: IAO:0000116 "replaced with SO:engineered_region" xsd:string +property_value: IAO:0000118 "extra-genomic sequence" xsd:string + +[Term] +id: GENO:0000458 +name: simple heterozygous +comment: a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a) +is_a: GENO:0000135 ! heterozygous + +[Term] +id: GENO:0000460 +name: transgene part +def: "A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc)" [] +is_a: GENO:0000666 ! gene part +intersection_of: GENO:0000666 ! gene part +intersection_of: RO:0002525 SO:0000902 ! is subsequence of transgene +relationship: RO:0002525 SO:0000902 ! is subsequence of transgene + +[Term] +id: GENO:0000476 +name: variant +def: "An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level" [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000477 +name: polymorphic +def: "An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000480 +name: mutant +def: "An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000481 +name: genomic feature +def: "A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)" [] +comment: 1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. \n\n2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). \n\n3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome. +is_a: GENO:0000897 ! genomic entity +is_a: SO:0000110 ! sequence_feature +intersection_of: SO:0000110 ! sequence_feature +intersection_of: GENO:0000903 GENO:0000902 ! has_location genomic feature location +relationship: BFO:0000050 SO:0001026 ! is part of genome +relationship: GENO:0000239 GENO:0000960 ! has_sequence genomic sequence +relationship: GENO:0000903 GENO:0000902 ! has_location genomic feature location +property_value: IAO:0000116 "This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology." xsd:string + +[Term] +id: GENO:0000482 +name: genetic material +def: "A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion)." [] +comment: This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material. +is_a: CHEBI:33696 ! nucleic acid +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000491 +name: obsolete_mutant allele +def: "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain." [] +comment: 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. +is_a: ObsoleteClass +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000119 "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" xsd:string +property_value: IAO:0000231 "Not required for any specific use case at this point so removed for simplicity. \nFormely asserted as allele and inferred as varaint allele. \nEq class definition:\nallele\n and (mutation or ('has subsequence' some mutation))" xsd:string + +[Term] +id: GENO:0000492 +name: mutation +def: "A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain." [] +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000683 GENO:0000501 ! varies_with wild-type allele + +[Term] +id: GENO:0000494 +name: extrachromosomal replicon +def: "A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon)" [] +is_a: GENO:0000481 ! genomic feature +relationship: GENO:0000207 GENO:0000139 ! has_sequence_attribute heritable +property_value: IAO:0000116 "Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element" xsd:string +property_value: IAO:0000118 "episomal replicon" xsd:string +property_value: IAO:0000231 "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'." xsd:string + +[Term] +id: GENO:0000495 +name: expression construct +is_a: GENO:0000856 ! engineered genetic construct +property_value: IAO:0000118 "expression construct feature" xsd:string + +[Term] +id: GENO:0000497 +name: polymorphic allele +def: "An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population." [] +comment: Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%). +is_a: GENO:0000512 ! allele +property_value: IAO:0000119 "PMID: 25741868 ACMG Guidelines" xsd:string + +[Term] +id: GENO:0000498 +name: major polymorphic allele +def: "A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location." [] +is_a: GENO:0000497 ! polymorphic allele +property_value: IAO:0000118 "major allele" xsd:string + +[Term] +id: GENO:0000499 +name: minor polymorphic allele +def: "A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location)." [] +is_a: GENO:0000497 ! polymorphic allele +property_value: IAO:0000118 "minor allele" xsd:string + +[Term] +id: GENO:0000500 +name: ancestral polymorphic allele +def: "A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree." [] +is_a: GENO:0000497 ! polymorphic allele +property_value: IAO:0000118 "ancestral allele" xsd:string + +[Term] +id: GENO:0000501 +name: wild-type allele +def: "An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared." [] +comment: 'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain.\n\nThe notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis. +is_a: GENO:0000512 ! allele +property_value: IAO:0000118 "wild-type allele" xsd:string + +[Term] +id: GENO:0000502 +name: wild-type gene +comment: A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation. +is_a: GENO:0000501 ! wild-type allele +is_a: SO:0000704 ! gene +property_value: IAO:0000118 "wild-type gene allele" xsd:string + +[Term] +id: GENO:0000504 +name: reagent targeted gene +def: "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." [] +comment: The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position. +is_a: GENO:0000529 ! expression-variant gene +relationship: GENO:0000231 GENO:0000534 ! has_proper_part reagent-targeted gene subregion +relationship: GENO:0000447 GENO:0000533 ! is_gene_target_of gene knockdown reagent + +[Term] +id: GENO:0000506 +name: transiently-expressed transgene +def: "A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome)." [] +is_a: GENO:0000529 ! expression-variant gene +property_value: IAO:0000118 "experimentally-expressed transgene" xsd:string +property_value: IAO:0000118 "extrinsic transgene" xsd:string + +[Term] +id: GENO:0000511 +name: wild-type +def: "An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000512 +name: allele +def: "One of a set of sequence features known to exist at a particular genomic location." [] +comment: An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations).\n\nAlleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence). +is_a: GENO:0000481 ! genomic feature +intersection_of: GENO:0000481 ! genomic feature +intersection_of: GENO:0000683 GENO:0000481 ! varies_with genomic feature +relationship: GENO:0000683 GENO:0000481 ! varies_with genomic feature +property_value: IAO:0000116 "A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene.\n\nTo be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene.\n \n[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17)\n[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17)\n[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17)\n[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17)\n[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17)\n[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17)\n[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483\n[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17)\n[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17)\n[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17)\n[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17)\n[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)" xsd:string +property_value: IAO:0000118 "variable feature" xsd:string + +[Term] +id: GENO:0000513 +name: aneusomic +def: "a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation." [] +is_a: GENO:0000773 ! variation attribute +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000515 +name: variant gene allele +def: "An allele of a gene that contains some sequence alteration." [] +comment: A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset. +is_a: GENO:0000002 ! variant allele +is_a: GENO:0000014 ! gene allele +intersection_of: GENO:0000014 ! gene allele +intersection_of: GENO:0000683 GENO:0000036 ! varies_with reference allele +relationship: GENO:0000382 SO:0001059 ! has_variant_part sequence_alteration +relationship: GENO:0000641 SO:0000704 ! is_variant_allele_of gene + +[Term] +id: GENO:0000516 +name: single locus complement +def: "A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes.\n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. +is_a: GENO:0000660 ! genomic feature set +property_value: IAO:0000112 "The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a.\n\nThe collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome." xsd:string +property_value: IAO:0000116 "TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label." xsd:string +property_value: IAO:0000118 "allelic complement" xsd:string +property_value: IAO:0000118 "homologous allele complement" xsd:string +property_value: IAO:0000118 "single locus feature complement" xsd:string + +[Term] +id: GENO:0000524 +name: extrinsic genotype +def: "A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state." [] +comment: An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment.\n\nThe 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations. +is_a: GENO:0000536 ! genotype +property_value: IAO:0000112 "In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as:\n\n shha; shhb\n\nThis notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct." xsd:string +property_value: IAO:0000116 "We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. \n\nOur rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. \n\nFinally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" xsd:string +property_value: IAO:0000118 "experimental genotype" xsd:string +property_value: IAO:0000118 "expression genotype" xsd:string + +[Term] +id: GENO:0000525 +name: effective genotype +def: "A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs)." [] +comment: An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment. +is_a: GENO:0000536 ! genotype +relationship: BFO:0000051 GENO:0000524 ! has part extrinsic genotype +relationship: BFO:0000051 GENO:0000719 ! has part intrinsic genotype +property_value: IAO:0000116 "Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" xsd:string + +[Term] +id: GENO:0000527 +name: reagent-targeted gene complement +def: "A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes)." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment. +is_a: GENO:0000715 ! qualified genomic feature set +relationship: RO:0002351 GENO:0000504 ! has member reagent targeted gene + +[Term] +id: GENO:0000528 +name: transiently-expressed transgene complement +def: "The set of all transgenes trransiently expressed in a biological system in the context of a given experiment." [] +is_a: GENO:0000715 ! qualified genomic feature set +relationship: GENO:0000382 GENO:0000506 ! has_variant_part transiently-expressed transgene +property_value: IAO:0000118 "experimental transgene complement" xsd:string + +[Term] +id: GENO:0000529 +name: expression-variant gene +def: "A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism)." [] +comment: Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism).\n\nThe identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system. +is_a: GENO:0000737 ! expression-qualified sequence feature +relationship: GENO:0000443 SO:0000704 ! is_expression_variant_of gene +property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes)." xsd:string +property_value: IAO:0000116 "See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself." xsd:string +property_value: IAO:0000118 "expression allele" xsd:string + +[Term] +id: GENO:0000533 +name: gene knockdown reagent +is_a: SO:0000804 ! engineered_region +property_value: IAO:0000118 "gene targeting reagent" xsd:string +property_value: IAO:0000118 "sequence targeting reagent" xsd:string + +[Term] +id: GENO:0000534 +name: reagent-targeted gene subregion +def: "A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent." [] +is_a: GENO:0000737 ! expression-qualified sequence feature +property_value: IAO:0000118 "targeted gene segment" xsd:string + +[Term] +id: GENO:0000536 +name: genotype +def: "A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference." [] +comment: 1. Scope of 'Genetic State': \n'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs.\n\n2. Genotype Subtypes:\nIn GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. \n\nTwo more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features.\n\n3. The Genotype Partonomy: \n'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a; fgf3[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements:\n\n - GVC: fgf8a; fgf3 (total intrinsic variation in the genome)\n - Genomic Background: AB (the reference against which the GVC is variant)\n - VSLC1: fgf8a (homozygous complement of gene alleles at one known variant locus)\n - VSLC2: fgf3 (heterozygous complement of gene alleles at another known variant locus)\n - Allele 1: fgf8a (variant version of the fgf8a gene, present in two copies)\n - Allele 2: fgf3 (variant version of the fgf3 gene, present in one copy)\n - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy)\n - Sequence Alteration1: (the specific mutation within the fgf8a gene that makes it variant)\n - Sequence Alteration2: (the specific mutation within the fgf3 gene that makes it variant)\n\nA graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md\n\nOne reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data. +is_a: IAO:0000030 ! information content entity +property_value: IAO:0000116 "As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above." xsd:string +property_value: IAO:0000119 "Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). \nNote however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO." xsd:string + +[Term] +id: GENO:0000575 +name: zebrafish phenotype +comment: ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl\nThis ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes. +is_a: UPHENO:0001001 ! Phenotype + +[Term] +id: GENO:0000602 +name: homoplasmic +def: "an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism." [] +is_a: GENO:0000918 ! organellar plasmy + +[Term] +id: GENO:0000603 +name: heteroplasmic +def: "an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism." [] +is_a: GENO:0000918 ! organellar plasmy + +[Term] +id: GENO:0000604 +name: hemizygous X-linked +is_a: GENO:0000134 ! hemizygous + +[Term] +id: GENO:0000605 +name: hemizygous Y-linked +is_a: GENO:0000134 ! hemizygous + +[Term] +id: GENO:0000606 +name: hemizygous insertion-linked +is_a: GENO:0000134 ! hemizygous + +[Term] +id: GENO:0000611 +name: genomic background +def: "A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations)." [] +is_a: GENO:0000899 ! genomic genotype +intersection_of: GENO:0000899 ! genomic genotype +intersection_of: RO:0000087 GENO:0000152 ! has_role reference +relationship: IAO:0000219 GENO:0000010 ! denotes background genome +relationship: RO:0000087 GENO:0000152 ! has_role reference +property_value: IAO:0000116 "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it." xsd:string +property_value: IAO:0000118 "background genotype" xsd:string + +[Term] +id: GENO:0000614 +name: chromosomal region +def: "An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band." [] +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 SO:0000105 ! is part of chromosome arm +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000116 "New term request for SO." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string + +[Term] +id: GENO:0000616 +name: chromosome sub-band +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 SO:0000341 ! is part of chromosome band +relationship: GENO:0000207 GENO:0000618 ! has_sequence_attribute chromosomal band intensity +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string + +[Term] +id: GENO:0000618 +name: chromosomal band intensity +is_a: GENO:0000788 ! sequence feature attribute +property_value: IAO:0000118 "chromosomal band brightness" xsd:string + +[Term] +id: GENO:0000619 +name: gpos +is_a: GENO:0000618 ! chromosomal band intensity + +[Term] +id: GENO:0000620 +name: gneg +is_a: GENO:0000618 ! chromosomal band intensity + +[Term] +id: GENO:0000621 +name: gvar +is_a: GENO:0000618 ! chromosomal band intensity + +[Term] +id: GENO:0000622 +name: gpos100 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000623 +name: gpos75 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000624 +name: gpos50 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000625 +name: gpos25 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000628 +name: short chromosome arm +def: "A chromosome arm that is the shorter of the two arms of a given chromosome." [] +is_a: SO:0000105 ! chromosome arm +property_value: IAO:0000118 "p-arm" xsd:string +property_value: IAO:0000118 "stalk" xsd:string + +[Term] +id: GENO:0000629 +name: long chromosome arm +def: "A chromosome arm that is the longer of the two arms of a given chromosome." [] +is_a: SO:0000105 ! chromosome arm +property_value: IAO:0000118 "q-arm" xsd:string + +[Term] +id: GENO:0000632 +name: gpos66 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000633 +name: gpos33 +is_a: GENO:0000619 ! gpos + +[Term] +id: GENO:0000637 +name: regulatory transgene region +def: "A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed." [] +is_a: GENO:0000460 ! transgene part +is_a: SO:0005836 ! regulatory_region + +[Term] +id: GENO:0000638 +name: expressed transgene region +def: "A transgene part whose sequence is expressed in a gene product through transcription and/or translation." [] +is_a: GENO:0000460 ! transgene part +property_value: IAO:0000118 "coding transgene feature" xsd:string + +[Term] +id: GENO:0000640 +name: reporter region +is_a: GENO:0000638 ! expressed transgene region + +[Term] +id: GENO:0000642 +name: selectable marker transgene +def: "A transgene whose product is used as a selectable marker." [] +is_a: SO:0000804 ! engineered_region +is_a: SO:0000902 ! transgene +intersection_of: SO:0000902 ! transgene +intersection_of: RO:0000087 GENO:0000911 ! has_role selectable marker role +relationship: RO:0000087 GENO:0000911 ! has_role selectable marker role + +[Term] +id: GENO:0000644 +name: karyotype +def: "A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell." [] +comment: Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). \n\nA base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation). +is_a: GENO:0000899 ! genomic genotype +property_value: IAO:0000119 "Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28)" xsd:string + +[Term] +id: GENO:0000645 +name: genomic genotype (sex-qualified) +def: "A genomic genotype where the genomic background specifies a male or female sex chromosome complement." [] +comment: We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances.\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. +is_a: GENO:0000899 ! genomic genotype +relationship: GENO:0000650 GENO:0000000 ! has_sex_agnostic_part genomic genotype (sex-agnostic) +property_value: IAO:0000116 "This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nIn the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former." xsd:string +property_value: IAO:0000118 "intrinsic genotype (sex-specific)" xsd:string +property_value: IAO:0000118 "sex-qualified genotype" xsd:string +property_value: IAO:0000118 "sex-qualified intrinsic genotype" xsd:string + +[Term] +id: GENO:0000646 +name: male intrinsic genotype +def: "A genomic genotype here the genomic background specifies a male sex chromosome complement." [] +is_a: GENO:0000645 ! genomic genotype (sex-qualified) + +[Term] +id: GENO:0000647 +name: female intrinsic genotype +def: "A genomic genotype here the genomic background specifies a female sex chromosome complement." [] +is_a: GENO:0000645 ! genomic genotype (sex-qualified) + +[Term] +id: GENO:0000649 +name: unspecified genomic background +def: "A background genotype whose sequence or identity is not known or specified." [] +is_a: GENO:0000611 ! genomic background +property_value: IAO:0000118 "unspecified background genotype" xsd:string + +[Term] +id: GENO:0000659 +name: sequence feature set +def: "A set of sequence features." [] +comment: 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature).\n\nThe notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles \{rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3].\n\n[1] https://www.snpedia.com/index.php/APOE-%CE%B54\n[2] https://www.snpedia.com/index.php/APOE-%CE%B52\n[3] https://www.snpedia.com/index.php/Gs270 +is_a: GENO:0000701 ! sequence feature or set +relationship: RO:0002351 SO:0000110 ! has member sequence_feature +property_value: IAO:0000112 "1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus\n\n2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele.\n\n3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y}" xsd:string + +[Term] +id: GENO:0000660 +name: genomic feature set +def: "A set of genomic features (i.e. sequence features that are of genomic origin)." [] +comment: A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature.\n\nThe notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. +is_a: GENO:0000659 ! sequence feature set +is_a: GENO:0000897 ! genomic entity +relationship: RO:0002351 GENO:0000481 ! has member genomic feature +property_value: IAO:0000116 "In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member." xsd:string +property_value: IAO:0000118 "genomic locus complement" xsd:string + +[Term] +id: GENO:0000666 +name: gene part +def: "A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc)." [] +xref: SO:0000831 (gene member region) +is_a: GENO:0000481 ! genomic feature +intersection_of: GENO:0000481 ! genomic feature +intersection_of: RO:0002525 GENO:0000014 ! is subsequence of gene allele +relationship: RO:0002525 GENO:0000014 ! is subsequence of gene allele +property_value: IAO:0000118 "defined gene part" xsd:string + +[Term] +id: GENO:0000667 +name: reporter transgene +def: "A transgene that codes for a product used as a reporter of gene expression or activity." [] +is_a: SO:0000804 ! engineered_region +is_a: SO:0000902 ! transgene +intersection_of: SO:0000902 ! transgene +intersection_of: RO:0000087 GENO:0000910 ! has_role reporter role +relationship: BFO:0000051 GENO:0000640 ! has part reporter region +relationship: RO:0000087 GENO:0000910 ! has_role reporter role + +[Term] +id: GENO:0000680 +name: obsolete_null feature +def: "A genomic feature that has an extent of zero." [] +is_a: ObsoleteClass +property_value: IAO:0000112 "A junction between bases, a deletion variant, a terminus at the end of a chromosome." xsd:string +property_value: IAO:0000116 "Former logical def: \n'genomic feature'\n and (has_extent value 0)" xsd:string + +[Term] +id: GENO:0000681 +name: novel extrachromosomal replicon +def: "An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found." [] +comment: Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. +is_a: GENO:0000494 ! extrachromosomal replicon +is_a: GENO:0000684 ! novel replicon +property_value: IAO:0000118 "aberrant extrachromosomal replicon" xsd:string +property_value: IAO:0000118 "exogenous extrachromosomal replicon" xsd:string +property_value: IAO:0000118 "transgenic extrachromosomal replicon" xsd:string + +[Term] +id: GENO:0000684 +name: novel replicon +def: "A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome." [] +comment: Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles. +is_a: SO:0001059 ! sequence_alteration +relationship: GENO:0000207 GENO:0000685 ! has_sequence_attribute novel +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature." xsd:string + +[Term] +id: GENO:0000685 +name: novel +def: "An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome." [] +is_a: GENO:0000773 ! variation attribute + +[Term] +id: GENO:0000688 +name: terminus +def: "A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide)." [] +is_a: SO:0000110 ! sequence_feature + +[Term] +id: GENO:0000701 +name: sequence feature or set +def: "A sequence feature or a set of such features." [] +comment: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location. +is_a: BFO:0000031 ! generically dependent continuant +union_of: GENO:0000701 ! sequence feature or set +union_of: SO:0000110 ! sequence_feature +property_value: IAO:0000118 "sequence feature or collection" xsd:string + +[Term] +id: GENO:0000702 +name: biological sequence +def: "A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides)." [] +comment: 'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome. +xref: VMC:State +is_a: GENO:0000921 ! biological sequence or set +disjoint_from: GENO:0000815 ! sequence feature location +disjoint_from: SO:0000110 ! sequence_feature +property_value: IAO:0000116 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." xsd:string +property_value: IAO:0000118 "biomacromolecular sequence" xsd:string +property_value: IAO:0000118 "state" xsd:string {http://purl.obolibrary.org/obo/IAO_0000116="In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele."} + +[Term] +id: GENO:0000713 +name: qualified sequence feature or collection +def: "A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification." [] +is_a: BFO:0000031 ! generically dependent continuant + +[Term] +id: GENO:0000714 +name: qualified genomic feature +def: "A qualified sequence feature that carries sequence derived from the genome of a cell or organism." [] +is_a: GENO:0000897 ! genomic entity +is_a: GENO:0000919 ! qualified sequence feature +relationship: GENO:0000726 GENO:0000481 {http://purl.obolibrary.org/obo/GENO_0000834="true", comment="Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position)."} ! has_sequence_feature genomic feature +property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." xsd:string + +[Term] +id: GENO:0000715 +name: qualified genomic feature set +def: "A set of qualified sequence features that carry genomic sequence." [] +comment: A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles \{rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele.\n\nA complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome. +is_a: GENO:0000897 ! genomic entity +is_a: GENO:0000920 ! qualified sequence feature set +relationship: GENO:0000726 GENO:0000660 ! has_sequence_feature genomic feature set +relationship: RO:0002351 GENO:0000714 ! has member qualified genomic feature +property_value: IAO:0000116 "Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member." xsd:string + +[Term] +id: GENO:0000719 +name: intrinsic genotype +def: "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype." [] +comment: 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. +is_a: GENO:0000536 ! genotype +property_value: IAO:0000116 "Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome." xsd:string + +[Term] +id: GENO:0000720 +name: DNA sequence +is_a: GENO:0000702 ! biological sequence +intersection_of: GENO:0000702 ! biological sequence +intersection_of: GENO:0000783 GENO:0000780 ! has_sequence_unit DNA residue +intersection_of: GENO:0000783 GENO:0000780 {all_only="true"} ! has_sequence_unit DNA residue +relationship: GENO:0000783 GENO:0000780 ! has_sequence_unit DNA residue + +[Term] +id: GENO:0000721 +name: RNA sequence +is_a: GENO:0000702 ! biological sequence +intersection_of: GENO:0000702 ! biological sequence +intersection_of: GENO:0000783 GENO:0000781 ! has_sequence_unit RNA residue +intersection_of: GENO:0000783 GENO:0000781 {all_only="true"} ! has_sequence_unit RNA residue +relationship: GENO:0000783 GENO:0000781 ! has_sequence_unit RNA residue + +[Term] +id: GENO:0000722 +name: amino acid sequence +is_a: GENO:0000702 ! biological sequence +intersection_of: GENO:0000702 ! biological sequence +intersection_of: GENO:0000783 GENO:0000782 ! has_sequence_unit amino acid residue +intersection_of: GENO:0000783 GENO:0000782 {all_only="true"} ! has_sequence_unit amino acid residue +relationship: GENO:0000783 GENO:0000782 ! has_sequence_unit amino acid residue + +[Term] +id: GENO:0000724 +name: obsolete_biological sequence or collection +is_a: ObsoleteClass + +[Term] +id: GENO:0000725 +name: obsolete_biological sequence collection +is_a: GENO:0000724 ! obsolete_biological sequence or collection + +[Term] +id: GENO:0000736 +name: location-qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature." [] +comment: As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell). +is_a: GENO:0000714 ! qualified genomic feature +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000737 +name: expression-qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct)" [] +is_a: GENO:0000714 ! qualified genomic feature + +[Term] +id: GENO:0000768 +name: obsolete_genomic position +def: "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence." [] +is_a: ObsoleteClass +property_value: IAO:0000116 "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature." xsd:string +property_value: IAO:0000118 "genomic coordinates" xsd:string +property_value: IAO:0000231 "remodeling notion of sequence feature position around the idea of a 'genomic locus'" xsd:string + +[Term] +id: GENO:0000770 +name: phenotypic inheritance process +is_a: GENO:0000351 ! biological process + +[Term] +id: GENO:0000772 +name: obsolete_unspecified +def: "A sequence attribute inhering in a feature whose identity is not specified." [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000773 +name: variation attribute +def: "An attribute describing a type of variation inhering in a sequence feature or collection." [] +is_a: GENO:0000788 ! sequence feature attribute +property_value: IAO:0000118 "allele attribute" xsd:string + +[Term] +id: GENO:0000777 +name: variant genomic genotype +def: "An intrinsic genotype that specifies variation from a defined reference genome." [] +is_a: GENO:0000899 ! genomic genotype +intersection_of: GENO:0000899 ! genomic genotype +intersection_of: IAO:0000219 GENO:0000033 ! denotes variant genome +relationship: IAO:0000219 GENO:0000033 ! denotes variant genome + +[Term] +id: GENO:0000778 +name: obsolete_sequence information entity +def: "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities." [] +is_a: ObsoleteClass +property_value: IAO:0000231 "eliminating classes that are not necessary or add uneeded complexity." xsd:string + +[Term] +id: GENO:0000779 +name: biological sequence unit +is_a: GENO:0000702 ! biological sequence +property_value: IAO:0000118 "biological sequence residue" xsd:string +property_value: IAO:0000118 "monomeric residue" xsd:string + +[Term] +id: GENO:0000780 +name: DNA residue +is_a: GENO:0000779 ! biological sequence unit +property_value: IAO:0000118 "deoxyribonucleic acid residue" xsd:string + +[Term] +id: GENO:0000781 +name: RNA residue +is_a: GENO:0000779 ! biological sequence unit +property_value: IAO:0000118 "ribonucleic acid residue" xsd:string + +[Term] +id: GENO:0000782 +name: amino acid residue +is_a: GENO:0000779 ! biological sequence unit + +[Term] +id: GENO:0000788 +name: sequence feature attribute +def: "An attribute, quality, or state of a sequence feature or collection." [] +comment: Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity. +xref: http://purl.obolibrary.org/obo/SO_0000400 +is_a: BFO:0000020 ! specifically dependent continuant + +[Term] +id: GENO:0000815 +name: sequence feature location +def: "The location of a sequence feature as defined by its start and end position on some reference coordinate system." [] +comment: 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms).\n\n2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there. +is_a: BFO:0000031 ! generically dependent continuant +disjoint_from: SO:0000110 ! sequence_feature + +[Term] +id: GENO:0000818 +name: modification-qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature)" [] +is_a: GENO:0000714 ! qualified genomic feature +property_value: IAO:0000114 GENO:0000484 + +[Term] +id: GENO:0000823 +name: allelic genotype +def: "A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes." [] +comment: An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location.\n\nThis contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background. +is_a: GENO:0000719 ! intrinsic genotype +is_a: GENO:0000897 ! genomic entity +intersection_of: GENO:0000719 ! intrinsic genotype +intersection_of: IAO:0000219 GENO:0000516 ! denotes single locus complement +relationship: IAO:0000219 GENO:0000516 ! denotes single locus complement +property_value: IAO:0000112 "1. The zebrafish \"fgf8a/fgf8a<+>\" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state).\n\n2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308.\n\n ##fileformat=VCFv4.2\n ##FORMAT=\n #CHROM POS REF ALT FILTER FORMAT SAMP001\n 20 2300608 C T PASS GT 0/1 \n 20 2301308 T G PASS GT 1/1\n (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html)\n\n3. Some allelic genotype formats encode the genotype as a single string - e.g. \"GRCh38 Chr12:258635(A;T)\" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12." xsd:string +property_value: IAO:0000118 "single locus genotype" xsd:string + +[Term] +id: GENO:0000833 +name: genotype-phenotype association +is_a: http://purl.org/oban/association ! association +relationship: GENO:0000580 ENVO:01000254 {http://purl.obolibrary.org/obo/GENO_0000834="true"} ! has_qualifier environmental system +relationship: http://purl.org/oban/association_has_object UPHENO:0001001 {http://purl.obolibrary.org/obo/GENO_0000834="true"} ! Phenotype +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000116 "Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each." xsd:string + +[Term] +id: GENO:0000839 +name: knockdown reagent targeted gene complement +is_a: GENO:0000527 ! reagent-targeted gene complement +relationship: GENO:0000382 GENO:0000504 ! has_variant_part reagent targeted gene + +[Term] +id: GENO:0000848 +name: obsolete_coding sequence alteration +def: "A sequence alteration within the coding sequence of a gene." [] +is_a: ObsoleteClass +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000231 "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." xsd:string + +[Term] +id: GENO:0000850 +name: P-element construct +def: "A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: GENO:0000856 +name: engineered genetic construct +def: "An engineered region that is used to transfer foreign genetic material into a host cell." [] +comment: Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. \n\nConstructs are typically packaged as part of delivery systems such as plasmids or viral vectors. +is_a: SO:0000804 ! engineered_region +property_value: IAO:0000118 "engineered_genetic_vector" xsd:string + +[Term] +id: GENO:0000861 +name: extra-chromosomal transgene +def: "A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct." [] +is_a: SO:0000902 ! transgene +property_value: IAO:0000118 "non-integrated transgene" xsd:string + +[Term] +id: GENO:0000870 +name: obsolete_sequence feature collection +def: "A collection of more than one sequence feature." [] +xref: http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection +is_a: ObsoleteClass + +[Term] +id: GENO:0000871 +name: haplotype +def: "A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block." [] +comment: A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. \n\nAs highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\n1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \n\n2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). "Star alleles" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/).\n\n3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. \n\nEach of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. +is_a: GENO:0000660 ! genomic feature set +relationship: RO:0002351 GENO:0000512 ! has member allele +property_value: http://purl.org/dc/terms/source "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype." xsd:string +property_value: IAO:0000116 "Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block.\n\nInstead, we can create an 'allele set' class as the haplotype parent?" xsd:string + +[Term] +id: GENO:0000872 +name: genomic sequence set +def: "A set of genomic sequences (a biological sequence that is of genomic origin)." [] +comment: A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. +is_a: GENO:0000922 ! biological sequence set +property_value: IAO:0000118 "copy number complement" xsd:string + +[Term] +id: GENO:0000873 +name: microsatellite alteration +def: "A relation used to describe an environment contextualizing the identity of an entity." [] +is_a: GENO:0000874 ! repeat region alteration + +[Term] +id: GENO:0000874 +name: repeat region alteration +def: "A relation used to describe a process contextualizing the identity of an entity." [] +is_a: SO:0001059 ! sequence_alteration + +[Term] +id: GENO:0000875 +name: allelic state +def: "A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism" [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: GENO:0000876 +name: obsolete_genetic dosage +comment: Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. +is_a: ObsoleteClass +property_value: IAO:0000118 "allelic dosage" xsd:string +property_value: IAO:0000118 "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome." xsd:string +property_value: IAO:0000118 "gene dosage" xsd:string +property_value: IAO:0000231 "Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute." xsd:string + +[Term] +id: GENO:0000877 +name: allele origin +def: "A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent." [] +is_a: GENO:0000788 ! sequence feature attribute +property_value: IAO:0000118 "genetic origin" xsd:string +property_value: IAO:0000118 "variant origin" xsd:string + +[Term] +id: GENO:0000878 +name: maternal allele origin +def: "Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg." [] +is_a: GENO:0000888 ! germline allele origin +property_value: IAO:0000118 "maternally inherited" xsd:string + +[Term] +id: GENO:0000879 +name: paternal allele origin +def: "Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm." [] +is_a: GENO:0000888 ! germline allele origin +property_value: IAO:0000118 "paternally inherited" xsd:string + +[Term] +id: GENO:0000880 +name: de novo allele origin +def: "Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis." [] +comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. \n \nDe novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder. +is_a: GENO:0000877 ! allele origin +property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string + +[Term] +id: GENO:0000881 +name: unknown allele origin +def: "Describes an allele whose origin is not known." [] +is_a: GENO:0000877 ! allele origin + +[Term] +id: GENO:0000882 +name: somatic allele origin +def: "Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body." [] +comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells.\n \nThese acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations. +is_a: GENO:0000877 ! allele origin +property_value: IAO:0000118 "acquired" xsd:string +property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string + +[Term] +id: GENO:0000883 +name: obsolete_gametic +def: "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells)." [] +is_a: ObsoleteClass +property_value: IAO:0000118 "germ-line" xsd:string +property_value: IAO:0000231 "replaced by GENO:0000900 ! 'germline'" xsd:string + +[Term] +id: GENO:0000885 +name: diplotype +def: "An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement')\n\nAlt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome." [] +comment: "Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes."\nFrom https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/ +is_a: GENO:0000823 ! allelic genotype + +[Term] +id: GENO:0000886 +name: allelic phase +def: "A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes." [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: GENO:0000887 +name: oryzias latipes strain +is_a: GENO:0000112 ! strain or breed +relationship: RO:0002351 NCBITaxon:8090 ! has member Oryzias latipes +relationship: RO:0002351 NCBITaxon:8090 ! has member Oryzias latipes + +[Term] +id: GENO:0000888 +name: germline allele origin +def: "Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg)." [] +comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells. +is_a: GENO:0000877 ! allele origin +property_value: IAO:0000118 "hereditary" xsd:string +property_value: IAO:0000118 "parental origin" xsd:string +property_value: IAO:0000118 "parentally inherited" xsd:string +property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string + +[Term] +id: GENO:0000889 +name: undetermined inheritance +def: "An inheritance pattern that is not determined or not known." [] +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000118 "unknown inheritance" xsd:string + +[Term] +id: GENO:0000890 +name: obsolete_canonical allele +def: "One of a set of sequence features or haplotypes that exist at a particular genetic locus. " [] +comment: As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand.\n\nIn the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) +is_a: ObsoleteClass +property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string +property_value: IAO:0000112 "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." xsd:string +property_value: IAO:0000116 "The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string +property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/ xsd:string +property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs." xsd:string + +[Term] +id: GENO:0000891 +name: obsolete_contextual allele +def: "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence." [] +comment: The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. +is_a: ObsoleteClass +property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string +property_value: IAO:0000116 "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string +property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ xsd:string +property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.\n\nFormer axiom: denotes some 'obsolete_canonical allele'" xsd:string + +[Term] +id: GENO:0000892 +name: heteroplasmic mitochondrial inheritance +def: "A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not." [] +is_a: GENO:0000949 ! mitochondrial inheritance + +[Term] +id: GENO:0000893 +name: homoplasmic mitochondrial inheritance +def: "A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited." [] +is_a: GENO:0000949 ! mitochondrial inheritance + +[Term] +id: GENO:0000897 +name: genomic entity +def: "An generically dependent continuant that carries biological sequence that is part of or derived from a genome." [] +is_a: BFO:0000031 ! generically dependent continuant +relationship: RO:0002162 OBI:0100026 ! in taxon organism +property_value: GENO:0000905 "true" xsd:boolean +property_value: IAO:0000116 "An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities." xsd:string + +[Term] +id: GENO:0000898 +name: haplotype block +def: "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations." [] +comment: A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000116 "Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as \n\"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.\" Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location.\n\nCurrent definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele." xsd:string +property_value: IAO:0000119 "Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424." xsd:string + +[Term] +id: GENO:0000899 +name: genomic genotype +def: "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype." [] +comment: 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. +is_a: GENO:0000719 ! intrinsic genotype +is_a: GENO:0000897 ! genomic entity +intersection_of: GENO:0000719 ! intrinsic genotype +intersection_of: IAO:0000219 SO:0001026 ! denotes genome +relationship: GENO:0000385 GENO:0000611 ! has_reference_part genomic background +relationship: IAO:0000219 SO:0001026 ! denotes genome +property_value: IAO:0000116 "'Genomic Genotype' vs 'Genome' in GENO: \nA genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome." xsd:string +property_value: IAO:0000118 "complete genotype" xsd:string + +[Term] +id: GENO:0000901 +name: obsolete_allele cellular context +def: "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)" [] +comment: Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. +is_a: ObsoleteClass +property_value: IAO:0000231 "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin" xsd:string + +[Term] +id: GENO:0000902 +name: genomic feature location +def: "The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system" [] +comment: 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. \n \n2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus.\n\n3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there. +xref: VMC:Location +is_a: GENO:0000815 ! sequence feature location +property_value: IAO:0000116 "In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future.\n\nWe don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences." xsd:string +property_value: IAO:0000116 "In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed.\n\nFor example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus)." xsd:string +property_value: IAO:0000118 "genomic location" xsd:string +property_value: IAO:0000118 "genomic locus" xsd:string + +[Term] +id: GENO:0000904 +name: organismal entity +def: "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc)." [] +is_a: BFO:0000040 ! material entity +property_value: GENO:0000905 "true" xsd:boolean +property_value: IAO:0000116 "useful organizational term to collect entities that have genomes/genotypes." xsd:string + +[Term] +id: GENO:0000907 +name: gene product +def: "The molecular product resulting from transcription of a single gene (either a protein or RNA molecule)" [] +is_a: SO:0000110 ! sequence_feature + +[Term] +id: GENO:0000910 +name: reporter role +is_a: OBI:0000086 ! reagent role + +[Term] +id: GENO:0000911 +name: selectable marker role +is_a: OBI:0000086 ! reagent role + +[Term] +id: GENO:0000912 +name: selectable marker region +is_a: GENO:0000638 ! expressed transgene region + +[Term] +id: GENO:0000914 +name: reference genome +def: "A genome whose sequence is identical to that of a genome sequence considered to be the reference." [] +is_a: SO:0001026 ! genome +relationship: GENO:0000239 SO:0001505 ! has_sequence reference genome sequence + +[Term] +id: GENO:0000915 +name: obsolete_haplotype +def: "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it." [] +comment: 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. +is_a: ObsoleteClass +property_value: IAO:0000116 "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"" xsd:string +property_value: IAO:0000119 "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype." xsd:string +property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" xsd:string + +[Term] +id: GENO:0000916 +name: obsolete_haplotype block +def: "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations." [] +comment: A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.\n\nThe boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.\n\n-----------------------\n\n* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. +is_a: ObsoleteClass +property_value: IAO:0000119 "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." xsd:string +property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets." xsd:string + +[Term] +id: GENO:0000918 +name: organellar plasmy +def: "An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell." [] +comment: Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene. +is_a: GENO:0000875 ! allelic state + +[Term] +id: GENO:0000919 +name: qualified sequence feature +def: "A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification." [] +comment: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). +comment: Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes. +is_a: GENO:0000713 ! qualified sequence feature or collection +property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." xsd:string + +[Term] +id: GENO:0000920 +name: qualified sequence feature set +def: "A set of qualified seqeunce features." [] +comment: 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'. +is_a: GENO:0000713 ! qualified sequence feature or collection +relationship: BFO:0000051 GENO:0000919 ! has part qualified sequence feature +relationship: GENO:0000726 GENO:0000659 ! has_sequence_feature sequence feature set + +[Term] +id: GENO:0000921 +name: biological sequence or set +def: "A biolocical sequence, or set of such sequences." [] +is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000118 "biological sequence or collection" xsd:string + +[Term] +id: GENO:0000922 +name: biological sequence set +def: "A set of biological sequences." [] +comment: 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. \n\nA set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence. +is_a: GENO:0000921 ! biological sequence or set + +[Term] +id: GENO:0000923 +name: obsolete_functional copy number complement +def: "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome." [] +comment: As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). +comment: The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. +is_a: ObsoleteClass +property_value: IAO:0000116 "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"" xsd:string +property_value: IAO:0000118 "functional feature complement" xsd:string +property_value: IAO:0000118 "genetic dosage" xsd:string +property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." xsd:string + +[Term] +id: GENO:0000924 +name: obsolete_intrinsic sequence feature attribute +def: "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form." [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000925 +name: obsolete_extrinsic sequence feature attribute +def: "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)" [] +is_a: ObsoleteClass + +[Term] +id: GENO:0000926 +name: allelic cellular distribution +def: "A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism)." [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: GENO:0000927 +name: constitutional +def: "A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin." [] +is_a: GENO:0000926 ! allelic cellular distribution + +[Term] +id: GENO:0000928 +name: clonal +def: "A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin." [] +is_a: GENO:0000926 ! allelic cellular distribution + +[Term] +id: GENO:0000929 +name: multifactorial inheritance +def: "An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors." [] +comment: Diseases inherited in this manner are termed 'complex diseases'. +xref: http://purl.obolibrary.org/obo/HP_0001426 +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000118 "complex inherritance" xsd:string +property_value: IAO:0000118 "multi-factorial inheritance" xsd:string +property_value: IAO:0000118 "multi-genic inheritance" xsd:string +property_value: IAO:0000118 "multi-locus inheritance" xsd:string +property_value: IAO:0000118 "multigenic inheritance" xsd:string + +[Term] +id: GENO:0000930 +name: digenic inheritance +def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes." [] +xref: http://purl.obolibrary.org/obo/HP_0010984 +is_a: GENO:0000929 ! multifactorial inheritance + +[Term] +id: GENO:0000931 +name: oligogenic inheritance +def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes." [] +comment: It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform. +xref: http://purl.obolibrary.org/obo/HP_0010983 +is_a: GENO:0000929 ! multifactorial inheritance + +[Term] +id: GENO:0000932 +name: polygenic inheritance +def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes." [] +comment: Typically used for traits/conditions governed by more than three gene loci. +xref: http://purl.obolibrary.org/obo/HP_0010982 +is_a: GENO:0000929 ! multifactorial inheritance + +[Term] +id: GENO:0000933 +name: monogenic inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors." [] +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000118 "single-gene inheritance" xsd:string + +[Term] +id: GENO:0000934 +name: autosomal inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome." [] +is_a: GENO:0000933 ! monogenic inheritance + +[Term] +id: GENO:0000935 +name: allosomal inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome." [] +xref: http://purl.obolibrary.org/obo/HP_0010985 +is_a: GENO:0000933 ! monogenic inheritance +property_value: IAO:0000118 "gonosomal inheritance" xsd:string + +[Term] +id: GENO:0000936 +name: X-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome." [] +xref: http://purl.obolibrary.org/obo/HP_0001417 +is_a: GENO:0000935 ! allosomal inheritance + +[Term] +id: GENO:0000937 +name: complete X-linked dominant inheritance +def: "An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." [] +is_a: GENO:0000146 ! X-linked dominant inheritance + +[Term] +id: GENO:0000938 +name: incomplete X-linked dominant inheritance +def: "An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." [] +is_a: GENO:0000146 ! X-linked dominant inheritance +property_value: IAO:0000118 "semi-dominant X-linked inheritance" xsd:string + +[Term] +id: GENO:0000939 +name: co-dominant X-linked inheritance +def: "An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." [] +is_a: GENO:0000146 ! X-linked dominant inheritance + +[Term] +id: GENO:0000941 +name: Y-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome." [] +xref: http://purl.obolibrary.org/obo/HP_0001450 +is_a: GENO:0000935 ! allosomal inheritance +property_value: IAO:0000118 "holandric inheritance" xsd:string + +[Term] +id: GENO:0000942 +name: Z-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome." [] +is_a: GENO:0000935 ! allosomal inheritance + +[Term] +id: GENO:0000943 +name: Z-linked dominant inheritance +def: "A Z-linked inheritance pattern wherein the trait manifests in heterozygotes." [] +is_a: GENO:0000942 ! Z-linked inheritance + +[Term] +id: GENO:0000944 +name: complete Z-linked dominant inheritance +def: "A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." [] +is_a: GENO:0000943 ! Z-linked dominant inheritance + +[Term] +id: GENO:0000945 +name: incomplete Z-linked dominant inheritance +def: "A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." [] +is_a: GENO:0000943 ! Z-linked dominant inheritance +property_value: IAO:0000118 "semi-dominant Z-linked inheritance" xsd:string + +[Term] +id: GENO:0000946 +name: co-dominant Z-linked inheritance +def: "An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." [] +is_a: GENO:0000943 ! Z-linked dominant inheritance + +[Term] +id: GENO:0000947 +name: Z-linked reccessive inheritance +def: "A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals." [] +is_a: GENO:0000942 ! Z-linked inheritance + +[Term] +id: GENO:0000948 +name: W-linked inheritance +def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome." [] +is_a: GENO:0000935 ! allosomal inheritance + +[Term] +id: GENO:0000949 +name: mitochondrial inheritance +def: "An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome." [] +comment: Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy). +xref: http://purl.obolibrary.org/obo/HP_0001427 +is_a: GENO:0000141 ! inheritance pattern + +[Term] +id: GENO:0000952 +name: sex-limited autosomal dominant inheritance +def: "An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females)." [] +xref: http://purl.obolibrary.org/obo/HP_0001470 +is_a: GENO:0000147 ! autosomal dominant inheritance + +[Term] +id: GENO:0000953 +name: sex-limited autosomal recessive inheritance +def: "An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females)." [] +xref: http://purl.obolibrary.org/obo/HP_0031362 +is_a: GENO:0000148 ! autosomal recessive inheritance + +[Term] +id: GENO:0000954 +name: allele set +def: "A set of discrete alleles within a particular genome." [] +comment: 'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An "Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'. +is_a: GENO:0000660 ! genomic feature set + +[Term] +id: GENO:0000955 +name: obsolete_variant copy number complement +def: "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s)." [] +comment: In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. +is_a: GENO:0000956 ! obsolete_copy number complement +property_value: IAO:0000118 "copy number variation" xsd:string +property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level." xsd:string + +[Term] +id: GENO:0000956 +name: obsolete_copy number complement +def: "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger." [] +comment: 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. +is_a: ObsoleteClass +property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." xsd:string + +[Term] +id: GENO:0000960 +name: genomic sequence +def: "A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)." [] +comment: A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. +is_a: GENO:0000702 ! biological sequence +relationship: GENO:0000251 GENO:0000481 ! is_sequence_of genomic feature + +[Term] +id: GENO:0000961 +name: copy number complement +def: "A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome." [] +comment: The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result.\n\nA 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. \n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. +comment: The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence. +is_a: GENO:0000872 ! genomic sequence set +property_value: IAO:0000116 "The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome.\n\nWe represent the notion of copy number at the \"sequence level\" (as opposed to the \"sequence feature level\") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The \"sequence level\" representation here supports this use case. By contrast, a \"feature level\" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity)." xsd:string + +[Term] +id: GENO:0000962 +name: variant copy number complement +def: "A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s)." [] +comment: 'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome. +is_a: GENO:0000961 ! copy number complement +property_value: IAO:0000116 "Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a \"sequence feature level\" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred).\n\nFor example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains." xsd:string + +[Term] +id: GENO:0000963 +name: functional copy complement +def: "A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome." [] +comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence.\n\n'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nAs we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele. +is_a: GENO:0000872 ! genomic sequence set +property_value: IAO:0000118 "functional genetic dosage" xsd:string + +[Term] +id: GENO:0000964 +name: mosaic +comment: A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type. +is_a: GENO:0000928 ! clonal + +[Term] +id: GENO:0000965 +name: sequence interval +def: "A pair of integers representing start and end position of a location on a sequence coordinate system." [] +is_a: IAO:0000030 ! information content entity + +[Term] +id: GO:0003674 +name: molecular function +is_a: BFO:0000034 ! function + +[Term] +id: GO:0032502 +name: developmental process +def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete]" [] +is_a: GENO:0000351 ! biological process + +[Term] +id: HP:0000118 +name: human phenotypic abnormality +comment: pulling in HP 'phenotypic abnormality' root here +is_a: UPHENO:0001001 ! Phenotype + +[Term] +id: HsapDv:0000000 +name: human life cycle stage +is_a: GENO:0000351 ! biological process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology." xsd:string +property_value: IAO:0000119 "A spatiotemporal region encompassing some part of the life cycle of an organism." xsd:string + +[Term] +id: IAO:0000027 +name: data item +is_a: IAO:0000030 ! information content entity + +[Term] +id: IAO:0000030 +name: information content entity +def: "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity" [] +is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000111 "information content entity" xsd:string +property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000119 "OBI_0000142" xsd:string + +[Term] +id: IAO:0000078 +name: curation status specification +def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string +property_value: IAO:0000118 "ontology metadata" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: IAO:8000000 +name: ontology module +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000116 "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000118 "ontology file" xsd:string +property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:03Z + +[Term] +id: IAO:8000001 +name: base ontology module +def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 +created_by: cjm +creation_date: 2018-05-20T20:55:30Z + +[Term] +id: IAO:8000002 +name: editors ontology module +def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "source ontology module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:47Z + +[Term] +id: IAO:8000003 +name: main release ontology module +def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:56:13Z + +[Term] +id: IAO:8000004 +name: bridge ontology module +def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies +created_by: cjm +creation_date: 2018-05-20T20:56:23Z + +[Term] +id: IAO:8000005 +name: import ontology module +def: "A subset ontology module that is intended to be imported from another ontology." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000118 "import file" xsd:string +property_value: seeAlso http://robot.obolibrary.org/extract +created_by: cjm +creation_date: 2018-05-20T20:56:47Z + +[Term] +id: IAO:8000006 +name: subset ontology module +def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "ontology slim" xsd:string +property_value: IAO:0000118 "subset ontology" xsd:string +property_value: seeAlso http://robot.obolibrary.org/filter +property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide +created_by: cjm +creation_date: 2018-05-20T20:58:11Z + +[Term] +id: IAO:8000007 +name: curation subset ontology module +def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:38Z + +[Term] +id: IAO:8000008 +name: analysis subset ontology module +def: "An ontology module that is intended for usage in analysis or discovery applications." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:49Z + +[Term] +id: IAO:8000009 +name: single layer subset ontology module +def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "ribbon subset" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:19Z + +[Term] +id: IAO:8000010 +name: exclusion subset ontology module +def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "antislim" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:57Z + +[Term] +id: IAO:8000011 +name: external import ontology module +def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] +is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000118 "external import" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:00:14Z + +[Term] +id: IAO:8000012 +name: species subset ontology module +def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "taxon subset" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +created_by: cjm +creation_date: 2018-05-20T21:14:16Z + +[Term] +id: IAO:8000013 +name: reasoned ontology module +def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso http://robot.obolibrary.org/reason +created_by: cjm +creation_date: 2018-05-20T21:20:33Z + +[Term] +id: IAO:8000014 +name: generated ontology module +def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:21:12Z + +[Term] +id: IAO:8000015 +name: template generated ontology module +def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] +is_a: IAO:8000014 ! generated ontology module +property_value: seeAlso http://robot.obolibrary.org/template +property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 +property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ +created_by: cjm +creation_date: 2018-05-20T21:21:21Z + +[Term] +id: IAO:8000016 +name: taxonomic bridge ontology module +is_a: IAO:8000004 ! bridge ontology module +created_by: cjm +creation_date: 2018-05-20T21:28:15Z + +[Term] +id: IAO:8000017 +name: ontology module subsetted by expressivity +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-22T04:15:54Z + +[Term] +id: IAO:8000018 +name: obo basic subset ontology module +def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: seeAlso "6.2" +created_by: cjm +creation_date: 2018-05-22T04:16:10Z + +[Term] +id: IAO:8000019 +name: ontology module subsetted by OWL profile +is_a: IAO:8000017 ! ontology module subsetted by expressivity +created_by: cjm +creation_date: 2018-05-22T04:16:28Z + +[Term] +id: IAO:8000020 +name: EL++ ontology module +is_a: IAO:8000019 ! ontology module subsetted by OWL profile +created_by: cjm +creation_date: 2018-05-22T04:16:48Z + +[Term] +id: MP:0000001 +name: mammalian phenotype +comment: where to place this depends on if we take the organismal view or the quality centric view. +is_a: UPHENO:0001001 ! Phenotype + +[Term] +id: NCBITaxon:10090 +name: Mus musculus +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:10239 +name: Viruses +comment: Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies. +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:7955 +name: Danio rerio +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:8090 +name: Oryzias latipes +is_a: OBI:0100026 ! organism + +[Term] +id: NCBITaxon:9606 +name: Homo sapiens +is_a: OBI:0100026 ! organism + +[Term] +id: OBI:0000011 +name: planned process +def: "A processual entity that realizes a plan which is the concretization of a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO." xsd:string + +[Term] +id: OBI:0000086 +name: reagent role +is_a: BFO:0000023 ! role + +[Term] +id: OBI:0000181 +name: population +def: "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area" [] +is_a: GENO:0000113 ! taxonomic group + +[Term] +id: OBI:0000435 +name: genotyping assay +def: "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions." [] +is_a: ERO:0000007 ! technique + +[Term] +id: OBI:0001148 +name: targeted gene knock-out technique +def: "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods." [] +comment: A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. +is_a: GENO:0000166 ! targeted gene mutation technique + +[Term] +id: OBI:0001149 +name: targeted gene knock-in technique +is_a: GENO:0000166 ! targeted gene mutation technique + +[Term] +id: OBI:0100026 +name: organism +is_a: GENO:0000904 ! organismal entity +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy." xsd:string + +[Term] +id: OBI:0600043 +name: genetic modification technique +def: "the introduction. alteration or integration of genetic material into a cell or organism" [] +is_a: ERO:0000007 ! technique + +[Term] +id: PATO:0000016 +name: obsolete_color brightness +is_a: ObsoleteClass +property_value: IAO:0000116 "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html" xsd:string +property_value: IAO:0000116 "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." xsd:string +property_value: IAO:0000118 "color value" xsd:string + +[Term] +id: PATO:0000383 +name: female +is_a: PATO:0001894 ! phenotypic sex + +[Term] +id: PATO:0000384 +name: male +is_a: PATO:0001894 ! phenotypic sex + +[Term] +id: PATO:0001894 +name: phenotypic sex +is_a: BFO:0000019 ! quality + +[Term] +id: PCO:0000000 +name: collection of organisms +def: "A material entity that consists of two or more organisms, viruses, or viroids." [] +comment: A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role). +is_a: GENO:0000904 ! organismal entity +relationship: RO:0002351 OBI:0100026 ! has member organism + +[Term] +id: PCO:0000020 +name: family +def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] +is_a: PCO:0000000 ! collection of organisms + +[Term] +id: Position +name: Position +def: "Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate." [] +is_a: GENO:0000902 ! genomic feature location +property_value: IAO:0000116 "We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region)." xsd:string +property_value: IAO:0000412 "FALDO" xsd:string + +[Term] +id: Region +name: Region +def: "A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene." [] +is_a: SO:0000110 ! sequence_feature +relationship: begin Position {cardinality="1"} ! Position +relationship: end Position {cardinality="1"} ! Position +property_value: IAO:0000116 "From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence." xsd:string + +[Term] +id: ReverseStrandPosition +name: Negative strand +is_a: StrandedPosition ! Stranded position + +[Term] +id: SO:0000034 +name: morpholino_oligo +def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [] +is_a: GENO:0000533 ! gene knockdown reagent + +[Term] +id: SO:0000105 +name: chromosome arm +def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [] +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 SO:0000830 ! is part of chromosome part +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000116 "Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string + +[Term] +id: SO:0000110 +name: sequence_feature +def: "Any extent of continuous biological sequence." [] +comment: A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome. +is_a: GENO:0000701 ! sequence feature or set +relationship: GENO:0000239 GENO:0000702 {http://purl.obolibrary.org/obo/GENO_0000834="true", comment="Formalizes the first identity criteria for a sequence feature of its sequence."} ! has_sequence biological sequence +relationship: GENO:0000903 GENO:0000815 {http://purl.obolibrary.org/obo/GENO_0000834="true", comment="Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property)."} ! has_location sequence feature location +property_value: IAO:0000116 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." xsd:string + +[Term] +id: SO:0000143 +name: obsolete_assembly_component +def: "A region of known length which may be used to manufacture a longer region." [] +is_a: SO:0001410 ! obsolete_experimental_feature + +[Term] +id: SO:0000149 +name: obsolete_contig +def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [] +is_a: SO:0000143 ! obsolete_assembly_component + +[Term] +id: SO:0000159 +name: deletion +def: "The point at which one or more contiguous nucleotides were excised." [] +xref: http://en.wikipedia.org/wiki/Nucleotide_deletion +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000033 xsd:string +property_value: IAO:0000118 "deleted_sequence" xsd:string +property_value: IAO:0000118 "nucleotide deletion" xsd:string +property_value: IAO:0000118 "nucleotide_deletion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0000165 +name: enhancer +is_a: SO:0005836 ! regulatory_region + +[Term] +id: SO:0000167 +name: promoter +def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [] +is_a: SO:0005836 ! regulatory_region + +[Term] +id: SO:0000199 +name: translocation +def: "A region of nucleotide sequence that has translocated to a new position." [] +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000118 "transchr" xsd:string +property_value: IAO:0000118 "translocated sequence" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0000207 +name: simple_sequence_length_variation +is_a: SO:0000248 ! sequence_length_variation +property_value: IAO:0000118 "simple sequence length polymorphism" xsd:string +property_value: IAO:0000118 "simple sequence length variation" xsd:string +property_value: IAO:0000118 "SSLP" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0000248 +name: sequence_length_variation +is_a: SO:1000002 ! substitution +property_value: IAO:0000118 "sequence length variation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0000281 +name: engineered_foreign_gene +is_a: SO:0000704 ! gene +is_a: SO:0000804 ! engineered_region +property_value: IAO:0000116 "See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25.\n\nIncludes things like loxP sites, inducible promoters, ires elements, etc." xsd:string + +[Term] +id: SO:0000289 +name: microsatellite +def: "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [] +comment: A defined feature that includes any type of VNTR or SSLP locus. +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000119 http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29 xsd:string + +[Term] +id: SO:0000337 +name: RNAi_reagent +is_a: GENO:0000533 ! gene knockdown reagent + +[Term] +id: SO:0000340 +name: chromosome +def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [] +comment: A complete chromosome sequence. +is_a: GENO:0000481 ! genomic feature + +[Term] +id: SO:0000341 +name: chromosome band +def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [] +comment: "Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. +is_a: SO:0000830 ! chromosome part +relationship: BFO:0000050 GENO:0000614 ! is part of chromosomal region +relationship: GENO:0000207 GENO:0000618 ! has_sequence_attribute chromosomal band intensity +property_value: IAO:0000112 "The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as \"one q two-two point three\", not \"one q twenty-two point three\"." xsd:string +property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band\n" xsd:string + +[Term] +id: SO:0000577 +name: centromere +is_a: SO:0000830 ! chromosome part + +[Term] +id: SO:0000637 +name: obsolete_engineered_plasmid +is_a: ObsoleteClass +property_value: IAO:0000116 "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." xsd:string + +[Term] +id: SO:0000667 +name: insertion +def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [] +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000034 xsd:string +property_value: IAO:0000118 "insertion" xsd:string +property_value: IAO:0000118 "nucleotide insertion" xsd:string +property_value: IAO:0000118 "nucleotide_insertion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0000694 +name: SNP +def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [] +is_a: SO:0001483 ! SNV +property_value: IAO:0000118 "single nucleotide polymorphism" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0000699 +name: junction +comment: A junction is a boundary between regions. A boundary has an extent of zero. +is_a: SO:0000110 ! sequence_feature + +[Term] +id: SO:0000704 +name: gene +def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [] +comment: A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion. +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000116 "Regarding the distinction between a 'gene' and a 'gene allele': \nEvery zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment)." xsd:string + +[Term] +id: SO:0000771 +name: QTL +def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [] +is_a: GENO:0000481 ! genomic feature +property_value: IAO:0000118 "quantitative trait locus" xsd:string + +[Term] +id: SO:0000783 +name: engineered +def: "An attribute to describe a region that was modified in vitro." [] +is_a: GENO:0000788 ! sequence feature attribute + +[Term] +id: SO:0000804 +name: engineered_region +is_a: SO:0000110 ! sequence_feature +intersection_of: SO:0000110 ! sequence_feature +intersection_of: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered +relationship: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered +property_value: IAO:0000118 "construct" xsd:string + +[Term] +id: SO:0000830 +name: chromosome part +def: "An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'." [] +is_a: GENO:0000481 ! genomic feature +intersection_of: GENO:0000481 ! genomic feature +intersection_of: GENO:0000248 SO:0000340 ! is_proper_part_of chromosome +relationship: GENO:0000248 SO:0000340 ! is_proper_part_of chromosome +property_value: IAO:0000118 "chromosomal feature" xsd:string +property_value: IAO:0000118 "gross chromosomal part" xsd:string + +[Term] +id: SO:0000902 +name: transgene +def: "A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome)." [] +comment: On the relationship between 'transgenic insertions', 'transgenes', and 'alleles'\nTransgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete.\n\nIn addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. \n\nFor the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach. +comment: Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism).\n\nNote that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome. +is_a: SO:0000704 ! gene + +[Term] +id: SO:0001013 +name: MNP +def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [] +is_a: SO:1000002 ! substitution +property_value: IAO:0000118 "multiple nucleotide polymorphism" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001019 +name: copy_number_variation +def: "A variation that increases or decreases the copy number of a given region." [] +xref: http://en.wikipedia.org/wiki/Copy_number_variation +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000118 "CNP" xsd:string +property_value: IAO:0000118 "CNV" xsd:string +property_value: IAO:0000118 "copy number polymorphism" xsd:string +property_value: IAO:0000118 "copy number variation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0001026 +name: genome +def: "A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny)" [] +comment: A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'. +is_a: GENO:0000660 ! genomic feature set +property_value: IAO:0000116 "Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence." xsd:string +property_value: IAO:0000118 "'genome sequence'" xsd:string + +[Term] +id: SO:0001059 +name: sequence_alteration +def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [] +comment: 1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. \n\nAlleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part.\n\n2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. \n\nFor a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference.\n\n3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism. +is_a: GENO:0000512 ! allele +intersection_of: GENO:0000512 ! allele +intersection_of: GENO:0000784 GENO:0000481 ! completely_varies_with genomic feature +relationship: GENO:0000784 GENO:0000481 ! completely_varies_with genomic feature +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000004 xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_alt_id SO:1000007 xsd:string +property_value: IAO:0000112 "A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': \n\n1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871.\n\n2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112.\n\n3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112." xsd:string +property_value: IAO:0000118 "sequence variation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0001218 +name: transgenic_insertion +def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [] +is_a: SO:0000667 ! insertion +relationship: BFO:0000051 GENO:0000093 ! has part integrated transgene +property_value: IAO:0000118 "transgenic insertion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001410 +name: obsolete_experimental_feature +def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [] +is_a: ObsoleteClass +property_value: IAO:0000231 "not currently needed to support modeling use cases. can re-introduce if becomes necessary." xsd:string + +[Term] +id: SO:0001477 +name: gene_trap_construct +def: "A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: SO:0001478 +name: promoter_trap_construct +def: "A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: SO:0001479 +name: enhancer_trap_construct +def: "A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [] +is_a: GENO:0000856 ! engineered genetic construct + +[Term] +id: SO:0001483 +name: SNV +def: "SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist." [] +is_a: SO:1000002 ! substitution +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Thu Oct 08 11:37:49 PDT 2009" xsd:string +property_value: IAO:0000118 "single nucleotide variant" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:0001500 +name: heritable_phenotypic_marker +def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [] +is_a: GENO:0000481 ! genomic feature + +[Term] +id: SO:0001505 +name: reference genome sequence +def: "A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced." [] +is_a: GENO:0000017 ! reference sequence +property_value: IAO:0000112 "'GRCh37.p10' (a human reference genome build)" xsd:string + +[Term] +id: SO:0001742 +name: copy_number_gain +def: "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [] +is_a: SO:0001019 ! copy_number_variation +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 01:54:09 PST 2011" xsd:string +property_value: IAO:0000118 "copy number gain" xsd:string +property_value: IAO:0000118 "gain" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001743 +name: copy_number_loss +def: "A sequence alteration whereby the copy number of a given region is less than the reference sequence." [] +is_a: SO:0001019 ! copy_number_variation +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 01:55:02 PST 2011" xsd:string +property_value: IAO:0000118 "copy number loss" xsd:string +property_value: IAO:0000118 "loss" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001744 +name: UPD +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [] +xref: http:http\\\://en.wikipedia.org/wiki/Uniparental_disomy +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:01:05 PST 2011" xsd:string +property_value: IAO:0000118 "uniparental disomy" xsd:string +property_value: IAO:0000118 "UPD" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001745 +name: maternal_uniparental_disomy +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [] +is_a: SO:0001744 ! UPD +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:03:01 PST 2011" xsd:string +property_value: IAO:0000118 "maternal uniparental disomy" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001746 +name: paternal_uniparental_disomy +def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [] +is_a: SO:0001744 ! UPD +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:03:30 PST 2011" xsd:string +property_value: IAO:0000118 "paternal uniparental disomy" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:0001784 +name: complex_structural_alteration +def: "A structural sequence alteration where there are multiple equally plausible explanations for the change." [] +is_a: SO:0001785 ! structural_alteration +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Wed Mar 23 03:21:19 PDT 2011" xsd:string +property_value: IAO:0000118 "complex" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0001785 +name: structural_alteration +is_a: SO:0001059 ! sequence_alteration +property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 25 02:27:41 PDT 2011" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: SO:0005836 +name: regulatory_region +is_a: GENO:0000666 ! gene part +property_value: IAO:0000116 "Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term." xsd:string +property_value: IAO:0000118 "regulatory element" xsd:string +property_value: IAO:0000118 "regulatory gene region" xsd:string + +[Term] +id: SO:1000002 +name: substitution +def: "Any change in genomic DNA caused by a single event." [] +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000005 +name: complex_substitution +def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\\"complex\\\" should be used. Usually there are multiple equally plausible explanations for the change." [] +is_a: SO:1000002 ! substitution +property_value: IAO:0000118 "complex substitution" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000008 +name: point_mutation +def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [] +xref: http://en.wikipedia.org/wiki/Point_mutation +is_a: SO:0001483 ! SNV +property_value: IAO:0000118 "point mutation" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000009 +name: transition +def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [] +is_a: SO:0001483 ! SNV +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000010 +name: pyrimidine_transition +def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [] +is_a: SO:1000009 ! transition +property_value: IAO:0000118 "pyrimidine transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000011 +name: C_to_T_transition +def: "A transition of a cytidine to a thymine." [] +is_a: SO:1000010 ! pyrimidine_transition +property_value: IAO:0000118 "C to T transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000012 +name: C_to_T_transition_at_pCpG_site +def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [] +is_a: SO:1000011 ! C_to_T_transition +property_value: IAO:0000118 "C to T transition at pCpG site" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000013 +name: T_to_C_transition +is_a: SO:1000010 ! pyrimidine_transition +property_value: IAO:0000118 "T to C transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000014 +name: purine_transition +def: "A substitution of a purine, A or G, for another purine." [] +is_a: SO:1000009 ! transition +property_value: IAO:0000118 "purine transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000015 +name: A_to_G_transition +def: "A transition of an adenine to a guanine." [] +is_a: SO:1000014 ! purine_transition +property_value: IAO:0000118 "A to G transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000016 +name: G_to_A_transition +def: "A transition of a guanine to an adenine." [] +is_a: SO:1000014 ! purine_transition +property_value: IAO:0000118 "G to A transition" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000017 +name: transversion +def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [] +xref: http://en.wikipedia.org/wiki/Transversion +is_a: SO:0001483 ! SNV +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000018 +name: pyrimidine_to_purine_transversion +def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [] +is_a: SO:1000017 ! transversion +property_value: IAO:0000118 "pyrimidine to purine transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000019 +name: C_to_A_transversion +def: "A transversion from cytidine to adenine." [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "C to A transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000020 +name: C_to_G_transversion +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "C to G transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000021 +name: T_to_A_transversion +def: "A transversion from T to A." [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "T to A transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000022 +name: T_to_G_transversion +def: "A transversion from T to G." [] +is_a: SO:1000018 ! pyrimidine_to_purine_transversion +property_value: IAO:0000118 "T to G transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000023 +name: purine_to_pyrimidine_transversion +def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [] +is_a: SO:1000017 ! transversion +property_value: IAO:0000118 "purine to pyrimidine transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000024 +name: A_to_C_transversion +def: "A transversion from adenine to cytidine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "A to C transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000025 +name: A_to_T_transversion +def: "A transversion from adenine to thymine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "A to T transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000026 +name: G_to_C_transversion +def: "A transversion from guanine to cytidine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "G to C transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000027 +name: G_to_T_transversion +def: "A transversion from guanine to thymine." [] +is_a: SO:1000023 ! purine_to_pyrimidine_transversion +property_value: IAO:0000118 "G to T transversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000032 +name: indel +def: "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [] +comment: Indels can have a different number of bases than the corresponding reference sequence. +xref: http://en.wikipedia.org/wiki/Indel +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000035 +name: duplication +def: "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point." [] +is_a: SO:0000667 ! insertion +property_value: IAO:0000118 "nucleotide duplication" xsd:string +property_value: IAO:0000118 "nucleotide_duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000036 +name: inversion +def: "A continuous nucleotide sequence is inverted in the same position." [] +is_a: SO:0001059 ! sequence_alteration +property_value: IAO:0000118 "inversion" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string +property_value: IAO:subset "SOFA" xsd:string + +[Term] +id: SO:1000039 +name: direct_tandem_duplication +def: "A tandem duplication where the individual regions are in the same orientation." [] +is_a: SO:1000173 ! tandem_duplication +property_value: IAO:0000118 "direct tandem duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000040 +name: inverted_tandem_duplication +def: "A tandem duplication where the individual regions are not in the same orientation." [] +is_a: SO:1000173 ! tandem_duplication +property_value: IAO:0000118 "inverted tandem duplication" xsd:string +property_value: IAO:0000118 "mirror duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl + +[Term] +id: SO:1000173 +name: tandem_duplication +def: "A duplication consisting of 2 identical adjacent regions." [] +is_a: SO:1000035 ! duplication +property_value: IAO:0000118 "erverted" xsd:string +property_value: IAO:0000118 "tandem duplication" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl +property_value: IAO:subset "DBVAR" xsd:string + +[Term] +id: StrandedPosition +name: Stranded position +comment: Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'. +is_a: Position ! Position + +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Synonym +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: SynonymType +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: UBERON:0000105 +name: life cycle stage +is_a: GENO:0000351 ! biological process +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms)" xsd:string + +[Term] +id: UBERON:0001062 +name: anatomical entity +xref: http://purl.obolibrary.org/obo/CARO_0000000 +is_a: GENO:0000904 ! organismal entity +relationship: RO:0001000 OBI:0100026 ! derives from organism +property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies." xsd:string + +[Term] +id: UPHENO:0001001 +name: Phenotype +comment: 1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition)\n\n2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000116 "Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework." xsd:string + +[Term] +id: WBPhenotype:0000886 +name: worm phenotype +def: "Animals exhibit variations compared to a given control." [] +is_a: UPHENO:0001001 ! Phenotype +property_value: IAO:0000116 "'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes." xsd:string +property_value: IAO:0000118 "c. elegans phenotype" xsd:string +property_value: IAO:0000118 "Variant" xsd:string + +[Term] +id: ZP:0000199 +name: abnormal(ly) malformed endocardium cell +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0000386 +name: abnormal(ly) absent dorso-rostral cluster +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0000755 +name: abnormal(ly) disrupted diencephalon development +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0005531 +name: abnormal(ly) disrupted neutrophil aggregation +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: ZP:0005692 +name: abnormal(ly) absent adaxial cell +is_a: GENO:0000575 ! zebrafish phenotype + +[Term] +id: http://purl.org/oban/association +name: association +is_a: IAO:0000030 ! information content entity + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/20423 +name: mus musculus shh gene +comment: Equivalent to: http://www.informatics.jax.org/marker/MGI:98297 +is_a: GENO:0000057 ! mus musculus gene +property_value: IAO:0000114 GENO:0000514 + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/30269 +name: danio rerio shha gene +xref: http://zfin.org/ZDB-GENE-980526-166 +is_a: GENO:0000047 ! danio rerio gene +property_value: IAO:0000114 GENO:0000514 + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/399483 +name: danio rerio cdkn1ca gene +xref: http://zfin.org/ZDB-GENE-040123-1 +is_a: GENO:0000047 ! danio rerio gene +property_value: IAO:0000114 GENO:0000514 + +[Term] +id: http://www.ncbi.nlm.nih.gov/gene/6469 +name: homo sapiens SHH gene +comment: Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690\n\nCodes for: http://www.uniprot.org/uniprot/Q15465 +is_a: GENO:0000054 ! homo sapiens gene +property_value: IAO:0000114 GENO:0000514 + +[Typedef] +id: BFO:0000050 +name: is part of +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: GENO:0000207 +name: has_sequence_attribute +def: "A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'." [] +xref: http://purl.obolibrary.org/obo/so_has_quality +property_value: IAO:0000116 "Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants." xsd:string + +[Typedef] +id: GENO:0000211 +name: bears_concretization_of +def: "A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes" [] +comment: Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence. +property_value: IAO:0000118 "materializes" xsd:string +holds_over_chain: RO:0000053 RO:0000059 + +[Typedef] +id: GENO:0000220 +name: is_genotype_of +inverse_of: GENO:0000222 ! has_genotype + +[Typedef] +id: GENO:0000222 +name: has_genotype +def: "A relationship that holds between a biological entity and some level of genetic variation present in its genome." [] +comment: The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations. +property_value: IAO:0000116 "This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype." xsd:string + +[Typedef] +id: GENO:0000231 +name: has_proper_part +def: "An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO)" [] +xref: http://semanticscience.org/resource/SIO_000053 +property_value: IAO:0000116 "No proper part relation anymore in RO/BFO?" xsd:string +is_transitive: true +is_a: BFO:0000051 ! has part +inverse_of: GENO:0000248 ! is_proper_part_of + +[Typedef] +id: GENO:0000239 +name: has_sequence +def: "A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears." [] +comment: 'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule. +xref: VMC:state +property_value: IAO:0000118 "has_sequence_component" xsd:string +property_value: IAO:0000118 "has_state" xsd:string +range: GENO:0000702 ! biological sequence +inverse_of: GENO:0000251 ! is_sequence_of + +[Typedef] +id: GENO:0000242 +name: obsolete_specifies +def: "A relationship between an information content entity representing a specification, and the entity it specifies." [] +property_value: IAO:0000112 "A geno:intrinnsic genotype 'specifies' a SO:genome.\nA geno:karyotype 'specifies' a geno:karyotype feature collection." xsd:string +is_a: ObsoleteProperty +inverse_of: GENO:0000253 ! obsolete_is_specified_by + +[Typedef] +id: GENO:0000243 +name: obsolete_approximates_sequence +property_value: IAO:0000116 "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000244 +name: obsolete_resolves_to_sequence +property_value: IAO:0000116 "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000248 +name: is_proper_part_of +def: "An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole." [] +xref: http://semanticscience.org/resource/SIO_000093 +is_a: BFO:0000050 ! is part of + +[Typedef] +id: GENO:0000251 +name: is_sequence_of +domain: GENO:0000702 ! biological sequence + +[Typedef] +id: GENO:0000252 +name: is_subject_of +inverse_of: IAO:0000136 ! is about + +[Typedef] +id: GENO:0000253 +name: obsolete_is_specified_by +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000359 +name: obsolete_is_phenotype_of_genotype +def: "shortcut relation used to link a phenotype directly to a genotype of an organism" [] +comment: Might expand to something like:\n\nphenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype))))))) +property_value: IAO:0000118 "is_phenotype_of_organism_with_genotype" xsd:string +property_value: IAO:0000118 "is_phenotype_with_genotype" xsd:string +property_value: IAO:0000118 "phenotype_has_genotype" xsd:string +domain: UPHENO:0001001 ! Phenotype +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000368 +name: obsolete_participates_in_inheritance_process +def: "A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next." [] +property_value: IAO:0000116 "Exploratory/temporary property, as we formalize our phenotypic inheritance model." xsd:string +range: GENO:0000141 ! inheritance pattern +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000382 +name: has_variant_part +def: "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression." [] +is_transitive: true +is_a: GENO:0000654 ! has_sequence_part +inverse_of: GENO:0000383 ! is_variant_part_of + +[Typedef] +id: GENO:0000383 +name: is_variant_part_of +is_transitive: true +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000385 +name: has_reference_part +def: "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant." [] +property_value: IAO:0000118 "has_reference_sequence_part" xsd:string +is_transitive: true +is_a: GENO:0000654 ! has_sequence_part +inverse_of: GENO:0000387 ! is_reference_part_of + +[Typedef] +id: GENO:0000387 +name: is_reference_part_of +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000408 +name: is_allele_of +def: "A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size." [] +comment: To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size).\n\nWhile conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like "fgf8a is an allele of the Danio rerio fgf8a gene", and we may create data where fgf8a is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene).\n\nIt is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. \n\nThis departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\\GAL4 gene.\n\nAt the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'. +property_value: IAO:0000112 " is_allele_of the 'danio rerio fgf8a' gene locus." xsd:string +property_value: IAO:0000116 "Domain = allele \nRange = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation)." xsd:string +property_value: IAO:0000116 "Note that the allele is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product." xsd:string +property_value: IAO:0000118 "is_sequence_variant_of" xsd:string +domain: GENO:0000481 ! genomic feature +is_a: GENO:0000418 ! has_affected_feature +inverse_of: GENO:0000413 ! has_allele + +[Typedef] +id: GENO:0000410 +name: obsolete_is_genetic_variant_of +def: "A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level)." [] +comment: Domain = genomic feature instance\nRange = punned gene class IRI +property_value: IAO:0000118 "is_variant_instance_of" xsd:string +property_value: IAO:0000231 "formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus)" xsd:string +is_a: ObsoleteProperty +inverse_of: GENO:0000411 ! obsolete_has_genetic_variant + +[Typedef] +id: GENO:0000411 +name: obsolete_has_genetic_variant +def: "A relation linking a gene class to a sequence-varaint or expression-variant of the gene." [] +comment: Domain = punned gene class\nRange = genomic feature +property_value: IAO:0000118 "has_variant_instance" xsd:string +property_value: IAO:0000231 "formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by)" xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000413 +name: has_allele +def: "A relation linking a gene class to one of its sequence-variant alleles." [] +property_value: IAO:0000116 "Domain = punned gene class\nRange = allele" xsd:string +property_value: IAO:0000118 "has_sequence_variant" xsd:string +is_a: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000414 +name: targets_gene +def: "A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets." [] +comment: This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets. +is_a: GENO:0000418 ! has_affected_feature +inverse_of: GENO:0000447 ! is_gene_target_of + +[Typedef] +id: GENO:0000418 +name: has_affected_feature +def: "A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression." [] +comment: This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset. +holds_over_chain: GENO:0000382 GENO:0000418 +holds_over_chain: GENO:0000383 GENO:0000418 +inverse_of: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000443 +name: is_expression_variant_of +def: "A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents." [] +comment: This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class. +property_value: IAO:0000116 "Domain = expression variant feature.\nRange = punned gene class" xsd:string +is_a: GENO:0000418 ! has_affected_feature +inverse_of: GENO:0000449 ! has_expression_variant + +[Typedef] +id: GENO:0000445 +name: is_feature_affected_by +def: "A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature." [] +comment: This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases) +property_value: IAO:0000118 "class_to_feature_relation" xsd:string + +[Typedef] +id: GENO:0000447 +name: is_gene_target_of +def: "A relation between a gene class and a gene targeting reagent that targets it." [] +comment: Domain = punned gene class\nRange = gene knockdown reagent +property_value: IAO:0000118 "is_target_of" xsd:string +is_a: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000449 +name: has_expression_variant +def: "A relation linking a gene class to one of an expression-variant of that gene.." [] +property_value: IAO:0000116 "Domain = punned gene class\nRange = expression variant feature" xsd:string +property_value: IAO:0000118 "has_expression_variant_instance" xsd:string +is_a: GENO:0000445 ! is_feature_affected_by + +[Typedef] +id: GENO:0000486 +name: obsolete_is_variant_with +def: "A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression." [] +comment: This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of. +property_value: IAO:0000231 "Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property." xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000488 +name: obsolete_is_expression_variant_with +def: "A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways)." [] +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000580 +name: has_qualifier +def: "A relation used to describe a context or conditions that define and/or identify an entity." [] +property_value: IAO:0000116 "Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association.\n\nUsed in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features." xsd:string +property_value: IAO:0000118 "has_qualifying_context" xsd:string + +[Typedef] +id: GENO:0000608 +name: has_zygosity +def: "a relation to link a single locus complement to its zygosity." [] +domain: GENO:0000516 ! single locus complement +range: GENO:0000133 ! zygosity +is_a: GENO:0000207 ! has_sequence_attribute + +[Typedef] +id: GENO:0000610 +name: is_reference_allele_of +def: "A relationship between a reference locus/allele and the gene class it is an allele of." [] +domain: GENO:0000036 ! reference allele +is_a: GENO:0000408 ! is_allele_of + +[Typedef] +id: GENO:0000626 +name: has_staining_intensity +comment: Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized. +property_value: IAO:0000116 "Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed." xsd:string +property_value: IAO:0000118 "has_color_value" xsd:string +is_a: GENO:0000207 ! has_sequence_attribute + +[Typedef] +id: GENO:0000634 +name: is_targeted_by +def: "relation between an molecular agent and its molecular target" [] +property_value: IAO:0000112 "Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant." xsd:string + +[Typedef] +id: GENO:0000639 +name: sequence_derives_from +def: "Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence." [] +property_value: IAO:0000112 "1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. \n\n2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds.\n\n3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC)" xsd:string +holds_over_chain: BFO:0000051 GENO:0000639 + +[Typedef] +id: GENO:0000641 +name: is_variant_allele_of +def: "A relationship between a variant allele and the gene class it is an allele of." [] +domain: GENO:0000002 ! variant allele +is_a: GENO:0000408 ! is_allele_of + +[Typedef] +id: GENO:0000650 +name: has_sex_agnostic_part +property_value: IAO:0000116 "Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases." xsd:string +is_a: GENO:0000654 ! has_sequence_part +inverse_of: GENO:0000661 ! is_sex_agnostic_part_of + +[Typedef] +id: GENO:0000651 +name: is_mutant_allele_of +comment: A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of. +domain: GENO:0000491 ! obsolete_mutant allele +is_a: GENO:0000641 ! is_variant_allele_of + +[Typedef] +id: GENO:0000652 +name: is_polymorphic_allele_of +def: "A relationship between a polymorphic allele and the gene class it is an allele of." [] +domain: GENO:0000497 ! polymorphic allele +is_a: GENO:0000641 ! is_variant_allele_of + +[Typedef] +id: GENO:0000653 +name: is_wild_type_allele_of +def: "A relationship between a wild-type allele and the gene class it is an allele of." [] +domain: GENO:0000501 ! wild-type allele +is_a: GENO:0000408 ! is_allele_of + +[Typedef] +id: GENO:0000654 +name: has_sequence_part +def: "An organizational class to hold relations of parthood between sequences/features." [] +is_a: BFO:0000051 ! has part +inverse_of: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000655 +name: is_sequence_part_of +is_a: BFO:0000050 ! is part of + +[Typedef] +id: GENO:0000661 +name: is_sex_agnostic_part_of +def: "Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases." [] +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000683 +name: varies_with +def: "A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part)." [] +comment: This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of) +is_symmetric: true + +[Typedef] +id: GENO:0000708 +name: faldo properties +comment: organizational property to hold imports from faldo. + +[Typedef] +id: GENO:0000726 +name: has_sequence_feature +def: "A relation linking a qualified sequence feature to its component sequence feature." [] +comment: In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism. +property_value: IAO:0000118 "has_sequence_feature_component" xsd:string +range: SO:0000110 ! sequence_feature + +[Typedef] +id: GENO:0000740 +name: has_inferred_phenotype +holds_over_chain: GENO:0000382 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype."} +holds_over_chain: GENO:0000383 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration."} +holds_over_chain: GENO:0000413 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations from a (sequence-)variant locus instance to a gene class (to support cases where the phenotype association is made at the level of the variant gene locus)."} +holds_over_chain: GENO:0000449 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations from an expression-variant gene instance to a gene class (to support cases where the phenotype association is made at the level of the expression-variant gene)."} +holds_over_chain: GENO:0000661 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)"} +is_a: RO:0002200 ! has phenotype + +[Typedef] +id: GENO:0000741 +name: obsolete_has_regulatory_part +comment: Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes. +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000742 +name: obsolete_is_alteration_within +def: "A relation linking a sequence_alteration to the gene it alters." [] +property_value: IAO:0000114 GENO:0000484 +property_value: IAO:0000118 "is_within_allele_of" xsd:string +holds_over_chain: GENO:0000383 GENO:0000408 +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000743 +name: has_asserted_phenotype +is_a: RO:0002200 ! has phenotype + +[Typedef] +id: GENO:0000761 +name: is_regulatory_part_of +property_value: IAO:0000116 "Proposal for a property linking regulatory elements to larger features of which they are a part." xsd:string +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: GENO:0000767 +name: obsolete_has_position_component +def: "A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances." [] +property_value: IAO:0000116 "For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them." xsd:string +is_a: ObsoleteProperty + +[Typedef] +id: GENO:0000783 +name: has_sequence_unit +def: "A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues)" [] +is_a: GENO:0000654 ! has_sequence_part + +[Typedef] +id: GENO:0000784 +name: completely_varies_with +def: "A relation between two seqeunces or features that are considered variant with each other along their entire extents." [] +is_symmetric: true +is_a: GENO:0000683 ! varies_with + +[Typedef] +id: GENO:0000790 +name: related_condition + +[Typedef] +id: GENO:0000791 +name: inferred_to_cause_condition +property_value: IAO:0000116 "Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene)" xsd:string +property_value: IAO:0000116 "The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains.\n\nBelow are the different kinds/paths of propagation we desire:\n1. Propagation 'down' a genotype (from larger components to smaller ones)\n2. Propagation 'up' a genotype (from smaller components to larger ones)\n3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype).\n4. From an effective genotype to its intrinsic and extrinsic components.\n5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele).\n6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this.\n\nNote that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha/shha [AB] to shha/shha [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition')" xsd:string +holds_over_chain: GENO:0000382 RO:0003303 {comment="Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype."} +holds_over_chain: GENO:0000383 RO:0003303 {comment="Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration."} +holds_over_chain: GENO:0000445 RO:0003303 {comment="Property chain to propagate inferred condition associations from a variant locus instance to a gene class (to support cases where the phenotype association is made directly at the level of the variant locus/allele)."} +holds_over_chain: GENO:0000661 RO:0003303 {comment="Property chain to propagate inferred condition associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)"} +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000793 +name: inferred_to_contribute_to_condition +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000794 +name: inferred_to_correlate_with_condition +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000840 +name: pathogenic_for_condition +xref: LOINC:LA6668-3 +is_a: RO:0003303 ! causes condition + +[Typedef] +id: GENO:0000841 +name: likely_pathogenic_for_condition +xref: LOINC:LA26332-9 +is_a: RO:0003303 ! causes condition + +[Typedef] +id: GENO:0000842 +name: non-causal_for_condition +def: "Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to." [] +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000843 +name: benign_for_condition +xref: LOINC:LA6675-8 +is_a: GENO:0000842 ! non-causal_for_condition + +[Typedef] +id: GENO:0000844 +name: likely_benign_for_condition +xref: LOINC:LA26334-5 +is_a: GENO:0000842 ! non-causal_for_condition + +[Typedef] +id: GENO:0000845 +name: has_uncertain_significance_for_condition +xref: LOINC:LA26333-7 +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000846 +name: has_qualifying_process +def: "A relation used to describe a process contextualizing the identity of an entity." [] +is_a: GENO:0000580 ! has_qualifier + +[Typedef] +id: GENO:0000847 +name: has_qualifying_environment +def: "A relation used to describe an environment contextualizing the identity of an entity." [] +is_a: GENO:0000580 ! has_qualifier + +[Typedef] +id: GENO:0000849 +name: is_candidate_variant_for +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: GENO:0000903 +name: has_location +def: "A relation linking a sequence feature to the location it occupies on some reference sequence." [] +property_value: IAO:0000118 "occupies" xsd:string +domain: SO:0000110 ! sequence_feature +range: GENO:0000815 ! sequence feature location + +[Typedef] +id: GENO:0000906 +name: on strand +comment: Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from. + +[Typedef] +id: GENO:0000957 +name: has_defining_location +def: "Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement." [] +comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location.\n\nFor copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. +range: GENO:0000815 ! sequence feature location + +[Typedef] +id: GENO:0000958 +name: has_defining_sequence +def: "Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement." [] +comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement. +range: GENO:0000702 ! biological sequence + +[Typedef] +id: GENO:0000959 +name: has_defining_feature +def: "Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement." [] +comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference.\n\nFor copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. +range: SO:0000110 ! sequence_feature + +[Typedef] +id: GENO:0000966 +name: has_interval +def: "Relates a sequence feature location to an interval that defines its start and end position." [] +comment: Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects. +domain: GENO:0000815 ! sequence feature location + +[Typedef] +id: GENO:0000967 +name: has_reference_sequence +def: "Relates a 'sequence feature location' to a sequence that it is anchored to." [] + +[Typedef] +id: IAO:0000136 +name: is about +def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." [] + +[Typedef] +id: IAO:0000219 +name: denotes +def: "Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" [] +property_value: IAO:0000116 "Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of." xsd:string +is_a: IAO:0000136 ! is about + +[Typedef] +id: OBI:0000293 +name: has_specified_input +def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +is_a: RO:0002233 ! has input + +[Typedef] +id: OBI:0000299 +name: has_specified_output +def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +is_a: RO:0002234 ! has output + +[Typedef] +id: RO:0000052 +name: inheres_in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] + +[Typedef] +id: RO:0000059 +name: concretizes +def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000087 +name: has_role +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0001000 +name: derives from + +[Typedef] +id: RO:0002091 +name: starts during +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002093 +name: ends during +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +is_symmetric: true + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] + +[Typedef] +id: RO:0002200 +name: has phenotype +def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] +range: UPHENO:0001001 ! Phenotype +inverse_of: RO:0002201 ! phenotype of + +[Typedef] +id: RO:0002201 +name: phenotype of +domain: UPHENO:0001001 ! Phenotype + +[Typedef] +id: RO:0002222 +name: temporally related to + +[Typedef] +id: RO:0002233 +name: has input +def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +is_a: RO:0000057 ! has participant + +[Typedef] +id: RO:0002234 +name: has output +def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." [] +is_a: RO:0000057 ! has participant +inverse_of: RO:0002353 ! output of + +[Typedef] +id: RO:0002350 +name: is member of +is_a: BFO:0000050 ! is part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000112 "Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes\n\nExample 2: a collection of information entities such as a genotype being comprised of a background component and a variant component" xsd:string +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002352 +name: input of +is_a: RO:0000056 ! participates in + +[Typedef] +id: RO:0002353 +name: output of +is_a: RO:0000056 ! participates in + +[Typedef] +id: RO:0002354 +name: obsolete_formed as result of +is_a: ObsoleteProperty + +[Typedef] +id: RO:000244 +name: molecularly controls +def: "Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b" [] + +[Typedef] +id: RO:0002522 +name: bounds sequence of +def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: GENO:0000654 ! has_sequence_part + +[Typedef] +id: RO:0002524 +name: has subsequence +def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +is_a: GENO:0000654 ! has_sequence_part +inverse_of: RO:0002525 ! is subsequence of + +[Typedef] +id: RO:0002525 +name: is subsequence of +is_a: GENO:0000655 ! is_sequence_part_of + +[Typedef] +id: RO:0002526 +name: overlaps sequence of +def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +property_value: http://purl.org/dc/terms/source http://biorxiv.org/content/early/2014/06/27/006650.abstract xsd:string +is_a: RO:0002131 ! overlaps + +[Typedef] +id: RO:0002528 +name: is upstream of sequence of +def: "inverse of downstream of sequence of" [] + +[Typedef] +id: RO:0002529 +name: is downstream of sequence of +def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] + +[Typedef] +id: RO:0003301 +name: is model of +def: "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] +comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. +property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" xsd:string +property_value: IAO:0000117 "Matthew Brush" xsd:string + +[Typedef] +id: RO:0003302 +name: causes or contributes to condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions. +property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." xsd:string +property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: RO:0003303 +name: causes condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003304 +name: contributes to condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003305 +name: contributes to severity of condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual." [] +property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003306 +name: contributes to frequency of condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population." [] +property_value: IAO:0000118 "contributes to penetrance of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003307 +name: is preventative for condition +def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions. +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: RO:0003308 +name: correlated with condition +def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] +is_a: GENO:0000790 ! related_condition + +[Typedef] +id: begin +name: begin +is_a: GENO:0000708 ! faldo properties + +[Typedef] +id: end +name: end +is_a: GENO:0000708 ! faldo properties + +[Typedef] +id: http://purl.org/oban/association_has_object +name: association has object + +[Typedef] +id: http://purl.org/oban/association_has_predicate +name: association has predicate + +[Typedef] +id: http://purl.org/oban/association_has_subject +name: association has subject + +[Typedef] +id: location +name: location +is_a: GENO:0000708 ! faldo properties + +[Typedef] +id: reference +name: reference +def: "The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly." [] +is_a: GENO:0000708 ! faldo properties + diff --git a/geno.owl b/geno.owl new file mode 100644 index 0000000..a70d2f3 --- /dev/null +++ b/geno.owl @@ -0,0 +1,9511 @@ + + + + + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. + +Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 + GENO ontology + Unspecified + + + + + + + + + + + + + + + + + + + Used to annotation axioms that define identity criteria for instances of a class. + is_identity_criteria + + + + + + + + + proabalistic_quantifier + + + + + + + + Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models. + mixin + + + + + + + + + gene symbol + + + + + + + + editor preferred term + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + editor preferred term + + + + + + + + example + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage + + + + + + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + + + + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition + + + + + + + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + editor note + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + alternative term + + + + + + + + definition source + + formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + + + + + + + + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + + + + + + is denotator type + relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from + + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + + + + + + + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + + + + + + + first order logic expression + PERSON:Alan Ruttenberg + first order logic expression + + + + + + + + antisymmetric property + part_of antisymmetric property xsd:true + use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + + + + + + OBO foundry unique label + + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + + + + + + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + has associated axiom(fol) + + + + + + + + is allocated id range + Add as annotation triples in the granting ontology + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + is allocated id range + + + + + + + + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + 2018-09-21T16:43:39Z + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + + + + + + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + https://github.com/geneontology/go-ontology/issues/15532 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + + + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + has axiom label + + + + + + + + term replaced by + + Add as annotation triples in the granting ontology + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + term replaced by + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + begin + + + + + + + + + end + + + + + + + + + location + + + + + + + + + The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly. + reference + + + + + + + + + + + is part of + + + + + + + + + + has part + + + + + + + + + + + + + + + + + + A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'. + Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants. + http://purl.obolibrary.org/obo/so_has_quality + has_sequence_attribute + + + + + + + + + + + + A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes + materializes + Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence. + bears_concretization_of + + + + + + + + + is_genotype_of + + + + + + + + + + + + + + + + + + + A relationship that holds between a biological entity and some level of genetic variation present in its genome. + This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype. + The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations. + has_genotype + + + + + + + + + + + An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO) + No proper part relation anymore in RO/BFO? + http://semanticscience.org/resource/SIO_000053 + has_proper_part + + + + + + + + + + A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears. + has_sequence_component + has_state + VMC:state + 'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule. + has_sequence + + + + + + + + + + A geno:intrinnsic genotype 'specifies' a SO:genome. +A geno:karyotype 'specifies' a geno:karyotype feature collection. + A relationship between an information content entity representing a specification, and the entity it specifies. + obsolete_specifies + + + + + + + + + Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. + obsolete_approximates_sequence + + + + + + + + + Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. + obsolete_resolves_to_sequence + + + + + + + + + An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole. + http://semanticscience.org/resource/SIO_000093 + is_proper_part_of + + + + + + + + + is_sequence_of + + + + + + + + + is_subject_of + + + + + + + + + obsolete_is_specified_by + + + + + + + + + + shortcut relation used to link a phenotype directly to a genotype of an organism + is_phenotype_of_organism_with_genotype + is_phenotype_with_genotype + phenotype_has_genotype + Might expand to something like: + +phenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype))))))) + obsolete_is_phenotype_of_genotype + + + + + + + + + + A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next. + Exploratory/temporary property, as we formalize our phenotypic inheritance model. + obsolete_participates_in_inheritance_process + + + + + + + + + + + A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression. + has_variant_part + + + + + + + + + + is_variant_part_of + + + + + + + + + + + A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant. + has_reference_sequence_part + has_reference_part + + + + + + + + + is_reference_part_of + + + + + + + + + + + <fgf8a^ti282a> is_allele_of the 'danio rerio fgf8a' gene locus. + A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size. + Domain = allele +Range = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation). + Note that the allele <fgf8a^ti282a> is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'. If the <fgf8a^ti282a> allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of a 'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product. + is_sequence_variant_of + To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size). + +While conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like "fgf8a<ti282a> is an allele of the Danio rerio fgf8a gene", and we may create data where fgf8a<ti282a> is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene). + +It is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. + +This departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\GAL4 gene. + +At the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'. + is_allele_of + + + + + + + + + + A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level). + is_variant_instance_of + formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus) + Domain = genomic feature instance +Range = punned gene class IRI + obsolete_is_genetic_variant_of + + + + + + + + + A relation linking a gene class to a sequence-varaint or expression-variant of the gene. + has_variant_instance + formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by) + Domain = punned gene class +Range = genomic feature + obsolete_has_genetic_variant + + + + + + + + + A relation linking a gene class to one of its sequence-variant alleles. + Domain = punned gene class +Range = allele + has_sequence_variant + has_allele + + + + + + + + + + A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets. + This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets. + targets_gene + + + + + + + + + + + + + + + + + A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression. + This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset. + has_affected_feature + + + + + + + + + + A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents. + Domain = expression variant feature. +Range = punned gene class + This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class. + is_expression_variant_of + + + + + + + + A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature. + class_to_feature_relation + This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases) + is_feature_affected_by + + + + + + + + + A relation between a gene class and a gene targeting reagent that targets it. + is_target_of + Domain = punned gene class +Range = gene knockdown reagent + is_gene_target_of + + + + + + + + + A relation linking a gene class to one of an expression-variant of that gene.. + Domain = punned gene class +Range = expression variant feature + has_expression_variant_instance + has_expression_variant + + + + + + + + + A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression. + Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property. + This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of. + obsolete_is_variant_with + + + + + + + + + A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways). + obsolete_is_expression_variant_with + + + + + + + + A relation used to describe a context or conditions that define and/or identify an entity. + Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association. + +Used in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features. + has_qualifying_context + has_qualifier + + + + + + + + + + + a relation to link a single locus complement to its zygosity. + has_zygosity + + + + + + + + + + A relationship between a reference locus/allele and the gene class it is an allele of. + is_reference_allele_of + + + + + + + + + Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed. + has_color_value + Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized. + has_staining_intensity + + + + + + + + Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant. + relation between an molecular agent and its molecular target + is_targeted_by + + + + + + + + + + + + + 1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. + +2. Used to specify the genetic background/strain of origin of an allele (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds. + +3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC) + Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence. + sequence_derives_from + + + + + + + + + + A relationship between a variant allele and the gene class it is an allele of. + is_variant_allele_of + + + + + + + + + + Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases. + has_sex_agnostic_part + + + + + + + + + + A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of. + is_mutant_allele_of + + + + + + + + + + A relationship between a polymorphic allele and the gene class it is an allele of. + is_polymorphic_allele_of + + + + + + + + + + A relationship between a wild-type allele and the gene class it is an allele of. + is_wild_type_allele_of + + + + + + + + + + An organizational class to hold relations of parthood between sequences/features. + has_sequence_part + + + + + + + + + is_sequence_part_of + + + + + + + + + Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases. + is_sex_agnostic_part_of + + + + + + + + + A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part). + This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of) + varies_with + + + + + + + + organizational property to hold imports from faldo. + faldo properties + + + + + + + + + + + + + + + + + A relation linking a qualified sequence feature to its component sequence feature. + has_sequence_feature_component + In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism. + has_sequence_feature + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_inferred_phenotype + + + + + + + + + Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype. + + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration. + + + + + + + + + + Property chain to propagate inferred phenotype associations from an intrinsic genotype component (e.g. a (sequence-)variant locus instance) to a gene class. + + + + + + + + + Property chain to propagate inferred phenotype associations from a (sequence-)variant locus instance to a gene class (to support cases where the phenotype association is made at the level of the variant gene locus). + + + + + + + + + + Property chain to propagate inferred phenotype associations from an extrinnsic genotype component (e.g. a expression-variant gene instance) to a gene class. + + + + + + + + + Property chain to propagate inferred phenotype associations from an expression-variant gene instance to a gene class (to support cases where the phenotype association is made at the level of the expression-variant gene). + + + + + + + + + Property chain to propagate inferred phenotype associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components) + + + + + + + + + Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes. + obsolete_has_regulatory_part + + + + + + + + + + + + + + A relation linking a sequence_alteration to the gene it alters. + is_within_allele_of + obsolete_is_alteration_within + + + + + + + + + has_asserted_phenotype + + + + + + + + + Proposal for a property linking regulatory elements to larger features of which they are a part. + is_regulatory_part_of + + + + + + + + + A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances. + For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them. + obsolete_has_position_component + + + + + + + + + A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues) + has_sequence_unit + + + + + + + + + + A relation between two seqeunces or features that are considered variant with each other along their entire extents. + completely_varies_with + + + + + + + + related_condition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene) + The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains. Where this is the case, it is noted in the annotations on the property chains. + +Below are the different kinds/paths of propagation we desire: +1. Propagation 'down' a genotype (from larger components to smaller ones) +2. Propagation 'up' a genotype (from smaller components to larger ones) +3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype). +4. From an effective genotype to its intrinsic and extrinsic components. +5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele). +6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this. + +Note that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha<tbx392>/shha<tbx392> [AB] to shha<tbx392>/shha<tbx392> [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background. So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as: has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition') + inferred_to_cause_condition + + + + + + + + + + This is a case of inter-gneotype phenotype propagation, requiring propagation down oen genotype and then up another. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to have this chain. + +This property chain propagates a phenotype asserted on a sex-qualified intrinsic genotype, down to its sex-agnostic genotype part, and then up to a parent effective genotype that has it as a variant part. I think this is OK in all cases, so we can implement this as the one case where we can have inter-genotype pheno propagation. But as noted, there will likely be no data that actually meets criteria to use this chain, so we can probably leave it out. + + + + + + + + + Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype. + + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, to the coompnent variant parts of this sex-agnostic genotype. + + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to move past the sex-agnostic genotype and down to its parts. + +The following shorter chain would also suffice here: +is_variant_part_of o inferred_to_cause_condition + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration. + + + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, through the coompnent variant parts of this sex-agnostic genotype, and to the affected gene. + + + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to propagate to genes. + +The shorter chain below would also suffice for this propagation: +has_allele o inferred_to_cause_condition + + + + + + + + + + Property chain to propagate inferred condition associations from an sequence alteration through the variant locus to a gene class. (separate chains are needed to propagate from the variant locus to the gene class, and another to propagate from a genotype, GVC, or VSLC to the gene class). + + +NOTE that i dont need this property chain if I have a property chain to infer a has_affected_locus link from a sequence alteration to a gene when the link is asserted from the variant locus to the gene: + +is_variant_part_of o has_affected_locus --> has_affected_locus + + + + + + + + + + Obsolete comment: Property chain to propagate inferred condition associations from an intrinsic genotype, GC, or VLSC to a gene class. (a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class). + +The following, shorter chain, would also suffice here: +has_allele o inferred_to_cause_condition -> inferred_to_cause_condition + Property chain to propagate inferred condition associations from an intrinsic genotype, GVC, or VLSC to an affected gene class, or from an extrinsic gneotype or component to an affected gene class. + +The following, shorter chain, would also suffice here: +has_affected_locus o inferred_to_cause_condition -> inferred_to_cause_condition + +Note that a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class in cases where the link to gene is through the variant locus rather than the seq alteration). + + + + + + + + + Property chain to propagate inferred condition associations from a variant locus instance to a gene class (to support cases where the phenotype association is made directly at the level of the variant locus/allele). + + + + + + + + + + Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype to a sex-agnostic intrinsic genotype. + + + + + + + + + Property chain to propagate inferred condition associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components) + + + + + + + + + inferred_to_contribute_to_condition + + + + + + + + + inferred_to_correlate_with_condition + + + + + + + + + LOINC:LA6668-3 + pathogenic_for_condition + + + + + + + + + LOINC:LA26332-9 + likely_pathogenic_for_condition + + + + + + + + + Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to. + non-causal_for_condition + + + + + + + + + LOINC:LA6675-8 + benign_for_condition + + + + + + + + + LOINC:LA26334-5 + likely_benign_for_condition + + + + + + + + + LOINC:LA26333-7 + has_uncertain_significance_for_condition + + + + + + + + + A relation used to describe a process contextualizing the identity of an entity. + has_qualifying_process + + + + + + + + + A relation used to describe an environment contextualizing the identity of an entity. + has_qualifying_environment + + + + + + + + + is_candidate_variant_for + + + + + + + + + + A relation linking a sequence feature to the location it occupies on some reference sequence. + occupies + has_location + + + + + + + + Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from. + on strand + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location. + +For copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. + has_defining_location + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement. + has_defining_sequence + + + + + + + + + + + + + + + + + Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement. + Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference. + +For copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement. + has_defining_feature + + + + + + + + + Relates a sequence feature location to an interval that defines its start and end position. + Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects. + has_interval + + + + + + + + Relates a 'sequence feature location' to a sequence that it is anchored to. + has_reference_sequence + + + + + + + + is_about is a (currently) primitive relation that relates an information artifact to an entity. + is about + + + + + + + + + Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically + Consdier if this is the best relation for linking genotypes to the genomic entities they specify. We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of. + denotes + + + + + + + + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + has_specified_input + + + + + + + + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + has_specified_output + + + + + + + + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + inheres_in + + + + + + + + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + bearer of + + + + + + + + + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates in + + + + + + + + a relation between a process and a continuant, in which the continuant is somehow involved in the process + has participant + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + has quality + + + + + + + + + has_role + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + derives from + + + + + + + + + starts during + + + + + + + + + ends during + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + overlaps + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + in taxon + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + has phenotype + + + + + + + + + phenotype of + + + + + + + + temporally related to + + + + + + + + + p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + has input + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + has output + + + + + + + + + + is member of + + + + + + + + + Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes + +Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component + has member is a mereological relation between a collection and an item. + has member + + + + + + + + + input of + + + + + + + + + output of + + + + + + + + + obsolete_formed as result of + + + + + + + + Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b + molecularly controls + + + + + + + + + x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + Chris Mungall + bounds sequence of + + + + + + + + + + x has subsequence y iff all of the sequence parts of x are sequence parts of y + has subsequence + + + + + + + + + is subsequence of + + + + + + + + + x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. + http://biorxiv.org/content/early/2014/06/27/006650.abstract + overlaps sequence of + + + + + + + + inverse of downstream of sequence of + is upstream of sequence of + + + + + + + + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + is downstream of sequence of + + + + + + + + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + Matthew Brush + The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + is model of + + + + + + + + + The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. + +An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition. + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. + causes or contributes to condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition. + causes condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition. + contributes to condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual. + contributes to expressivity of condition + contributes to severity of condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population. + contributes to penetrance of condition + contributes to frequency of condition + + + + + + + + + A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions. + is preventative for condition + + + + + + + + + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + correlated with condition + + + + + + + + association has object + + + + + + + + association has predicate + + + + + + + + association has subject + + + + + + + + + + + + + + + + + + + The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is. + position + + + + + + + + + Property linking a sequence or sequence feature to an integer representing its length in terms of the number of units in the sequence. + has_extent + + + + + + + + + + Shortcut relation linking a sequence feature directly to a string representing the 'state' of its sequence - i.e. the ordering of units that comprise it (e.g. 'atgcagctagctaccgtcgatcg'). + has_sequence_string + + + + + + + + ObsoleteDataProperty + + + + + + + + The 'rank' quantifier in Bgee gene-anatomy associations, that indicates the imporatnace/specificity of a gene expression in a given anatommy relative to expressionin other anatomies for the same gene. + Property to link an assertion or association with some value quantifying its relevance or ranking. + has_quantifier + + + + + + + + The starting position of a sequence feature or interval. + start_position + + + + + + + + The ending position of a sequence feature or interval. + end_position + + + + + + + + + + Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg'). + has_string + + + + + + + + Describes the number of members in some set. + has_count + In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'. + has_member_count + + + + + + + + + + + + + + Both strands + + + + + + + + + A position that is exactly known. + Exact position + + + + + + + + + Positive strand + + + + + + + + + Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate. + We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region). + FALDO + Position + + + + + + + + + + + + + + 1 + + + + + 1 + + + + + + A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene. + From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence. + Region + + + + + + + + + Negative strand + + + + + + + + + Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'. + Stranded position + + + + + + + + + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + + + + + + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + continuant + continuant + + + + + + + + + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + occurrent + occurrent + + + + + + + + + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + independent continuant + independent continuant + + + + + + + + + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + + process + process + + + + + + + + + + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocitosis and exocitosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89 + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + + disposition + disposition + + + + + + + + + + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + realizable entity + realizable entity + + + + + + + + + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + + quality + quality + + + + + + + + + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + specifically dependent continuant + specifically dependent continuant + + + + + + + + + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + role + role + + + + + + + + + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + generically dependent continuant + generically dependent continuant + + + + + + + + + the function of a hammer to drive in nails + the function of a heart pacemaker to regulate the beating of a heart through electricity + the function of amylase in saliva to break down starch into sugar + BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + + function + + + + + + + + + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + material entity + material entity + + + + + + + + + Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology. + molecular entity + + + + + + + + + nucleic acid + + + + + + + + + + + + + + + A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). + cell line + + + + + + + + + Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies. + cell + + + + + + + + + 1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions. + +2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity). + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system + + + + + + + + + A technique is a planned process used to accomplish a specific activity or task. + technique + + + + + + + + + A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo. + embryonic stem cell line + + + + + + + + + A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types. + stem cell line + + + + + + + + + Example zebrafish intrinsic genotype: + +Genotype = fgf8a<ti282a/+>; shha<tb392/tb392> (AB) +reference component (genomic background) = AB +variant component ('genomic variation complement') = fgf8a<ti282a/+>; shha<tb392/tb392> + +. . . and within this variant component, there are two 'variant single locus complements' represented: + +allele complement 1 = fgf8a<ti282a/+> +allele complement 2 = shha<tb392/tb392> + +and within each of these 'variant single locus complements' there is one or more variant gene locus member: + +in complement 1: fgf8a<ti282a> +in complement 2: shha<ttb392> + A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement) + This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). + +Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. + genotype + organismal genotype + sex-agnostic intrinsic genotype + In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances). + genomic genotype (sex-agnostic) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An allele that varies in it sequence from what is considered the reference or canonical sequence at that location. + The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles. + alternate allele + sequence-variant feature + variant feature + Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another. + +A variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence. + variant allele + + + + + + + + + + + + + + + + + + + + + + + + + + A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype. + Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases. + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation. + +In model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a<t1282a/+>(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)). + genomic variation complement + + + + + + + + + The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB) + A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). + Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it. + genomic background + OBI:genetic population background information + background genome + + + + + + + + + + + + + + + The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The "mn004Gt" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome. + +http://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722 + +http://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8 + A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene) + Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment). + +This design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not. + http://purl.obolibrary.org/obo/SO_0001023 ! allele + In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion. + +A genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene. + gene allele + + + + + + + + + + + + + + + + + + + + + + + + + + A sequence that serves as a standard against which other sequences at the same location are compared. + The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant. + reference sequence + A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence. + reference sequence + + + + + + + + + a collection more than one sequence features (ie a collection of discontinuous sequence features) + perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one) + 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. + obsolete_sequence feature collection + + + + + + + + + A sequence feature collection comprised of discontiguous sequences from a single genome + Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system. + genomic feature collection + Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. + obsolete_genomic feature collection + + + + + + + + + A single locus complement that serves as a standard against which 'variant' sequences are compared + reference allelic complement + reference single locus feature complement + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class axiom: +'single locus complement' + and (has_sequence_attribute some reference) + +SC axioms: +'has member' exactly 0 'variant allele' +'has member' only 'reference genomic feature' +'has member' some 'reference genomic feature' + obsolete_reference single locus complement + + + + + + + + + + + + + + + + + + + + + + + + + + A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13). + variant allelic complement + Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members. + +Note that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant. + variant single locus complement + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A genome that varies at one or more loci from the sequence of some reference genome. + http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here) + variant genome + + + + + + + + + + + + + + + + + + + + + + + + + + An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome. + Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population. + +In model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared. + reference allele + + + + + + + + + + A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus). + Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '. + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class def: 'genomic feature' + and (has_sequence_attribute some unspecified) + An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). + obsolete_unspecified feature + + + + + + + + + A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature. + hemizygous reference junction + Eliminating unecessary defined/organizational classes. Former logical def: + +junction + and (has_sequence_attribute some reference) + +Subclass axiom: +is_variant_with some insertion + In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. + +The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. + obsolete_reference junction + + + + + + + + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a danio rerio. + danio rerio gene + + + + + + + + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a homo sapiens. + homo sapiens gene + + + + + + + + + + + + + + + + + + + + + + + + + + A gene that originates from the genome of a mus musculus. + mus musculus gene + + + + + + + + + A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development. +http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690 + +Note that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469 + A version/allele of a gene that serves as a standard against which variant genes are compared. + reference gene + Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. + +Eq Class axiom: +'gene allele' + and (has_sequence_attribute some reference) + +SC axioms: +is_variant_with some 'gene allele' +is_reference_allele_of some gene + Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. + +In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. + obsolete_reference gene allele + + + + + + + + + obsolete_experimental insertion + + + + + + + + + + + + + + + gene trap insertion + + + + + + + + + + + + + + + A transgene that has been integrated into a chrromosome in the host genome. + An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion. + +An 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome. + integrated transgene + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny. + 1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. + +2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way. + 1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. + +2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms. + genomic material + + + + + + + + + A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion. + physical genome + A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements. + +Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome. + material genome + + + + + + + + + a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role) + Consider http://semanticscience.org/resource/SIO_001062 ! human population ("A human population refers to a collection of human beings"). + homo sapiens population + human population + + + + + + + + + + + + + + + A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical. + organism strain or breed + Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR) + strain or breed + + + + + + + + + A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon) + taxonomic group + + + + + + + + + mus musculus strain + + + + + + + + + + + + + + + + + + + + + danio rerio strain + + + + + + + + + sequence attribute that can inhere only in a collection of more than one sequence features + obsolete_sequence feature collection attribute + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes). + in cis + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes). + in trans + + + + + + + + + + + + + + + An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different). + allelic state + derived from https://en.wikipedia.org/wiki/Zygosity + http://semanticscience.org/resource/SIO_001263 + zygosity + + + + + + + + + hemizygous + + + + + + + + + heterozygous + + + + + + + + + homozygous + + + + + + + + + indeterminite zygosity + no-call zygosity + unknown zygosity + unspecified zygosity + + + + + indeterminite zygosity + MGI uses this term when zygosity is not known. + + + + + no-call zygosity + (this is how the GVF10 format/standard refers to loci without enough data to make an accurate call . . . see http://www.sequenceontology.org/resources/gvf.html#quick_gvf_examples) + + + + + + + + + The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event. + We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells). + +We can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms. + heritabililty + + + + + + + + + heritable + + + + + + + + + non-heritable + + + + + + + + + The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment. + The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family. + mode of inheritance + phenotypic inheritance pattern + http://purl.obolibrary.org/obo/HP_0000005 + http://purl.obolibrary.org/obo/NCIT_C45827 + An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, "genetic context" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. + +These genetic and environmental "interactions" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y. + inheritance pattern + + + + + + + + + disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes + Triage until decide if want to define this as grouping class that would result in multiple-inheritance. + obsolete_dominant inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant autosomal inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + pure dominant inheritance + complete autosomal dominant inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + intermediate dominant autosomal inheritance + semi-dominant autosomal inheritance + incomplete autosomal dominant inheritance + + + + + + + + + An X-linked inheritance pattern wherein the trait manifests in heterozygotes. + http://purl.obolibrary.org/obo/HP_0001423 + X-linked dominant inheritance + + + + + + + + + An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes. + vertical inheritance + http://purl.obolibrary.org/obo/HP_0000006 + autosomal dominant inheritance + + + + + + + + + An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals. + autosomal recessive inheritance + + + + + + + + + An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals. + http://purl.obolibrary.org/obo/HP_0001419 + X-linked recessive inheritance + + + + + + + + + duplicate term, use GENO:0000148 + obsolete_autosomal recessive inheritance + + + + + + + + + An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared. + Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another. + reference + + + + + + + + + unspecified life cycle stage + + + + + + + + + objective is to insert some specified sequence into the genome of a cell or virus + genetic insertion technique + + + + + + + + + mutagen treatment technique + + + + + + + + + + + + + + + a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). + This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. + targeted gene mutation technique + + + + + + + + + Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. + random genetic insertion technique + + + + + + + + + + + + + + + targeted genetic insertion technique + + + + + + + + + enhancer trapping technique + + + + + + + + + gene trapping technique + + + + + + + + + promoter trapping technique + + + + + + + + + targeted knock-in technique + + + + + + + + + random transgene insertion technique + + + + + + + + + A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome + obsolete_chromosome complement + + + + + + + + + + + + + + + + A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation + duplicate chromosome + This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome. + gained aneusomic chromosome + + + + + + + + + + + + 0 + + + + A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation. + This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as "the point at which one or more contiguous nucleotides were excised". + absent aneusomic chromosome + lost aneusomic chromosome + + + + + + + + + + + + + + + + + A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation. + Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism. + aneuploid chromosomal segment + aneusomic chromosomal subregion/segment + partial aneusomic chromosomal element + Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome." + aneusomic chromosomal part + + + + + + + + + + A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event. + duplicate partial aneuploid chromosomal element + translocated duplicate chromosomal element + translocated duplicate chromosomal segment + Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location. + gained aneusomic chromosomal segment + + + + + + + + + + + + 0 + + + + A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome. + In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement + dropped partial anneuploid chromosomal element + translocated absent chromosomal segment + truncated chromosome terminus + This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome. + +Loss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus. + lost aneusomic chromosomal segment + + + + + + + + + + + + + + + + + A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation + complete aneusomic chromosome + Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism. + +Similarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication. + aneusomic chromosome + + + + + + + + + Stub class to serve as root of hierarchy for imports of biological processes from GO-BP. + biological process + + + + + + + + + disomic zygosity + + + + + + + + + aneusomic zygosity + + + + + + + + + trisomic homozygous + + + + + + + + + trisomic heterozygous + + + + + + + + + A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a<ti282a>/fgf8a<x15>) + trans-heterozygous + compound heterozygous + + + + + + + + + A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe) + replaced with SO:engineered_region + extra-genomic sequence + obsolete_reagent sequence feature + + + + + + + + + a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a<ti282a/+>) + simple heterozygous + + + + + + + + + + + + + + + + + + + + + + + + + + A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc) + transgene part + + + + + + + + + An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level + variant + + + + + + + + + An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant. + polymorphic + + + + + + + + + An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence. + mutant + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism) + This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology. + 1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. + +2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). + +3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome. + genomic feature + + + + + + + + + + A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion). + This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material. + genetic material + + + + + + + + + + An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain. + Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines + Not required for any specific use case at this point so removed for simplicity. +Formely asserted as allele and inferred as varaint allele. +Eq class definition: +allele + and (mutation or ('has subsequence' some mutation)) + 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. + obsolete_mutant allele + + + + + + + + + + + + + + + A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain. + mutation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon) + Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element + episomal replicon + Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. + extrachromosomal replicon + + + + + + + + + expression construct feature + expression construct + + + + + + + + + An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population. + PMID: 25741868 ACMG Guidelines + Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%). + polymorphic allele + + + + + + + + + A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location. + major allele + major polymorphic allele + + + + + + + + + A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location). + minor allele + minor polymorphic allele + + + + + + + + + A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree. + ancestral allele + ancestral polymorphic allele + + + + + + + + + An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared. + wild-type allele + 'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain. + +The notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis. + wild-type allele + + + + + + + + + + wild-type gene allele + A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation. + wild-type gene + + + + + + + + + + + + + + + + + + + + + A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi. + The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position. + reagent targeted gene + + + + + + + + + A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome). + experimentally-expressed transgene + extrinsic transgene + transiently-expressed transgene + + + + + + + + + An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared. + wild-type + + + + + + + + + + + + + + + + + + + + + + + + + + One of a set of sequence features known to exist at a particular genomic location. + A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene. + +To be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene. + +[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17) +[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17) +[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17) +[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17) +[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17) +[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17) +[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483 +[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17) +[8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17) +[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17) +[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17) +[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17) + variable feature + An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). + +Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence). + allele + + + + + + + + + + a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation. + aneusomic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An allele of a gene that contains some sequence alteration. + A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset. + variant gene allele + + + + + + + + + The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a<ti282a/+>. + +The collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome. + A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism. + TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label. + allelic complement + homologous allele complement + single locus feature complement + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes. + +The fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. + single locus complement + + + + + + + + + In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as: + + shha<MO1-1ng/ul>; shhb<pFLAG-mmusShhb> + +This notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct. + A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state. + We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. + +Our rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally applied rather than inherent to the genome. + +Finally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." + experimental genotype + expression genotype + An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment. + +The 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations. + extrinsic genotype + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs). + Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." + An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment. + effective genotype + + + + + + + + + + + + + + + A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes). + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment. + reagent-targeted gene complement + + + + + + + + + + + + + + + The set of all transgenes trransiently expressed in a biological system in the context of a given experiment. + experimental transgene complement + transiently-expressed transgene complement + + + + + + + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes). + A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism). + See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself. + expression allele + Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism). + +The identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system. + expression-variant gene + + + + + + + + + gene targeting reagent + sequence targeting reagent + gene knockdown reagent + + + + + + + + + A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent. + targeted gene segment + reagent-targeted gene subregion + + + + + + + + + + + + + + + + + + + + + + A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference. + As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh<tbx292>, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above. + Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). +Note however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO. + 1. Scope of 'Genetic State': +'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs. + +2. Genotype Subtypes: +In GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. + +Two more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features. + +3. The Genotype Partonomy: +'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a<ti282a/ti282a>; fgf3<t24149/+>[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements: + + - GVC: fgf8a<ti282a/ti282a>; fgf3<t24149/+> (total intrinsic variation in the genome) + - Genomic Background: AB (the reference against which the GVC is variant) + - VSLC1: fgf8a<ti282a/ti282a> (homozygous complement of gene alleles at one known variant locus) + - VSLC2: fgf3<t24149/+> (heterozygous complement of gene alleles at another known variant locus) + - Allele 1: fgf8a<ti282a> (variant version of the fgf8a gene, present in two copies) + - Allele 2: fgf3<t24149> (variant version of the fgf3 gene, present in one copy) + - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy) + - Sequence Alteration1: <ti282a> (the specific mutation within the fgf8a gene that makes it variant) + - Sequence Alteration2: <t24149> (the specific mutation within the fgf3 gene that makes it variant) + +A graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md + +One reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data. + genotype + + + + + + + + + ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl +This ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes. + zebrafish phenotype + + + + + + + + + an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. + homoplasmic + + + + + + + + + an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. + heteroplasmic + + + + + + + + + hemizygous X-linked + + + + + + + + + hemizygous Y-linked + + + + + + + + + hemizygous insertion-linked + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). + Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it. + background genotype + genomic background + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. + New term request for SO. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosomal region + + + + + + + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosome sub-band + + + + + + + + + chromosomal band brightness + chromosomal band intensity + + + + + + + + + gpos + + + + + + + + + gneg + + + + + + + + + gvar + + + + + + + + + gpos100 + + + + + + + + + gpos75 + + + + + + + + + gpos50 + + + + + + + + + gpos25 + + + + + + + + + A chromosome arm that is the shorter of the two arms of a given chromosome. + p-arm + stalk + short chromosome arm + + + + + + + + + A chromosome arm that is the longer of the two arms of a given chromosome. + q-arm + long chromosome arm + + + + + + + + + gpos66 + + + + + + + + + gpos33 + + + + + + + + + + A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed. + regulatory transgene region + + + + + + + + + A transgene part whose sequence is expressed in a gene product through transcription and/or translation. + coding transgene feature + expressed transgene region + + + + + + + + + reporter region + + + + + + + + + + + + + + + + + + + + + + + + + + + A transgene whose product is used as a selectable marker. + selectable marker transgene + + + + + + + + + A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell. + Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28) + Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). + +A base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation). + karyotype + + + + + + + + + + + + + + + A genomic genotype where the genomic background specifies a male or female sex chromosome complement. + This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). + +In the genotype partonomy, a sex qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former. + intrinsic genotype (sex-specific) + sex-qualified genotype + sex-qualified intrinsic genotype + We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances. + +Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. + genomic genotype (sex-qualified) + + + + + + + + + A genomic genotype here the genomic background specifies a male sex chromosome complement. + male intrinsic genotype + + + + + + + + + A genomic genotype here the genomic background specifies a female sex chromosome complement. + female intrinsic genotype + + + + + + + + + A background genotype whose sequence or identity is not known or specified. + unspecified background genotype + unspecified genomic background + + + + + + + + + + + + + + + + + + + + + 1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus + +2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele. + +3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y} + A set of sequence features. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature). + +The notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3]. + +[1] https://www.snpedia.com/index.php/APOE-%CE%B54 +[2] https://www.snpedia.com/index.php/APOE-%CE%B52 +[3] https://www.snpedia.com/index.php/Gs270 + sequence feature set + + + + + + + + + + + + + + + + A set of genomic features (i.e. sequence features that are of genomic origin). + In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member. + genomic locus complement + A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature. + +The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. + genomic feature set + + + + + + + + + + + + + + + + + + + + + + + + + + A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc). + defined gene part + SO:0000831 (gene member region) + gene part + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A transgene that codes for a product used as a reporter of gene expression or activity. + reporter transgene + + + + + + + + + A junction between bases, a deletion variant, a terminus at the end of a chromosome. + A genomic feature that has an extent of zero. + Former logical def: +'genomic feature' + and (has_extent value 0) + obsolete_null feature + + + + + + + + + + + + + + + + + + + + An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found. + aberrant extrachromosomal replicon + exogenous extrachromosomal replicon + transgenic extrachromosomal replicon + Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'. + novel extrachromosomal replicon + + + + + + + + + + + + + + + + A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome. + This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature. + Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles. + novel replicon + + + + + + + + + An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome. + novel + + + + + + + + + A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide). + terminus + + + + + + + + + + + + + + + + + A sequence feature or a set of such features. + sequence feature or collection + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location. + sequence feature or set + + + + + + + + + + + + + + + + + A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides). + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + biomacromolecular sequence + state + VMC:State + 'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome. + biological sequence + + + + + + + + + + + true + + + + + state + In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele. + + + + + + + + + A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position). This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification. + qualified sequence feature or collection + + + + + + + + + + + + + + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes). + A qualified sequence feature that carries sequence derived from the genome of a cell or organism. + qualified genomic feature + + + + + + + + + + + true + This axiom is an initial attempt to formalize the identity criteria of an extrinnsic context that separates qualified sequence features from sequence features (i.e. the context of its material bearer). As we further develop our efforts here this will get refined and more precise. + + + + + + + + + + + true + Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position). + + + + + + + + + + + + + + + + + + + + + + A set of qualified sequence features that carry genomic sequence. + Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member. + A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele. + +A complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome. + qualified genomic feature set + + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. + Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence. This syntax has reference and variant components - a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence. Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'. So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome. + 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. + +2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. + intrinsic genotype + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + DNA sequence + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + RNA sequence + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + amino acid sequence + + + + + + + + + obsolete_biological sequence or collection + + + + + + + + + obsolete_biological sequence collection + + + + + + + + + + A sequence feature whose identity is additionally dependent on the cellular or anatomical location of the genetic material bearing the feature. + As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell). + location-qualified sequence feature + + + + + + + + + A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct) + expression-qualified sequence feature + + + + + + + + + A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence. + This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature. + genomic coordinates + remodeling notion of sequence feature position around the idea of a 'genomic locus' + obsolete_genomic position + + + + + + + + + phenotypic inheritance process + + + + + + + + + A sequence attribute inhering in a feature whose identity is not specified. + obsolete_unspecified + + + + + + + + + An attribute describing a type of variation inhering in a sequence feature or collection. + allele attribute + variation attribute + + + + + + + + + + + + + + + + + + + + + + + + + + An intrinsic genotype that specifies variation from a defined reference genome. + variant genomic genotype + + + + + + + + + An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities. + eliminating classes that are not necessary or add uneeded complexity. + obsolete_sequence information entity + + + + + + + + + + + + + + 1 + + + + + + biological sequence residue + monomeric residue + biological sequence unit + + + + + + + + + deoxyribonucleic acid residue + DNA residue + + + + + + + + + ribonucleic acid residue + RNA residue + + + + + + + + + amino acid residue + + + + + + + + + An attribute, quality, or state of a sequence feature or collection. + http://purl.obolibrary.org/obo/SO_0000400 + Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity. + sequence feature attribute + + + + + + + + + + The location of a sequence feature as defined by its start and end position on some reference coordinate system. + 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). + +2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there. + sequence feature location + + + + + + + + + + A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature) + modification-qualified sequence feature + + + + + + + + + + + + + + + + + + + + + + + + + + + 1. The zebrafish "fgf8a<ti282a>/fgf8a<+>" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus - which here has a heterozygous state). + +2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308. + + ##fileformat=VCFv4.2 + ##FORMAT=<ID=GT, Description="Genotype, 0=REF, 1=ALT"> + #CHROM POS REF ALT FILTER FORMAT SAMP001 + 20 2300608 C T PASS GT 0/1 + 20 2301308 T G PASS GT 1/1 + (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html) + +3. Some allelic genotype formats encode the genotype as a single string - e.g. "GRCh38 Chr12:258635(A;T)" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12. + A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes. + single locus genotype + An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location. + +This contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background. + allelic genotype + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each. + genotype-phenotype association + + + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + + + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + true + + + + + + + + + + + + + + + knockdown reagent targeted gene complement + + + + + + + + + + A sequence alteration within the coding sequence of a gene. + Not required at this poitn, so marked exploratory and obsoleted. +Asserted under sequence_alteration. + obsolete_coding sequence alteration + + + + + + + + + A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome. + P-element construct + + + + + + + + + An engineered region that is used to transfer foreign genetic material into a host cell. + engineered_genetic_vector + Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. + +Constructs are typically packaged as part of delivery systems such as plasmids or viral vectors. + engineered genetic construct + + + + + + + + + A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct. + non-integrated transgene + extra-chromosomal transgene + + + + + + + + + A collection of more than one sequence feature. + http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection + obsolete_sequence feature collection + + + + + + + + + + + + + + + A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block. + Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type. But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block. + +Instead, we can create an 'allele set' class as the haplotype parent? + Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype. + A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. + +As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': + +1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. + +2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). "Star alleles" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/). + +3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. + +Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. + haplotype + + + + + + + + + A set of genomic sequences (a biological sequence that is of genomic origin). + copy number complement + A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. + genomic sequence set + + + + + + + + + A relation used to describe an environment contextualizing the identity of an entity. + microsatellite alteration + + + + + + + + + A relation used to describe a process contextualizing the identity of an entity. + repeat region alteration + + + + + + + + + A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism + allelic state + + + + + + + + + allelic dosage + an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome. + gene dosage + Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute. + Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. + +Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. + obsolete_genetic dosage + + + + + + + + + A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent. + genetic origin + variant origin + allele origin + + + + + + + + + Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg. + maternally inherited + maternal allele origin + + + + + + + + + Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm. + paternally inherited + paternal allele origin + + + + + + + + + Describes an attribute describing an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis. + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. + +De novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder. + de novo allele origin + + + + + + + + + Describes an allele whose origin is not known. + unknown allele origin + + + + + + + + + Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body. + acquired + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells. + +These acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations. + somatic allele origin + + + + + + + + + a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells). + germ-line + replaced by GENO:0000900 ! 'germline' + obsolete_gametic + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement') + +Alt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome. + "Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes." +From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/ +https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/ + diplotype + + + + + + + + + A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes. + allelic phase + + + + + + + + + + + + + + + + + + + + + oryzias latipes strain + + + + + + + + + Describes an allele that is inherited from a parent in virtue of the allele being present in one or both of the parent's germ cells (sperm or egg). + hereditary + parental origin + parentally inherited + Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation + We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (passed down from a parent) and *heritable* (passable down to offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells. + germline allele origin + + + + + + + + + An inheritance pattern that is not determined or not known. + unknown inheritance + undetermined inheritance + + + + + + + + + The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”. + One of a set of sequence features or haplotypes that exist at a particular genetic locus. <see ClinGen Allele Model> + The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. + http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/ + No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. + ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) + As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. + +In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) + obsolete_canonical allele + + + + + + + + + An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence. + The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. + http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ + No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. + +Former axiom: denotes some 'obsolete_canonical allele' + ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) + The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. + obsolete_contextual allele + + + + + + + + + A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not. + heteroplasmic mitochondrial inheritance + + + + + + + + + A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited. + homoplasmic mitochondrial inheritance + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + An generically dependent continuant that carries biological sequence that is part of or derived from a genome. + An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities. + genomic entity + + + + + + + + + A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations. + Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as +"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations." Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then could define haplotype block as a location. + +Current definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele. + Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424. + A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. + haplotype block + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. + 'Genomic Genotype' vs 'Genome' in GENO: +A genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence. Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'. So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome. + complete genotype + 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. + +2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons. + genomic genotype + + + + + + + + + A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells) + decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin + Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. + obsolete_allele cellular context + + + + + + + + + The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system + In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. + +We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences. + In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. + +For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus). + genomic location + genomic locus + VMC:Location + 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. + +2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. + +3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there. + genomic feature location + + + + + + + + + + + + + + + + + + + + + + + + true + A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc). + useful organizational term to collect entities that have genomes/genotypes. + organismal entity + + + + + + + + + The molecular product resulting from transcription of a single gene (either a protein or RNA molecule) + gene product + + + + + + + + + reporter role + + + + + + + + + selectable marker role + + + + + + + + + selectable marker region + + + + + + + + + + + + + + + A genome whose sequence is identical to that of a genome sequence considered to be the reference. + reference genome + + + + + + + + + A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it. + Former comment: "Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project." + Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype. + Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. + +Former SC axioms: +- is_allele_of some 'haplotype block' +- 'has part' some sequence_alteration + 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene). + +2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. + +GENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. + +3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': + +a. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. +b. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. +c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. + +The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. + obsolete_haplotype + + + + + + + + + A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations. + Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block. + Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. + A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. + +The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. + +----------------------- + +* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. + obsolete_haplotype block + + + + + + + + + An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell. + Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene. + organellar plasmy + + + + + + + + + Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes). + A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification. + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each. We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes. + qualified sequence feature + + + + + + + + + + + + + + + + + + + + + A set of qualified seqeunce features. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'matehmatical sets'. + qualified sequence feature set + + + + + + + + + A biolocical sequence, or set of such sequences. + biological sequence or collection + biological sequence or set + + + + + + + + + A set of biological sequences. + 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. + +A set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence. + biological sequence set + + + + + + + + + A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome. + Formerly considered modeling this as an informational entity, defined as "An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome." + functional feature complement + genetic dosage + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963. + As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). + The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. + obsolete_functional copy number complement + + + + + + + + + A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form. + obsolete_intrinsic sequence feature attribute + + + + + + + + + A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.) + obsolete_extrinsic sequence feature attribute + + + + + + + + + A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism). + allelic cellular distribution + + + + + + + + + A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin. + constitutional + + + + + + + + + A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin. + clonal + + + + + + + + + An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors. + complex inherritance + multi-factorial inheritance + multi-genic inheritance + multi-locus inheritance + multigenic inheritance + http://purl.obolibrary.org/obo/HP_0001426 + Diseases inherited in this manner are termed 'complex diseases'. + multifactorial inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes. + http://purl.obolibrary.org/obo/HP_0010984 + digenic inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes. + http://purl.obolibrary.org/obo/HP_0010983 + It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform. + oligogenic inheritance + + + + + + + + + A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes. + http://purl.obolibrary.org/obo/HP_0010982 + Typically used for traits/conditions governed by more than three gene loci. + polygenic inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors. + single-gene inheritance + monogenic inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome. + autosomal inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome. + gonosomal inheritance + http://purl.obolibrary.org/obo/HP_0010985 + allosomal inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome. + http://purl.obolibrary.org/obo/HP_0001417 + X-linked inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + complete X-linked dominant inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + semi-dominant X-linked inheritance + incomplete X-linked dominant inheritance + + + + + + + + + An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant X-linked inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome. + holandric inheritance + http://purl.obolibrary.org/obo/HP_0001450 + Y-linked inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome. + Z-linked inheritance + + + + + + + + + A Z-linked inheritance pattern wherein the trait manifests in heterozygotes. + Z-linked dominant inheritance + + + + + + + + + A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus. + complete Z-linked dominant inheritance + + + + + + + + + A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus. + semi-dominant Z-linked inheritance + incomplete Z-linked dominant inheritance + + + + + + + + + An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus. + co-dominant Z-linked inheritance + + + + + + + + + A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals. + Z-linked reccessive inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome. + W-linked inheritance + + + + + + + + + An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome. + http://purl.obolibrary.org/obo/HP_0001427 + Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy). + mitochondrial inheritance + + + + + + + + + An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females). + http://purl.obolibrary.org/obo/HP_0001470 + sex-limited autosomal dominant inheritance + + + + + + + + + An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females). + http://purl.obolibrary.org/obo/HP_0031362 + sex-limited autosomal recessive inheritance + + + + + + + + + A set of discrete alleles within a particular genome. + 'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An "Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'. + allele set + + + + + + + + + A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s). + copy number variation + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. + In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). + +Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. + obsolete_variant copy number complement + + + + + + + + + A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger. + Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961. + 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. + +2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. + +3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. + obsolete_copy number complement + + + + + + + + + + + + + + + + + + + + + A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism). + A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. + genomic sequence + + + + + + + + + A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome. + The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome. + +We represent the notion of copy number at the "sequence level" (as opposed to the "sequence feature level") because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome. In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15. When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The "sequence level" representation here supports this use case. By contrast, a "feature level" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity). + The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result. + +A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. + +The fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus. + The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence. + copy number complement + + + + + + + + + A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s). + Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a "sequence feature level" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of a 'variant copy number complement'. The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred). + +For example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'. But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/). In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'. This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains. + 'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome. + variant copy number complement + + + + + + + + + A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome. + functional genetic dosage + A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence. + +'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. + +As we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele. + functional copy complement + + + + + + + + + A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type. + mosaic + + + + + + + + + A pair of integers representing start and end position of a location on a sequence coordinate system. + sequence interval + + + + + + + + + molecular function + + + + + + + + + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete] + developmental process + + + + + + + + + pulling in HP 'phenotypic abnormality' root here + human phenotypic abnormality + + + + + + + + + Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology. + A spatiotemporal region encompassing some part of the life cycle of an organism. + human life cycle stage + + + + + + + + + data item + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + information content entity + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + ontology metadata + data about an ontology part + data about an ontology part + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification + + + + + + + + + + + + + + + + + + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + + + + + + + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + cjm + 2018-05-20T20:55:03Z + ontology module + + + + + + + + + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + cjm + 2018-05-20T20:55:30Z + base ontology module + + + + + + + + + + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + cjm + 2018-05-20T20:55:47Z + editors ontology module + + + + + + + + + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + cjm + 2018-05-20T20:56:13Z + main release ontology module + + + + + + + + + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + cjm + 2018-05-20T20:56:23Z + bridge ontology module + + + + + + + + + + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + cjm + 2018-05-20T20:56:47Z + import ontology module + + + + + + + + + + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + cjm + 2018-05-20T20:58:11Z + subset ontology module + + + + + + + + + + + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + cjm + 2018-05-20T20:58:38Z + curation subset ontology module + + + + + + + + + An ontology module that is intended for usage in analysis or discovery applications. + cjm + 2018-05-20T20:58:49Z + analysis subset ontology module + + + + + + + + + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + cjm + 2018-05-20T20:59:19Z + single layer subset ontology module + + + + + + + + + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + cjm + 2018-05-20T20:59:57Z + exclusion subset ontology module + + + + + + + + + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + cjm + 2018-05-20T21:00:14Z + external import ontology module + + + + + + + + + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + cjm + 2018-05-20T21:14:16Z + species subset ontology module + + + + + + + + + + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + cjm + 2018-05-20T21:20:33Z + reasoned ontology module + + + + + + + + + + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + cjm + 2018-05-20T21:21:12Z + generated ontology module + + + + + + + + + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + cjm + 2018-05-20T21:21:21Z + template generated ontology module + + + + + + + + + + + + cjm + 2018-05-20T21:28:15Z + taxonomic bridge ontology module + + + + + + + + + cjm + 2018-05-22T04:15:54Z + ontology module subsetted by expressivity + + + + + + + + + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + cjm + 2018-05-22T04:16:10Z + obo basic subset ontology module + + + + + + + + + + cjm + 2018-05-22T04:16:28Z + ontology module subsetted by OWL profile + + + + + + + + + cjm + 2018-05-22T04:16:48Z + EL++ ontology module + + + + + + + + + where to place this depends on if we take the organismal view or the quality centric view. + mammalian phenotype + + + + + + + + + Mus musculus + + + + + + + + + Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies. + Viruses + + + + + + + + + Danio rerio + + + + + + + + + Oryzias latipes + + + + + + + + + Homo sapiens + + + + + + + + + A processual entity that realizes a plan which is the concretization of a plan specification. + Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO. + planned process + + + + + + + + + reagent role + + + + + + + + + a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area + population + + + + + + + + + An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. + genotyping assay + + + + + + + + + A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. + A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. + targeted gene knock-out technique + + + + + + + + + targeted gene knock-in technique + + + + + + + + + Stub class to serve as root of hierarchy for imports from NCBI Taxonomy. + organism + + + + + + + + + + + + + + + + + + + + + + + + + the introduction. alteration or integration of genetic material into a cell or organism + genetic modification technique + + + + + + + + + 'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html + Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute. + color value + obsolete_color brightness + + + + + + + + + female + + + + + + + + + male + + + + + + + + + phenotypic sex + + + + + + + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role). + collection of organisms + + + + + + + + + A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. + family + + + + + + + + + Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. + morpholino_oligo + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. + Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + chromosome arm + + + + + + + + + + + + + + + + + + + + + Any extent of continuous biological sequence. + GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. +1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. +2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). +3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern). + A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome. + sequence_feature + + + + + + + + + + + true + Formalizes the first identity criteria for a sequence feature of its sequence. + + + + + + + + + + + true + Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property). + + + + + + + + + A region of known length which may be used to manufacture a longer region. + obsolete_assembly_component + + + + + + + + + A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. + obsolete_contig + + + + + + + + + + + + 0 + + + The point at which one or more contiguous nucleotides were excised. + deleted_sequence + nucleotide deletion + nucleotide_deletion + + SO:1000033 + SO:0000159 + SOFA + http://en.wikipedia.org/wiki/Nucleotide_deletion + deletion + + + + + + + + + enhancer + + + + + + + + + A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. + promoter + + + + + + + + + A region of nucleotide sequence that has translocated to a new position. + transchr + translocated sequence + + SO:0000199 + DBVAR + translocation + + + + + + + + + SSLP + simple sequence length polymorphism + simple sequence length variation + + SO:0000207 + simple_sequence_length_variation + + + + + + + + + sequence length variation + + SO:0000248 + sequence_length_variation + + + + + + + + + + See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25. + +Includes things like loxP sites, inducible promoters, ires elements, etc. + engineered_foreign_gene + + + + + + + + + A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. + http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29 + A defined feature that includes any type of VNTR or SSLP locus. + microsatellite + + + + + + + + + RNAi_reagent + + + + + + + + + Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. + A complete chromosome sequence. + chromosome + + + + + + + + + + + + + + + + + + + + + The descriptor 1p22.3 = chromosome 1, short arm, region 2, band 2, sub-band 3. This is read as "one q two-two point three", not "one q twenty-two point three". + A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. + http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here: +chromosome > arm > region > band > sub-band + +Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): +chromosome > arm > band > sub-band > sub-sub-band + + "Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band. + chromosome band + + + + + + + + + centromere + + + + + + + + + Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct. + obsolete_engineered_plasmid + + + + + + + + + The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. + insertion + nucleotide insertion + nucleotide_insertion + + SO:1000034 + SO:0000667 + DBVAR + SOFA + insertion + + + + + + + + + SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. + single nucleotide polymorphism + + SO:0000694 + SOFA + SNP + + + + + + + + + A junction is a boundary between regions. A boundary has an extent of zero. + junction + + + + + + + + + A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. + Regarding the distinction between a 'gene' and a 'gene allele': +Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment). + A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion. + gene + + + + + + + + + A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. + quantitative trait locus + QTL + + + + + + + + + An attribute to describe a region that was modified in vitro. + engineered + + + + + + + + + + + + + + + + + + + + + + + + + + construct + engineered_region + + + + + + + + + + + + + + + + + + + + + + + + + + An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'. + chromosomal feature + gross chromosomal part + chromosome part + + + + + + + + + A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome). + On the relationship between 'transgenic insertions', 'transgenes', and 'alleles' +Transgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete. + +In addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. + +For the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach. + Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors. What matters is that they are active in the context of a foreign biological system (typically a cell or organism). + +Note that transgenes as defined here are not necessarily from a different taxon than that of the host genome. For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome. + transgene + + + + + + + + + A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. + multiple nucleotide polymorphism + + SO:0001013 + MNP + + + + + + + + + A variation that increases or decreases the copy number of a given region. + CNP + CNV + copy number polymorphism + copy number variation + + SO:0001019 + SOFA + http://en.wikipedia.org/wiki/Copy_number_variation + copy_number_variation + + + + + + + + + A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny) + Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. + 'genome sequence' + A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'. + genome + + + + + + + + + + + + + + + + + + + + + + + + + + A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': + +1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene. This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/80358871. + +2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene. This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'. See https://www.ncbi.nlm.nih.gov/snp/483353112. + +3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene. This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero. See https://www.ncbi.nlm.nih.gov/snp/483353112. + A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. + sequence variation + + SO:1000004 + SO:1000007 + SO:0001059 + SOFA + 1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. + +Alleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part. + +2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. + +For a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference. + +3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism. + sequence_alteration + + + + + + + + + + + + + + + An insertion that derives from another organism, via the use of recombinant DNA technology. + transgenic insertion + + SO:0001218 + transgenic_insertion + + + + + + + + + A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. + not currently needed to support modeling use cases. can re-introduce if becomes necessary. + obsolete_experimental_feature + + + + + + + + + A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. + gene_trap_construct + + + + + + + + + A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. + promoter_trap_construct + + + + + + + + + A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. + enhancer_trap_construct + + + + + + + + + SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist. + single nucleotide variant + + kareneilbeck + Thu Oct 08 11:37:49 PDT 2009 + SO:0001483 + SOFA + SNV + + + + + + + + + A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. + heritable_phenotypic_marker + + + + + + + + + 'GRCh37.p10' (a human reference genome build) + A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced. + reference genome sequence + + + + + + + + + A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. + copy number gain + gain + + kareneilbeck + Mon Feb 28 01:54:09 PST 2011 + SO:0001742 + DBVAR + copy_number_gain + + + + + + + + + A sequence alteration whereby the copy number of a given region is less than the reference sequence. + copy number loss + loss + + kareneilbeck + Mon Feb 28 01:55:02 PST 2011 + SO:0001743 + DBVAR + copy_number_loss + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. + UPD + uniparental disomy + + kareneilbeck + Mon Feb 28 02:01:05 PST 2011 + SO:0001744 + DBVAR + http:http\://en.wikipedia.org/wiki/Uniparental_disomy + UPD + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. + maternal uniparental disomy + + kareneilbeck + Mon Feb 28 02:03:01 PST 2011 + SO:0001745 + maternal_uniparental_disomy + + + + + + + + + Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. + paternal uniparental disomy + + kareneilbeck + Mon Feb 28 02:03:30 PST 2011 + SO:0001746 + paternal_uniparental_disomy + + + + + + + + + A structural sequence alteration where there are multiple equally plausible explanations for the change. + complex + + kareneilbeck + Wed Mar 23 03:21:19 PDT 2011 + SO:0001784 + DBVAR + complex_structural_alteration + + + + + + + + + + kareneilbeck + Fri Mar 25 02:27:41 PDT 2011 + SO:0001785 + DBVAR + structural_alteration + + + + + + + + + Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term. + regulatory element + regulatory gene region + regulatory_region + + + + + + + + + Any change in genomic DNA caused by a single event. + + SO:1000002 + SOFA + substitution + + + + + + + + + When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change. + complex substitution + + SO:1000005 + SOFA + complex_substitution + + + + + + + + + A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. + point mutation + + SO:1000008 + SOFA + http://en.wikipedia.org/wiki/Point_mutation + point_mutation + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. + + SO:1000009 + transition + + + + + + + + + A substitution of a pyrimidine, C or T, for another pyrimidine. + pyrimidine transition + + SO:1000010 + pyrimidine_transition + + + + + + + + + A transition of a cytidine to a thymine. + C to T transition + + SO:1000011 + C_to_T_transition + + + + + + + + + The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine. + C to T transition at pCpG site + + SO:1000012 + C_to_T_transition_at_pCpG_site + + + + + + + + + T to C transition + + SO:1000013 + T_to_C_transition + + + + + + + + + A substitution of a purine, A or G, for another purine. + purine transition + + SO:1000014 + purine_transition + + + + + + + + + A transition of an adenine to a guanine. + A to G transition + + SO:1000015 + A_to_G_transition + + + + + + + + + A transition of a guanine to an adenine. + G to A transition + + SO:1000016 + G_to_A_transition + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. + + SO:1000017 + http://en.wikipedia.org/wiki/Transversion + transversion + + + + + + + + + Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. + pyrimidine to purine transversion + + SO:1000018 + pyrimidine_to_purine_transversion + + + + + + + + + A transversion from cytidine to adenine. + C to A transversion + + SO:1000019 + C_to_A_transversion + + + + + + + + + C to G transversion + + SO:1000020 + C_to_G_transversion + + + + + + + + + A transversion from T to A. + T to A transversion + + SO:1000021 + T_to_A_transversion + + + + + + + + + A transversion from T to G. + T to G transversion + + SO:1000022 + T_to_G_transversion + + + + + + + + + Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. + purine to pyrimidine transversion + + SO:1000023 + purine_to_pyrimidine_transversion + + + + + + + + + A transversion from adenine to cytidine. + A to C transversion + + SO:1000024 + A_to_C_transversion + + + + + + + + + A transversion from adenine to thymine. + A to T transversion + + SO:1000025 + A_to_T_transversion + + + + + + + + + A transversion from guanine to cytidine. + G to C transversion + + SO:1000026 + G_to_C_transversion + + + + + + + + + A transversion from guanine to thymine. + G to T transversion + + SO:1000027 + G_to_T_transversion + + + + + + + + + A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. + + SO:1000032 + http://en.wikipedia.org/wiki/Indel + Indels can have a different number of bases than the corresponding reference sequence. + indel + + + + + + + + + One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point. + nucleotide duplication + nucleotide_duplication + + SO:1000035 + duplication + + + + + + + + + A continuous nucleotide sequence is inverted in the same position. + inversion + + SO:1000036 + DBVAR + SOFA + inversion + + + + + + + + + A tandem duplication where the individual regions are in the same orientation. + direct tandem duplication + + SO:1000039 + direct_tandem_duplication + + + + + + + + + A tandem duplication where the individual regions are not in the same orientation. + inverted tandem duplication + mirror duplication + + SO:1000040 + inverted_tandem_duplication + + + + + + + + + A duplication consisting of 2 identical adjacent regions. + erverted + tandem duplication + + SO:1000173 + DBVAR + tandem_duplication + + + + + + + + + Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms) + life cycle stage + + + + + + + + + + + + + + + Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies. + http://purl.obolibrary.org/obo/CARO_0000000 + anatomical entity + + + + + + + + + Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework. + 1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition) + +2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment + Phenotype + + + + + + + + + Animals exhibit variations compared to a given control. + 'Variant' is the given label of the root class in the Worm Phenotype ontology. Renamng it here to be consisent with our hierarchy of phenotype classes. + Variant + c. elegans phenotype + worm phenotype + + + + + + + + + abnormal(ly) malformed endocardium cell + + + + + + + + + abnormal(ly) absent dorso-rostral cluster + + + + + + + + + abnormal(ly) disrupted diencephalon development + + + + + + + + + abnormal(ly) disrupted neutrophil aggregation + + + + + + + + + abnormal(ly) absent adaxial cell + + + + + + + + + association + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Equivalent to: http://www.informatics.jax.org/marker/MGI:98297 + mus musculus shh gene + + + + + + + + + + http://zfin.org/ZDB-GENE-980526-166 + danio rerio shha gene + + + + + + + + + + http://zfin.org/ZDB-GENE-040123-1 + danio rerio cdkn1ca gene + + + + + + + + + + Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690 + +Codes for: http://www.uniprot.org/uniprot/Q15465 + homo sapiens SHH gene + + + + + + + + + + + + + + exploratory term + + + + + + + + + exemplar term + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + core + + + + + + + + + placeholder removed + + + + + + + + + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + + + + + + + + + Initially created such that integrated transgene infers as child of sequence_alteration. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/imports/iao_import.json b/imports/iao_import.json new file mode 100644 index 0000000..ee7a9ee --- /dev/null +++ b/imports/iao_import.json @@ -0,0 +1,3550 @@ +{ + "graphs" : [ { + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "term imported" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "term split" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this cell derives from this parent cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this nucleus derives from this parent nucleus (nuclear division)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "derives from" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent cell derives into this cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent nucleus derives into this nucleus (nuclear division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + } ] + }, + "type" : "PROPERTY", + "lbl" : "derives into" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000230", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We expect to be able to mine these new reasons and add instances as required." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "other" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + } ] + }, + "type" : "PROPERTY", + "lbl" : "part of" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "meta" : { + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor note" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "editor note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "meta" : { + "definition" : { + "val" : "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term editor" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term editor" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000235", + "meta" : { + "definition" : { + "val" : "inverse of the relation 'denotes'", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Mike Conlon" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/206" + } ] + }, + "type" : "PROPERTY", + "lbl" : "denoted by" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000281" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has curation status" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has curation status" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000598", + "meta" : { + "definition" : { + "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID policy for" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000599", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID prefix" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "meta" : { + "definition" : { + "val" : "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "textual definition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has part" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "meta" : { + "definition" : { + "val" : "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "example" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + } ] + }, + "type" : "PROPERTY", + "lbl" : "example of usage" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term tracker item" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The 'tracker item' can associate a tracker with a specific ontology term." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term tracker item" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000596", + "meta" : { + "definition" : { + "val" : "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID digit count" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000597", + "meta" : { + "definition" : { + "val" : "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ID range allocated to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000234", + "meta" : { + "definition" : { + "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The 'term requester' can credit the person, organization or project who request the ontology term." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "ontology term requester" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000113", + "meta" : { + "definition" : { + "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "in branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000277" + } ] + }, + "type" : "PROPERTY", + "lbl" : "in branch" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "meta" : { + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has obsolescence reason" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has obsolescence reason" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "meta" : { + "definition" : { + "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term~editor preferred label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "editor preferred term" + } ] + }, + "type" : "PROPERTY", + "lbl" : "editor preferred label" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000078", + "meta" : { + "definition" : { + "val" : "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bill Bug" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curation status specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000266" + } ] + }, + "type" : "CLASS", + "lbl" : "curation status specification" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "meta" : { + "definition" : { + "val" : "An administrative note of use for a curator but of no use for a user", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "curator note" + } ] + }, + "type" : "PROPERTY", + "lbl" : "curator note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "alternative term" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "alternative term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "meta" : { + "definition" : { + "val" : "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "definition source" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Daniel Schober" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition source" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000312", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is_specified_output_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is_specified_output_of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_specified_output_of" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "metadata complete" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "pending final vetting" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "metadata incomplete" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "meta" : { + "definition" : { + "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the undetached arm of a human being" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a puff of smoke" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an epidemic" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a forest fire" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a hurricane" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a flame" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a sea wave" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "material" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a tornado" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an aggregate of human beings." + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "MaterialEntity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an energy wave" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a human being" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a photon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "material entity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "type" : "INDIVIDUAL", + "lbl" : "example to be eventually removed" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term.", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "uncurated" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "meta" : { + "definition" : { + "val" : "term created to ease viewing/sort terms for development purpose, and will not be included in a release", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "organizational term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"", + "xrefs" : [ ] + } + }, + "type" : "INDIVIDUAL", + "lbl" : "ready for release" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000409", + "meta" : { + "definition" : { + "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Barry Smith, Werner Ceusters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "CLASS", + "lbl" : "denotator type" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "type" : "PROPERTY", + "lbl" : "disposition of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000020", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:48Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "EL++ ontology module" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass", + "type" : "CLASS", + "lbl" : "Obsolete Class" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000019", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module subsetted by OWL profile" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000011", + "meta" : { + "definition" : { + "val" : "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:00:14Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "external import" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "external import ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000012", + "meta" : { + "definition" : { + "val" : "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:14:16Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "taxon subset" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + }, + "type" : "CLASS", + "lbl" : "species subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000136", + "meta" : { + "definition" : { + "val" : "is_about is a (currently) primitive relation that relates an information artifact to an entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This document is about information artifacts and their representations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is about" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000015", + "meta" : { + "definition" : { + "val" : "A quality of an information bearer that imparts the information content", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "information carrier" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "CLASS", + "lbl" : "information carrier" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000411", + "meta" : { + "definition" : { + "val" : "relates an class defined in an ontology, to the type of it's denotator", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is denotator type" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is denotator type" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000013", + "meta" : { + "definition" : { + "val" : "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:20:33Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/reason" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "reasoned ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000014", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:21:12Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" + } ] + }, + "type" : "CLASS", + "lbl" : "generated ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000412", + "meta" : { + "definition" : { + "val" : "For external terms/classes, the ontology from which the term was imported", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBI:" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "imported from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "imported from" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000015", + "meta" : { + "definition" : { + "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://doi.org/10.1186/s13326-017-0126-0" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/template" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:21:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "template generated ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "universal" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T21:28:15Z" + } ] + }, + "type" : "CLASS", + "lbl" : "taxonomic bridge ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000017", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:15:54Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module subsetted by expressivity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000018", + "meta" : { + "definition" : { + "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T04:16:10Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" + } ] + }, + "type" : "CLASS", + "lbl" : "obo basic subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000293", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has_specified_input" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Coutot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Larry Hunter" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has_specified_input" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "see is_input_of example_of_usage" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_specified_input" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "meta" : { + "definition" : { + "val" : "Add as annotation triples in the granting ontology", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term replaced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term replaced by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "role of" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000295", + "type" : "PROPERTY", + "lbl" : "is_specified_input_of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + } ] + }, + "type" : "PROPERTY", + "lbl" : "quality of" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000010", + "meta" : { + "definition" : { + "val" : "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:59:57Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "antislim" + } ] + }, + "type" : "CLASS", + "lbl" : "exclusion subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000299", + "meta" : { + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has_specified_output" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has_specified_output" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Larry Hunter" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has_specified_output" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has role" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has quality" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000008", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended for usage in analysis or discovery applications.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:49Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "analysis subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000009", + "meta" : { + "definition" : { + "val" : "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:59:19Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ribbon subset" + } ] + }, + "type" : "CLASS", + "lbl" : "single layer subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:03Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology file" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." + } ] + }, + "type" : "CLASS", + "lbl" : "ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000028", + "meta" : { + "definition" : { + "val" : "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "based on Oxford English Dictionary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: James A. Overton" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "symbol" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "20091104, MC: this needs work and will most probably change" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Jonathan Rees" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a written proper name such as \"OBI\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a serial number such as \"12324X\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a stop sign" + } ] + }, + "type" : "CLASS", + "lbl" : "symbol" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand expression to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + } ] + }, + "type" : "PROPERTY", + "lbl" : "expand expression to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000001", + "meta" : { + "definition" : { + "val" : "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:30Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "base ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000425", + "meta" : { + "definition" : { + "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "expand assertion to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + } ] + }, + "type" : "PROPERTY", + "lbl" : "expand assertion to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000002", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:55:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "source ontology module" + } ] + }, + "type" : "CLASS", + "lbl" : "editors ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000003", + "meta" : { + "definition" : { + "val" : "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:13Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" + } ] + }, + "type" : "CLASS", + "lbl" : "main release ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "meta" : { + "definition" : { + "val" : "Terms with this status should eventually replaced with a term from another ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "to be replaced with external ontology term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000027", + "meta" : { + "definition" : { + "val" : "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Jonathan Rees" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data item" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Chris Stoeckert" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Data items include counts of things, analyte concentrations, and statistical summaries." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "data" + } ] + }, + "type" : "CLASS", + "lbl" : "data item" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000004", + "meta" : { + "definition" : { + "val" : "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:23Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "bridge ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "meta" : { + "definition" : { + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "defined class" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000005", + "meta" : { + "definition" : { + "val" : "A subset ontology module that is intended to be imported from another ontology.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add axioms that indicate this is the output of a module extraction process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "import file" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/extract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:56:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "CLASS", + "lbl" : "import ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "meta" : { + "definition" : { + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "named class expression" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000006", + "meta" : { + "definition" : { + "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ontology slim" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:11Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "subset ontology" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://robot.obolibrary.org/filter" + } ] + }, + "type" : "CLASS", + "lbl" : "subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_8000007", + "meta" : { + "definition" : { + "val" : "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-20T20:58:38Z" + } ] + }, + "type" : "CLASS", + "lbl" : "curation subset ontology module" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of your nose" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the mass of this piece of gold." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the color of a tomato" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "quality" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the length of the circumference of your waist" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the ambient temperature of this portion of air" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Quality" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the shape of your nostril" + } ] + }, + "type" : "CLASS", + "lbl" : "quality" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "meta" : { + "definition" : { + "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the life of an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the flight of a bird" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "process" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of cell-division, \\ a beating of the heart" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of meiosis" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a process of sleeping" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "your process of aging." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the course of a disease" + } ] + }, + "type" : "CLASS", + "lbl" : "process" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "group:OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "requires discussion" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "disposition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "children are innately disposed to categorize objects in certain ways." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Disposition" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "certain people have a predisposition to colon cancer" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an atom of element X has the disposition to decay to an atom of element Y" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" + } ] + }, + "type" : "CLASS", + "lbl" : "disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "meta" : { + "definition" : { + "val" : "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of your blood to coagulate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the disposition of this piece of metal to conduct electricity." + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "realizable" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "RealizableEntity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of being a doctor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of your reproductive organs" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of this boundary to delineate where Utah and Colorado meet" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "realizable entity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "first order logic expression" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "first order logic expression" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000427", + "meta" : { + "definition" : { + "val" : "use boolean value xsd:true to indicate that the property is an antisymmetric property", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part_of antisymmetric property xsd:true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "antisymmetric property" + } ] + }, + "type" : "PROPERTY", + "lbl" : "antisymmetric property" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000030", + "meta" : { + "definition" : { + "val" : "A generically dependent continuant that is about some thing.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI_0000142" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "information content entity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples of information content entites include journal articles, data, graphical layouts, and graphs." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Chris Stoeckert" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." + } ] + }, + "type" : "CLASS", + "lbl" : "information content entity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006011", + "meta" : { + "definition" : { + "val" : "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "#40" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "VFB" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-21T16:43:39Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "may be identical to" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0006012", + "meta" : { + "definition" : { + "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/15532" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "GO ontology" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall, Jie Zheng" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/32" + } ] + }, + "type" : "PROPERTY", + "lbl" : "scheduled for obsoletion on or after" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", + "meta" : { + "definition" : { + "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a spatial region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the bottom right portion of a human torso" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "ic" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a leg" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "IndependentContinuant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an orchestra." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an atom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the interior of your mouth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a chair" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a molecule" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a heart" + } ] + }, + "type" : "CLASS", + "lbl" : "independent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0010000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has axiom id" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has axiom label" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "meta" : { + "definition" : { + "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." + } ] + }, + "type" : "PROPERTY", + "lbl" : "concretizes" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "meta" : { + "definition" : { + "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is concretized as" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has participant" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000600", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "elucidation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Barry Smith" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + } ] + }, + "type" : "PROPERTY", + "lbl" : "elucidation" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Julius Caesar" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Verdi’s Requiem" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "entity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Entity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "your body mass index" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the Second World War" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" + } ] + }, + "type" : "CLASS", + "lbl" : "entity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000601", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom associated with a term expressed using natural language" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(nl)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has associated axiom(nl)" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000002", + "meta" : { + "definition" : { + "val" : "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "continuant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Continuant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" + } ] + }, + "type" : "CLASS", + "lbl" : "continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "meta" : { + "definition" : { + "val" : "An entity that has temporal parts and that happens, unfolds or develops through time.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "occurrent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Occurrent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", + "val" : "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." + } ] + }, + "type" : "CLASS", + "lbl" : "occurrent" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000602", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An axiom expressed in first order logic using CLIF syntax" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has associated axiom(fol)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has associated axiom(fol)" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000603", + "meta" : { + "definition" : { + "val" : "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\"", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is allocated id range" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is allocated id range" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color inheres in this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility inheres in this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A dependent inheres in its bearer at all times for which the dependent exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + } ] + }, + "type" : "PROPERTY", + "lbl" : "inheres in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + } ] + }, + "type" : "PROPERTY", + "lbl" : "participates in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "meta" : { + "definition" : { + "val" : "is member of is a mereological relation between a item and a collection.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "member part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An organism that is a member of a population of organisms" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is member of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "member of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "bearer of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "meta" : { + "definition" : { + "val" : "has member is a mereological relation between a collection and an item.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has member" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000578", + "meta" : { + "definition" : { + "val" : "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bill Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000120" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "CRID" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records')." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. \n" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Original proposal from Bjoern, discussions at IAO calls" + } ] + }, + "type" : "CLASS", + "lbl" : "centrally registered identifier" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000579", + "meta" : { + "definition" : { + "val" : "A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "CRID registry" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Original proposal from Bjoern, discussions at IAO calls" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bill Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000120" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + } ] + }, + "type" : "CLASS", + "lbl" : "centrally registered identifier registry" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "function" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of a hammer to drive in nails" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of amylase in saliva to break down starch into sugar" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Function" + } ] + }, + "type" : "CLASS", + "lbl" : "function" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000577", + "meta" : { + "definition" : { + "val" : "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Original proposal from Bjoern, discussions at IAO calls" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bill Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000120" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "CRID symbol" + } ] + }, + "type" : "CLASS", + "lbl" : "centrally registered identifier symbol" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000178", + "meta" : { + "definition" : { + "val" : "A material entity in which a concretization of an information content entity inheres.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a hard drive" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a brain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP: IAO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "material information bearer" + } ] + }, + "type" : "CLASS", + "lbl" : "material information bearer" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000031", + "meta" : { + "definition" : { + "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "gdc" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "GenericallyDependentContinuant" + } ] + }, + "type" : "CLASS", + "lbl" : "generically dependent continuant" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#Subset", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000219", + "meta" : { + "definition" : { + "val" : "denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.\ng denotes r =def \nr is a portion of reality\nthere is some c that is a concretization of g \nevery c that is a concretization of g specifically denotes r" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named." + } ] + }, + "type" : "PROPERTY", + "lbl" : "denotes" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000011", + "meta" : { + "definition" : { + "val" : "A processual entity that realizes a plan which is the concretization of a plan specification.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "planned process" + } ] + }, + "type" : "CLASS", + "lbl" : "planned process" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "type" : "INDIVIDUAL", + "lbl" : "placeholder removed" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "meta" : { + "definition" : { + "val" : "An alternative name for a class or property which is unique across the OBO Foundry.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP:OBO Foundry " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "OBO foundry unique label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Melanie Courtot" + } ] + }, + "type" : "PROPERTY", + "lbl" : "OBO foundry unique label" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000023", + "meta" : { + "definition" : { + "val" : "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", + "val" : "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a stone in marking a property boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", + "val" : "Role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the student role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a building in serving as a military target" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of subject in a clinical trial" + }, { + "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", + "val" : "role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the priest role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the role of a boundary to demarcate two neighboring administrative territories" + } ] + }, + "type" : "CLASS", + "lbl" : "role" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "terms merged" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "meta" : { + "definition" : { + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "failed exploratory term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000224", + "meta" : { + "definition" : { + "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "core" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "meta" : { + "definition" : { + "val" : "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "obsolescence reason specification" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolescence reason specification" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000102", + "meta" : { + "definition" : { + "val" : "data about an ontology part is a data item about a part of an ontology, for example a term", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person:Alan Ruttenberg" + } ] + }, + "type" : "CLASS", + "lbl" : "data about an ontology part" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000020", + "meta" : { + "definition" : { + "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. 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: "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000027" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_8000011", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_8000005" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000080", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0000030", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000001" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0000578", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000577" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000293", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000295" + }, { + "sub" : "http://www.geneontology.org/formats/oboInOwl#DbXref", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000016", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" + } ], + "id" : "http://purl.obolibrary.org/obo/geno/imports/iao_import.owl", + "meta" : { + "subsets" : [ ], + "xrefs" : [ ], + "basicPropertyValues" : [ ], + "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-09-09/imports/iao_import.owl" + }, + "equivalentNodesSets" : [ ], + "logicalDefinitionAxioms" : [ { + "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0000015", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000019" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000059", + "fillerId" : "http://purl.obolibrary.org/obo/IAO_0000030" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0000178", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "restrictions" : [ null ] + } ], + "domainRangeAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000293", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000219", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000030" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000091", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000299", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000312", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000087", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000086", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000019" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000059", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000235", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000001" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000030" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000136", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000030" ] + } ], + "propertyChainAxioms" : [ ] + } ] +} \ No newline at end of file diff --git a/imports/iao_import.obo b/imports/iao_import.obo new file mode 100644 index 0000000..bfff057 --- /dev/null +++ b/imports/iao_import.obo @@ -0,0 +1,940 @@ +format-version: 1.2 +data-version: geno/releases/2019-09-09/imports/iao_import.owl +ontology: geno/imports/iao_import +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (denotes)\n\nAnnotationAssertion(rdfs:comment \"\"@en)\n\n# Object Property: (has_specified_input)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (has_specified_output)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (is_specified_output_of)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (curation status specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (material information bearer)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))\n\n# Class: (obsolescence reason specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (denotator type)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (centrally registered identifier)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: ()\n\nEquivalentClasses( ObjectOneOf())\n\n\n############################\n# Named Individuals\n############################\n\n# Individual: (metadata complete)\n\n\n# Individual: (organizational term)\n\n\n# Individual: (ready for release)\n\n\n# Individual: (metadata incomplete)\n\n\n# Individual: (uncurated)\n\n\n# Individual: (pending final vetting)\n\n\n# Individual: (placeholder removed)\n\n\n# Individual: (terms merged)\n\n\n# Individual: (term imported)\n\n\n# Individual: (term split)\n\n\n# Individual: (to be replaced with external ontology term)\n\n\n# Individual: (requires discussion)\n\n\n\nDifferentIndividuals( )\nDifferentIndividuals( )\n) + +[Term] +id: BFO:0000001 +name: entity +property_value: BFO:0000179 "entity" xsd:string +property_value: BFO:0000180 "Entity" xsd:string +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +property_value: BFO:0000179 "continuant" xsd:string +property_value: BFO:0000180 "Continuant" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +is_a: BFO:0000001 ! entity +property_value: BFO:0000179 "occurrent" xsd:string +property_value: BFO:0000180 "Occurrent" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} +property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "ic" xsd:string +property_value: BFO:0000180 "IndependentContinuant" xsd:string +property_value: IAO:0000112 "a chair" xsd:string +property_value: IAO:0000112 "a heart" xsd:string +property_value: IAO:0000112 "a leg" xsd:string +property_value: IAO:0000112 "a molecule" xsd:string +property_value: IAO:0000112 "a spatial region" xsd:string +property_value: IAO:0000112 "an atom" xsd:string +property_value: IAO:0000112 "an orchestra." xsd:string +property_value: IAO:0000112 "an organism" xsd:string +property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string +property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +is_a: BFO:0000003 ! occurrent +property_value: BFO:0000179 "process" xsd:string +property_value: BFO:0000180 "Process" xsd:string +property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string +property_value: IAO:0000112 "a process of meiosis" xsd:string +property_value: IAO:0000112 "a process of sleeping" xsd:string +property_value: IAO:0000112 "the course of a disease" xsd:string +property_value: IAO:0000112 "the flight of a bird" xsd:string +property_value: IAO:0000112 "the life of an organism" xsd:string +property_value: IAO:0000112 "your process of aging." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string +property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role +property_value: BFO:0000179 "disposition" xsd:string +property_value: BFO:0000180 "Disposition" xsd:string +property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string +property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string +property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string +property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string +property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000017 +name: realizable entity +def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality +property_value: BFO:0000179 "realizable" xsd:string +property_value: BFO:0000180 "RealizableEntity" xsd:string +property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string +property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string +property_value: IAO:0000112 "the function of your reproductive organs" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: BFO:0000179 "quality" xsd:string +property_value: BFO:0000180 "Quality" xsd:string +property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string +property_value: IAO:0000112 "the color of a tomato" xsd:string +property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string +property_value: IAO:0000112 "the mass of this piece of gold." xsd:string +property_value: IAO:0000112 "the shape of your nose" xsd:string +property_value: IAO:0000112 "the shape of your nostril" xsd:string +property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "sdc" xsd:string +property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string +property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000023 +name: role +def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] +is_a: BFO:0000017 ! realizable entity +property_value: BFO:0000179 "role" xsd:string +property_value: BFO:0000180 "Role" xsd:string +property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string +property_value: IAO:0000112 "the priest role" xsd:string +property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string +property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string +property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string +property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string +property_value: IAO:0000112 "the student role" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string +property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +is_a: BFO:0000002 ! continuant +property_value: BFO:0000179 "gdc" xsd:string +property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string +property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition +property_value: BFO:0000179 "function" xsd:string +property_value: BFO:0000180 "Function" xsd:string +property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string +property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string +property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string +property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant +property_value: BFO:0000179 "material" xsd:string +property_value: BFO:0000180 "MaterialEntity" xsd:string +property_value: IAO:0000112 "a flame" xsd:string +property_value: IAO:0000112 "a forest fire" xsd:string +property_value: IAO:0000112 "a human being" xsd:string +property_value: IAO:0000112 "a hurricane" xsd:string +property_value: IAO:0000112 "a photon" xsd:string +property_value: IAO:0000112 "a puff of smoke" xsd:string +property_value: IAO:0000112 "a sea wave" xsd:string +property_value: IAO:0000112 "a tornado" xsd:string +property_value: IAO:0000112 "an aggregate of human beings." xsd:string +property_value: IAO:0000112 "an energy wave" xsd:string +property_value: IAO:0000112 "an epidemic" xsd:string +property_value: IAO:0000112 "the undetached arm of a human being" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: DbXref +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Definition +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: IAO:0000015 +name: information carrier +def: "A quality of an information bearer that imparts the information content" [] +is_a: BFO:0000019 ! quality +intersection_of: BFO:0000019 ! quality +intersection_of: RO:0000059 IAO:0000030 ! concretizes information content entity +property_value: IAO:0000111 "information carrier" xsd:string +property_value: IAO:0000112 "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'." xsd:string +property_value: IAO:0000116 "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string + +[Term] +id: IAO:0000027 +name: data item +def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] +is_a: IAO:0000030 ! information content entity +property_value: IAO:0000111 "data item" xsd:string +property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string +property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string +property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string +property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string +property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000118 "data" xsd:string + +[Term] +id: IAO:0000028 +name: symbol +def: "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." [] +is_a: IAO:0000030 ! information content entity +property_value: IAO:0000111 "symbol" xsd:string +property_value: IAO:0000112 "a serial number such as \"12324X\"" xsd:string +property_value: IAO:0000112 "a stop sign" xsd:string +property_value: IAO:0000112 "a written proper name such as \"OBI\"" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "20091104, MC: this needs work and will most probably change" xsd:string +property_value: IAO:0000116 "2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154)." xsd:string +property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000119 "based on Oxford English Dictionary" xsd:string + +[Term] +id: IAO:0000030 +name: information content entity +def: "A generically dependent continuant that is about some thing." [] +is_a: BFO:0000031 ! generically dependent continuant +relationship: IAO:0000136 BFO:0000001 ! is about entity +property_value: IAO:0000111 "information content entity" xsd:string +property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." xsd:string +property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000119 "OBI_0000142" xsd:string + +[Term] +id: IAO:0000078 +name: curation status specification +def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000100 +name: data set +def: "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets." [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000111 "data set" xsd:string +property_value: IAO:0000112 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" xsd:string +property_value: IAO:0000116 "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction." xsd:string +property_value: IAO:0000117 "person:Allyson Lister" xsd:string +property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string +property_value: IAO:0000119 group:OBI xsd:string +property_value: IAO:0000119 "OBI_0000042" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string + +[Term] +id: IAO:0000178 +name: material information bearer +def: "A material entity in which a concretization of an information content entity inheres." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000111 "material information bearer" xsd:string +property_value: IAO:0000112 "a brain" xsd:string +property_value: IAO:0000112 "a hard drive" xsd:string +property_value: IAO:0000112 "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "GROUP: IAO" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: IAO:0000577 +name: centrally registered identifier symbol +def: "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry." [] +is_a: IAO:0000028 ! symbol +relationship: BFO:0000050 IAO:0000578 ! part of centrally registered identifier +property_value: IAO:0000112 "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000118 "CRID symbol" xsd:string +property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string + +[Term] +id: IAO:0000578 +name: centrally registered identifier +def: "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs." [] +is_a: IAO:0000030 ! information content entity +relationship: BFO:0000051 IAO:0000577 ! has part centrally registered identifier symbol +property_value: IAO:0000112 "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records')." xsd:string +property_value: IAO:0000116 "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. \n" xsd:string +property_value: IAO:0000116 "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000118 "CRID" xsd:string +property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string + +[Term] +id: IAO:0000579 +name: centrally registered identifier registry +def: "A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process." [] +is_a: IAO:0000100 ! data set +property_value: IAO:0000112 "PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. " xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bill Hogan" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000118 "CRID registry" xsd:string +property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string + +[Term] +id: IAO:8000000 +name: ontology module +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000116 "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000118 "ontology file" xsd:string +property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:03Z + +[Term] +id: IAO:8000001 +name: base ontology module +def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 +created_by: cjm +creation_date: 2018-05-20T20:55:30Z + +[Term] +id: IAO:8000002 +name: editors ontology module +def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "source ontology module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:47Z + +[Term] +id: IAO:8000003 +name: main release ontology module +def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:56:13Z + +[Term] +id: IAO:8000004 +name: bridge ontology module +def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies +created_by: cjm +creation_date: 2018-05-20T20:56:23Z + +[Term] +id: IAO:8000005 +name: import ontology module +def: "A subset ontology module that is intended to be imported from another ontology." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000118 "import file" xsd:string +property_value: seeAlso http://robot.obolibrary.org/extract +created_by: cjm +creation_date: 2018-05-20T20:56:47Z + +[Term] +id: IAO:8000006 +name: subset ontology module +def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "ontology slim" xsd:string +property_value: IAO:0000118 "subset ontology" xsd:string +property_value: seeAlso http://robot.obolibrary.org/filter +property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide +created_by: cjm +creation_date: 2018-05-20T20:58:11Z + +[Term] +id: IAO:8000007 +name: curation subset ontology module +def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:38Z + +[Term] +id: IAO:8000008 +name: analysis subset ontology module +def: "An ontology module that is intended for usage in analysis or discovery applications." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:49Z + +[Term] +id: IAO:8000009 +name: single layer subset ontology module +def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "ribbon subset" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:19Z + +[Term] +id: IAO:8000010 +name: exclusion subset ontology module +def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "antislim" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:57Z + +[Term] +id: IAO:8000011 +name: external import ontology module +def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] +is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000118 "external import" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:00:14Z + +[Term] +id: IAO:8000012 +name: species subset ontology module +def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "taxon subset" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +created_by: cjm +creation_date: 2018-05-20T21:14:16Z + +[Term] +id: IAO:8000013 +name: reasoned ontology module +def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso http://robot.obolibrary.org/reason +created_by: cjm +creation_date: 2018-05-20T21:20:33Z + +[Term] +id: IAO:8000014 +name: generated ontology module +def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:21:12Z + +[Term] +id: IAO:8000015 +name: template generated ontology module +def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] +is_a: IAO:8000014 ! generated ontology module +property_value: seeAlso http://robot.obolibrary.org/template +property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 +property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ +created_by: cjm +creation_date: 2018-05-20T21:21:21Z + +[Term] +id: IAO:8000016 +name: taxonomic bridge ontology module +is_a: IAO:8000004 ! bridge ontology module +created_by: cjm +creation_date: 2018-05-20T21:28:15Z + +[Term] +id: IAO:8000017 +name: ontology module subsetted by expressivity +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-22T04:15:54Z + +[Term] +id: IAO:8000018 +name: obo basic subset ontology module +def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: seeAlso "6.2" +created_by: cjm +creation_date: 2018-05-22T04:16:10Z + +[Term] +id: IAO:8000019 +name: ontology module subsetted by OWL profile +is_a: IAO:8000017 ! ontology module subsetted by expressivity +created_by: cjm +creation_date: 2018-05-22T04:16:28Z + +[Term] +id: IAO:8000020 +name: EL++ ontology module +is_a: IAO:8000019 ! ontology module subsetted by OWL profile +created_by: cjm +creation_date: 2018-05-22T04:16:48Z + +[Term] +id: OBI:0000011 +name: planned process +def: "A processual entity that realizes a plan which is the concretization of a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + +[Term] +id: ObsoleteClass +name: Obsolete Class + +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Synonym +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: SynonymType +is_a: IAO:0000102 ! data about an ontology part + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true + +[Typedef] +id: IAO:0000136 +name: is about +def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." [] +property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string +domain: IAO:0000030 ! information content entity + +[Typedef] +id: IAO:0000219 +name: denotes +def: "denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" [] +property_value: IAO:0000112 "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named." xsd:string +property_value: IAO:0000116 "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.\ng denotes r =def \nr is a portion of reality\nthere is some c that is a concretization of g \nevery c that is a concretization of g specifically denotes r" xsd:string +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan" xsd:string +domain: IAO:0000030 ! information content entity +range: BFO:0000001 ! entity +is_a: IAO:0000136 ! is about +inverse_of: IAO:0000235 ! denoted by + +[Typedef] +id: IAO:0000235 +name: denoted by +def: "inverse of the relation 'denotes'" [] +property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Mike Conlon" xsd:string +property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/206 +domain: BFO:0000001 ! entity +range: IAO:0000030 ! information content entity + +[Typedef] +id: OBI:0000293 +name: has_specified_input +def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "has_specified_input" xsd:string +property_value: IAO:0000111 "has_specified_input" xsd:string +property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl +domain: OBI:0000011 ! planned process +is_a: RO:0000057 ! has participant +inverse_of: OBI:0000295 ! is_specified_input_of + +[Typedef] +id: OBI:0000295 +name: is_specified_input_of + +[Typedef] +id: OBI:0000299 +name: has_specified_output +def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "has_specified_output" xsd:string +property_value: IAO:0000111 "has_specified_output" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl +domain: OBI:0000011 ! planned process +is_a: RO:0000057 ! has participant +inverse_of: OBI:0000312 ! is_specified_output_of + +[Typedef] +id: OBI:0000312 +name: is_specified_output_of +def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "is_specified_output_of" xsd:string +property_value: IAO:0000111 "is_specified_output_of" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl +range: OBI:0000011 ! planned process +is_a: RO:0000056 ! participates in + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: RO:0000053 ! bearer of +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +is_a: RO:0000052 ! inheres in + +[Typedef] +id: RO:0001000 +name: derives from +def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string +property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string +property_value: IAO:0000118 "derives_from" xsd:string +inverse_of: RO:0001001 ! derives into + +[Typedef] +id: RO:0001001 +name: derives into +def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string +property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string +property_value: IAO:0000118 "derives_into" xsd:string + +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000050 ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000051 ! has part + diff --git a/imports/iao_import.owl b/imports/iao_import.owl new file mode 100644 index 0000000..56b32ee --- /dev/null +++ b/imports/iao_import.owl @@ -0,0 +1,2638 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + + + + + + + example + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + + + + + + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + + + + + + + + definition + definition + textual definition + + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + textual definition + + + + + + + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + + editor note + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + alternative term + + + + + + + + definition source + + formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + + + + + + + + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + + + + + + is denotator type + relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + imported from + + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + + + + + + + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + + + + + + + first order logic expression + PERSON:Alan Ruttenberg + first order logic expression + + + + + + + + antisymmetric property + part_of antisymmetric property xsd:true + use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + + + + + + OBO foundry unique label + + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + + + + + + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + + has associated axiom(fol) + + + + + + + + is allocated id range + Add as annotation triples in the granting ontology + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + is allocated id range + + + + + + + + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + 2018-09-21T16:43:39Z + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + + + + + + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + https://github.com/geneontology/go-ontology/issues/15532 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + + has axiom label + + + + + + + + term replaced by + + Add as annotation triples in the granting ontology + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + term replaced by + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + has part + + + + + + + + + This document is about information artifacts and their representations + + is_about is a (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + + + + + + A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. + denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically + 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. +g denotes r =def +r is a portion of reality +there is some c that is a concretization of g +every c that is a concretization of g specifically denotes r + person:Alan Ruttenberg + Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan + + denotes + + + + + + + + + + inverse of the relation 'denotes' + Person: Jie Zheng, Chris Stoeckert, Mike Conlon + + denoted by + + + + + + + + + + + + + + + + has_specified_input + has_specified_input + see is_input_of example_of_usage + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot + + has_specified_input + + + + + + + + is_specified_input_of + + + + + + + + + + + + + + + + has_specified_output + has_specified_output + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot + + has_specified_output + + + + + + + + + + + + + + + is_specified_output_of + is_specified_output_of + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters + + is_specified_output_of + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + role of + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + disposition of + + + + + + + + + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + derives from + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + derives into + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + + + + + + + continuant + Continuant + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + + + + + + + + + + + occurrent + Occurrent + An entity that has temporal parts and that happens, unfolds or develops through time. + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + + + + + + + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process + + + + + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + + + + + + + + + + disposition + Disposition + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocytosis and exocytosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + disposition + + + + + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + + + + + + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + + + + + + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + + + + + + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + + + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + + + + + + + + + quality + Quality + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + quality + + + + + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + + + + + + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + + + + + + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + + + + + + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + + + + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + + + + + + + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant + + + + + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + + + + + + + + + function + Function + the function of a hammer to drive in nails + the function of a heart pacemaker to regulate the beating of a heart through electricity + the function of amylase in saliva to break down starch into sugar + BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + function + + + + + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + + + + + + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + + + + + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + + + + + + + + + + + + + + + + + + + + information carrier + In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. + + A quality of an information bearer that imparts the information content + 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. + 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. + PERSON: Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + information carrier + + + + + + + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item + + + + + + + + + symbol + a serial number such as "12324X" + a stop sign + a written proper name such as "OBI" + + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + 20091104, MC: this needs work and will most probably change + 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). + PERSON: James A. Overton + PERSON: Jonathan Rees + based on Oxford English Dictionary + symbol + + + + + + + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + A generically dependent continuant that is about some thing. + 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data set + Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). + + A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. + 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type + 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000042 + group:OBI + data set + + + + + + + + + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part + + + + + + + + + + + + + + + + + + + + + + + + + material information bearer + A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. + a brain + a hard drive + + A material entity in which a concretization of an information content entity inheres. + GROUP: IAO + material information bearer + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification + + + + + + + + + + + + + + + + + + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + + + + + + + + + + + + + The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. + + A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID symbol + Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier symbol + + + + + + + + + + + + + + + + + + + + + + + + + + The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. + + An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. + 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). + Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. + + Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID + Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier + + + + + + + + + PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. + + A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID registry + Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier registry + + + + + + + + + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + cjm + 2018-05-20T20:55:03Z + ontology module + + + + + + + + + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + cjm + 2018-05-20T20:55:30Z + base ontology module + + + + + + + + + + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + cjm + 2018-05-20T20:55:47Z + editors ontology module + + + + + + + + + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + cjm + 2018-05-20T20:56:13Z + main release ontology module + + + + + + + + + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + cjm + 2018-05-20T20:56:23Z + bridge ontology module + + + + + + + + + + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + cjm + 2018-05-20T20:56:47Z + import ontology module + + + + + + + + + + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + cjm + 2018-05-20T20:58:11Z + subset ontology module + + + + + + + + + + + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + cjm + 2018-05-20T20:58:38Z + curation subset ontology module + + + + + + + + + An ontology module that is intended for usage in analysis or discovery applications. + cjm + 2018-05-20T20:58:49Z + analysis subset ontology module + + + + + + + + + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + cjm + 2018-05-20T20:59:19Z + single layer subset ontology module + + + + + + + + + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + cjm + 2018-05-20T20:59:57Z + exclusion subset ontology module + + + + + + + + + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + cjm + 2018-05-20T21:00:14Z + external import ontology module + + + + + + + + + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + cjm + 2018-05-20T21:14:16Z + species subset ontology module + + + + + + + + + + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + cjm + 2018-05-20T21:20:33Z + reasoned ontology module + + + + + + + + + + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + cjm + 2018-05-20T21:21:12Z + generated ontology module + + + + + + + + + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + cjm + 2018-05-20T21:21:21Z + template generated ontology module + + + + + + + + + + + + cjm + 2018-05-20T21:28:15Z + taxonomic bridge ontology module + + + + + + + + + cjm + 2018-05-22T04:15:54Z + ontology module subsetted by expressivity + + + + + + + + + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + cjm + 2018-05-22T04:16:10Z + obo basic subset ontology module + + + + + + + + + + cjm + 2018-05-22T04:16:28Z + ontology module subsetted by OWL profile + + + + + + + + + cjm + 2018-05-22T04:16:48Z + EL++ ontology module + + + + + + + + + planned process + A processual entity that realizes a plan which is the concretization of a plan specification. + + planned process + + + + + + + + + + + + + + + + + + + + + + + + Obsolete Class + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + core + + + + + + + + + placeholder removed + + + + + + + + + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + + This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. + We expect to be able to mine these new reasons and add instances as required. + other + true + + + + + + + + + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/imports/ro_import.json b/imports/ro_import.json new file mode 100644 index 0000000..19e4750 --- /dev/null +++ b/imports/ro_import.json @@ -0,0 +1,4812 @@ +{ + "graphs" : [ { + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/GO_0003674", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "molecular process" + } ] + }, + "type" : "CLASS", + "lbl" : "molecular_function" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + }, + "type" : "PROPERTY", + "lbl" : "results in formation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "results in developmental progression of" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000000", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/cl.owl" + } ] + }, + "type" : "CLASS", + "lbl" : "cell" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0000001", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "quality (PATO)" + } ] + }, + "type" : "CLASS", + "lbl" : "quality" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0016740", + "type" : "CLASS", + "lbl" : "transferase activity" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002608", + "meta" : { + "definition" : { + "val" : "Inverse of 'causal agent in process'", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + }, + "type" : "PROPERTY", + "lbl" : "process has causal agent" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0010002", + "meta" : { + "definition" : { + "val" : "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Molecules of DNA are carriers of genetic information." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This hard drive is carrier of these data items." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "[072-ISO]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This copy of *War and Peace* is carrier of the novel written by Tolstoy." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is carrier of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0010001", + "meta" : { + "definition" : { + "val" : "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "g-depends on", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Genetic information generically depend on molecules of DNA." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The novel *War and Peace* generically depends on this copy of the novel." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The pattern shared by chess boards generically depends on any chess board." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The score of a symphony g-depends on a copy of the score." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This pdf file generically depends on this server." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "[072-ISO]" + } ] + }, + "type" : "PROPERTY", + "lbl" : "generically depends on" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "developmentally succeeded by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Connects a biological entity to its taxon of origin." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Jennifer Deegan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + } ] + }, + "type" : "PROPERTY", + "lbl" : "in taxon" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", + "type" : "PROPERTY", + "lbl" : "has_related_synonym" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "meta" : { + "definition" : { + "val" : "inverse of has disposition", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + }, + "type" : "PROPERTY", + "lbl" : "disposition of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003001", + "meta" : { + "definition" : { + "val" : "a produced_by b iff some process that occurs_in b has_output a.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Melissa Haendel" + } ] + }, + "type" : "PROPERTY", + "lbl" : "produced by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003000", + "meta" : { + "definition" : { + "val" : "a produces b if some process that occurs_in a has_output b, where a and b are material entities. 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entity" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002584", + "meta" : { + "definition" : { + "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has part structure that is capable of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : 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It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "temporally related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002464", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "helper property (not for use in curation)" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002581", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is a defining property chain axiom" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "is a defining property chain axiom where second argument is reflexive" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002217", + "meta" : { + "definition" : { + "val" : "x actively participates in y if and only if x participates in y and x realizes some active role", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "agent in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "actively participates in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003307", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preventative for condition" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." + } ] + }, + "type" : "PROPERTY", + "lbl" : "ameliorates condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003306", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to penetrance of condition" + } ] + }, + "type" : "PROPERTY", + "lbl" : "contributes to frequency of condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002218", + "meta" : { + "definition" : { + "val" : "x has participant y if and only if x realizes some active role that inheres in y", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This may be obsoleted and replaced by the original 'has agent' relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'heart development' has active participant some Shh protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has agent" + } ] + }, + "type" : "PROPERTY", + "lbl" : "obsolete has active participant" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003308", + "meta" : { + "definition" : { + "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "correlated with condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "meta" : { + "definition" : { + "val" : "inverse of regulates", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "regulated by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "meta" : { + "definition" : { + "val" : "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "positively regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003303", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "causes condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003302", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." + } ] + }, + "type" : "PROPERTY", + "lbl" : "causes or contributes to condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "negatively regulated by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002577", + "meta" : { + "definition" : { + "val" : "A material entity consisting of multiple components that are causally integrated.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.jbiomedsem.com/content/4/1/43" + } ] + }, + "type" : "CLASS", + "lbl" : "system" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002578", + "meta" : { + "definition" : { + "val" : "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "directly regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to expressivity of condition" + } ] + }, + "type" : "PROPERTY", + "lbl" : "contributes to severity of condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "positively regulated by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "RO_0000053 some (RO_0000054 only ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + } ] + }, + "type" : "PROPERTY", + "lbl" : "capable of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003304", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "contributes to condition" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity" + } ] + }, + "type" : "PROPERTY", + "lbl" : "capable of part of" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001010", + "type" : "CLASS", + "lbl" : "organism or virus or viroid" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this cell derives from this parent cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this nucleus derives from this parent nucleus (nuclear division)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "derives from" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "involved in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "meta" : { + "definition" : { + "val" : "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Hill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Tanya Berardini" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent cell derives into this cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent nucleus derives into this nucleus (nuclear division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + } ] + }, + "type" : "PROPERTY", + "lbl" : "derives into" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "meta" : { + "definition" : { + "val" : "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Brush" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is model of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "meta" : { + "definition" : { + "val" : "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "negatively regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "meta" : { + "definition" : { + "val" : "inverse of enables", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "enabled by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002450", + "meta" : { + "definition" : { + "val" : "Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly increases activity of", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "activates" + } ] + }, + "type" : "PROPERTY", + "lbl" : "activity directly positively regulates activity of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "meta" : { + "definition" : { + "val" : "Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "activity directly regulates activity of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "enables" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "meta" : { + "definition" : { + "val" : "Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly decreases activity of", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inhibits" + } ] + }, + "type" : "PROPERTY", + "lbl" : "activity directly negatively regulates activity of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + } ] + }, + "type" : "PROPERTY", + "lbl" : "functionally related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "part of structure that is capable of" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + } ] + }, + "type" : "PROPERTY", + "lbl" : "part of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "mereotopologically related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "This is the transitive form of the develops from relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Terry Meehan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Melissa Haendel" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "develops from" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + } ] + }, + "type" : "PROPERTY", + "lbl" : "developmentally related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "meta" : { + "definition" : { + "val" : "inverse of develops from", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Terry Meehan" + } ] + }, + "type" : "PROPERTY", + "lbl" : "develops into" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "meta" : { + "definition" : { + "val" : "Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influences (material entity to material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally influences" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002447", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + } ] + }, + "type" : "PROPERTY", + "lbl" : "phosphorylates" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "editor note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000117", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "term editor" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "type" : "PROPERTY", + "lbl" : "has curation status" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has part" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "example of usage" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000232", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "curator note" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "type" : "PROPERTY", + "lbl" : "editor preferred term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "alternative term" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + } ] + }, + "type" : "PROPERTY", + "lbl" : "definition source" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some environmental process", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + } ] + }, + "type" : "PROPERTY", + "lbl" : "evolutionarily related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://xmlns.com/foaf/0.1/page", + "val" : "https://github.com/oborel/obo-relations/wiki/InteractionRelations" + } ] + }, + "type" : "PROPERTY", + "lbl" : "interaction relation helper property" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "molecular interaction relation helper property" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "phenotype of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002559", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influenced by (material entity to material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally influenced by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://xmlns.com/foaf/0.1/page", + "val" : "https://github.com/oborel/obo-relations/wiki/InteractionRelations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + } ] + }, + "type" : "PROPERTY", + "lbl" : "interacts with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "meta" : { + "definition" : { + "val" : "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "inheres in part of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/MI_0915" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "molecularly binds with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "binds" + } ] + }, + "type" : "PROPERTY", + "lbl" : "molecularly interacts with" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "pending final vetting" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "meta" : { + "definition" : { + "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "material entity" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "ready for release" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + }, + "type" : "PROPERTY", + "lbl" : "involved in negative regulation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + } ] + }, + "type" : "PROPERTY", + "lbl" : "involved in or involved in regulation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is active in" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass", + "type" : "CLASS", + "lbl" : "Obsolete Class" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of, negative effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally downstream of or within" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0008150", + "type" : "CLASS", + "lbl" : "biological_process" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "involved in regulation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + }, + "type" : "PROPERTY", + "lbl" : "involved in positive regulation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of, positive effect" + }, { + "id" : "http://purl.obolibrary.org/obo/UPHENO_0001001", + "type" : "CLASS", + "lbl" : "phenotype" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of or within, positive effect" + }, { + "id" : "http://purl.obolibrary.org/obo/OGMS_0000031", + "meta" : { + "definition" : { + "val" : "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "disease" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of or within, negative effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "meta" : { + "definition" : { + "val" : "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of or within" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002532", + "meta" : { + "definition" : { + "val" : "Any entity that is ordered in discrete units along a linear axis.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "CLASS", + "lbl" : "sequentially ordered entity" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally upstream of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002533", + "meta" : { + "definition" : { + "val" : "Any individual unit of a collection of like units arranged in a linear order", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." + } ] + }, + "type" : "CLASS", + "lbl" : "sequence atomic unit" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "immediately causally upstream of" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "meta" : { + "definition" : { + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occurs_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "occurs in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" + } ] + }, + "type" : "PROPERTY", + "lbl" : "occurs in" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "site of" + } ] + }, + "type" : "PROPERTY", + "lbl" : "contains process" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + } ] + }, + "type" : "PROPERTY", + "lbl" : "preceded by" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + } ] + }, + "type" : "PROPERTY", + "lbl" : "precedes" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0003824", + "type" : "CLASS", + "lbl" : "catalytic activity" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + }, + "type" : "PROPERTY", + "lbl" : "starts during" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "type" : "CLASS", + "lbl" : "quality" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " + } ] + }, + "type" : "PROPERTY", + "lbl" : "ends during" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "meta" : { + "definition" : { + "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "process" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "INDIVIDUAL", + "lbl" : "requires discussion" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "type" : "CLASS", + "lbl" : "disposition" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "first order logic expression" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "meta" : { + "definition" : { + "val" : "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "realizable entity" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + } ] + }, + "type" : "PROPERTY", + "lbl" : "immediately precedes" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + } ] + }, + "type" : "PROPERTY", + "lbl" : "acts upstream of, negative effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "meta" : { + "definition" : { + "val" : "This relation groups causal relations between material entities and causal relations between processes", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally related to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:30Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "acts upstream of or within, positive effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004031", + "meta" : { + "definition" : { + "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-25T23:20:13Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "enables subfunction" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:14Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "acts upstream of, positive effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:51Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "acts upstream of or within, negative effect" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "meta" : { + "definition" : { + "val" : "inverse of upstream of", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causally downstream of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "meta" : { + "definition" : { + "val" : "inverse of has subsequence", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is subsequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + } ] + }, + "type" : "PROPERTY", + "lbl" : "immediately causally downstream of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "meta" : { + "definition" : { + "val" : "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "overlaps sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002527", + "meta" : { + "definition" : { + "val" : "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "disconnected from" + } ] + }, + "type" : "PROPERTY", + "lbl" : "does not overlap sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "meta" : { + "definition" : { + "val" : "inverse of downstream of sequence of", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is upstream of sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0016301", + "type" : "CLASS", + "lbl" : "kinase activity" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "meta" : { + "definition" : { + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "bounds sequence of" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", + "type" : "PROPERTY", + "lbl" : "in_subset" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002523", + "meta" : { + "definition" : { + "val" : "inverse of bounds sequence of", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is bound by sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "meta" : { + "definition" : { + "val" : "x has subsequence y iff all of the sequence parts of x are sequence parts of y", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contains" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has subsequence" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "meta" : { + "definition" : { + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "is downstream of sequence of" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", + "meta" : { + "definition" : { + "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "independent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + }, + "type" : "PROPERTY", + "lbl" : "during which starts" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + }, + "type" : "PROPERTY", + "lbl" : "during which ends" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "ends after" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts_at_end_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + }, + "type" : "PROPERTY", + "lbl" : "immediately preceded by" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002514", + "meta" : { + "definition" : { + "val" : "A relation that holds between two entities that have the property of being sequences or having sequences. ", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + }, + "type" : "PROPERTY", + "lbl" : "sequentially related to" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", + "type" : "PROPERTY", + "lbl" : "has_broad_synonym" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000002", + "meta" : { + "definition" : { + "val" : "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "meta" : { + "definition" : { + "val" : "An entity that has temporal parts and that happens, unfolds or develops through time.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "occurrent" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", + "type" : "PROPERTY", + "lbl" : "has_exact_synonym" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", + "type" : "PROPERTY", + "lbl" : "database_cross_reference" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002630", + "meta" : { + "definition" : { + "val" : "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + }, + "type" : "PROPERTY", + "lbl" : "directly negatively regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002506", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causal relation between material entities" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + }, + "type" : "PROPERTY", + "lbl" : "causal agent in process" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + }, + "type" : "PROPERTY", + "lbl" : "causal relation between processes" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/BFO_0000169" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + }, + "type" : "PROPERTY", + "lbl" : "depends on" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "type" : "CLASS", + "lbl" : "function" + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", + "type" : "CLASS", + "lbl" : "environmental system" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002629", + "meta" : { + "definition" : { + "val" : "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + }, + "type" : "PROPERTY", + "lbl" : "directly positively regulates" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000031", + "meta" : { + "definition" : { + "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "generically dependent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has component" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002615", + "meta" : { + "definition" : { + "val" : "Inverse of is-model-of", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "has model" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002610", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Groups both positive and negative correlation" + } ] + }, + "type" : "PROPERTY", + "lbl" : "correlated with" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + }, + "type" : "PROPERTY", + "lbl" : "OBO foundry unique label" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000023", + "meta" : { + "definition" : { + "val" : "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "role" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0016772", + "type" : "CLASS", + "lbl" : "transferase activity, transferring phosphorus-containing groups" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", + "type" : "PROPERTY", + "lbl" : "subset_property" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000020", + "meta" : { + "definition" : { + "val" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "specifically dependent continuant" + } ], + "edges" : [ { + "sub" : "http://purl.obolibrary.org/obo/RO_0002162", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002320" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002203" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002384", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002324" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002529", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002527" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002411", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002131", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002323" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002200", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002201" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002353", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002328" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000066", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000067" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002501", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002410" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002431", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0003303", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0003302" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002525", + "pred" 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"http://purl.obolibrary.org/obo/RO_0002162" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/RO_0000058" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002314", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000063", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/BFO_0000063" ] + } ] + } ] +} \ No newline at end of file diff --git a/imports/ro_import.obo b/imports/ro_import.obo new file mode 100644 index 0000000..d864e3b --- /dev/null +++ b/imports/ro_import.obo @@ -0,0 +1,1804 @@ +format-version: 1.2 +data-version: geno/releases/2019-09-09/imports/ro_import.owl +subsetdef: ro-eco "" +subsetdef: RO:0002259 "" +ontology: geno/imports/ro_import +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (is model of)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +disjoint_from: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000002 ! part of continuant + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +relationship: BFO:0000050 BFO:0000003 ! part of occurrent + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000004 ! part of independent continuant + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +is_a: BFO:0000003 ! occurrent + +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role + +[Term] +id: BFO:0000017 +name: realizable entity +def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality +relationship: BFO:0000050 BFO:0000017 ! part of realizable entity + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +relationship: BFO:0000050 BFO:0000019 ! part of quality + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant + +[Term] +id: BFO:0000023 +name: role +def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] +is_a: BFO:0000017 ! realizable entity + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] +is_a: BFO:0000002 ! continuant +relationship: BFO:0000050 BFO:0000031 ! part of generically dependent continuant + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant + +[Term] +id: CARO:0000000 +name: anatomical entity +is_a: CARO:0030000 ! biological entity +property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl + +[Term] +id: CARO:0000003 +name: connected anatomical structure +is_a: CARO:0000006 ! material anatomical entity +property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl + +[Term] +id: CARO:0000006 +name: material anatomical entity +is_a: BFO:0000040 ! material entity +is_a: CARO:0000000 ! anatomical entity +property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl + +[Term] +id: CARO:0001010 +name: organism or virus or viroid +is_a: BFO:0000040 ! material entity + +[Term] +id: CARO:0030000 +name: biological entity +is_a: BFO:0000004 ! independent continuant + +[Term] +id: CL:0000000 +name: cell +is_a: CARO:0000003 ! connected anatomical structure +property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl + +[Term] +id: ENVO:01000254 +name: environmental system +is_a: RO:0002577 ! system + +[Term] +id: GO:0003674 +name: molecular_function +is_a: BFO:0000015 ! process +property_value: IAO:0000589 "molecular process" xsd:string + +[Term] +id: GO:0003824 +name: catalytic activity +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0008150 +name: biological_process +is_a: BFO:0000015 ! process + +[Term] +id: GO:0016301 +name: kinase activity +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups + +[Term] +id: GO:0016740 +name: transferase activity +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +is_a: GO:0016740 ! transferase activity + +[Term] +id: OGMS:0000031 +name: disease +def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [] +is_a: BFO:0000016 ! disposition + +[Term] +id: ObsoleteClass +name: Obsolete Class + +[Term] +id: PATO:0000001 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000589 "quality (PATO)" xsd:string + +[Term] +id: RO:0002532 +name: sequentially ordered entity +def: "Any entity that is ordered in discrete units along a linear axis." [] +relationship: RO:0002524 RO:0002533 ! has subsequence sequence atomic unit +property_value: IAO:0000117 "Chris Mungall" xsd:string + +[Term] +id: RO:0002533 +name: sequence atomic unit +def: "Any individual unit of a collection of like units arranged in a linear order" [] +is_a: RO:0002532 ! sequentially ordered entity +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." xsd:string + +[Term] +id: RO:0002577 +name: system +def: "A material entity consisting of multiple components that are causally integrated." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string + +[Term] +id: UPHENO:0001001 +name: phenotype +is_a: PATO:0000001 ! quality + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: BFO:0000062 +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: BFO:0000050 BFO:0000062 +holds_over_chain: RO:0002091 BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + +[Typedef] +id: BFO:0000063 +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: BFO:0000050 BFO:0000063 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: BFO:0000066 +name: occurs in +def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "occurs in" xsd:string +property_value: IAO:0000118 "occurs_in" xsd:string +property_value: IAO:0000118 "unfolds in" xsd:string +property_value: IAO:0000118 "unfolds_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000050 BFO:0000066 +inverse_of: BFO:0000067 ! contains process +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: RO:0002314 ! inheres in part of +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: BFO:0000051 RO:0000057 + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: RO:0000053 ! bearer of +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +def: "inverse of has disposition" [] +subset: RO:0002259 +is_a: RO:0000052 ! inheres in + +[Typedef] +id: RO:0001000 +name: derives from +def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +subset: ro-eco +property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string +property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string +property_value: IAO:0000118 "derives_from" xsd:string +property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +inverse_of: RO:0001001 ! derives into + +[Typedef] +id: RO:0001001 +name: derives into +def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +subset: ro-eco +property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string +property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string +property_value: IAO:0000118 "derives_into" xsd:string + +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + +[Typedef] +id: RO:0002019 +name: has ligand +def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] +domain: GO:0004872 +is_a: RO:0002233 ! has input +created_by: dos +creation_date: 2017-07-19T17:30:36Z + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +is_a: RO:0002334 ! regulated by +inverse_of: RO:0002578 ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002630 ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002629 ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002025 +name: has effector activity +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. +is_functional: true +is_a: RO:0002017 ! has component activity +is_a: RO:0002211 ! regulates +created_by: dos +creation_date: 2017-09-22T14:14:36Z + +[Typedef] +id: RO:0002084 +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: RO:0002222 ! temporally related to +inverse_of: RO:0002093 ! ends during + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +holds_over_chain: RO:0002093 BFO:0000062 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002087 +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes + +[Typedef] +id: RO:0002088 +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: RO:0002222 ! temporally related to +inverse_of: RO:0002091 ! starts during + +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: RO:0002575 BFO:0000063 +is_a: BFO:0000063 ! precedes + +[Typedef] +id: RO:0002091 +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002093 +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: RO:0001900 RO:0001901 +holds_over_chain: BFO:0000050 BFO:0000050 +holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 RO:0002131 +is_a: RO:0002323 ! mereotopologically related to +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Jennifer Deegan" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +range: CARO:0001010 ! organism or virus or viroid +holds_over_chain: BFO:0000050 RO:0002162 +holds_over_chain: BFO:0000051 RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002215 RO:0002162 +holds_over_chain: RO:0002217 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002180 +name: has component +def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002200 +name: has phenotype +def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +range: UPHENO:0001001 ! phenotype +inverse_of: RO:0002201 ! phenotype of + +[Typedef] +id: RO:0002201 +name: phenotype of +def: "inverse of has phenotype" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_functional: true + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 "Melissa Haendel" xsd:string +property_value: IAO:0000117 "Terry Meehan" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 "Terry Meehan" xsd:string +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + +[Typedef] +id: RO:0002211 +name: regulates +def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Hill" xsd:string +property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000119 "GO" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string +property_value: IAO:0000589 "regulates (processual)" xsd:string +property_value: IAO:0000600 "false" xsd:boolean +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: RO:0002578 RO:0002578 +is_transitive: true +is_a: RO:0002411 ! causally upstream of +inverse_of: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002212 +name: negatively regulates +def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +property_value: RO:0004050 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect +inverse_of: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002213 +name: positively regulates +def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +property_value: RO:0004049 RO:0002211 +holds_over_chain: RO:0002212 RO:0002212 +is_transitive: true +is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect +inverse_of: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002215 +name: capable of +def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] +subset: ro-eco +property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string +property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function realized in" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 +property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of +expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso "defining-property-chains-involving-reflexivity" +holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process +expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] + +[Typedef] +id: RO:0002217 +name: actively participates in +def: "x actively participates in y if and only if x participates in y and x realizes some active role" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "agent in" xsd:string +is_a: RO:0000056 ! participates in +inverse_of: RO:0002218 ! obsolete has active participant + +[Typedef] +id: RO:0002218 +name: obsolete has active participant +def: "x has participant y if and only if x realizes some active role that inheres in y" [] +subset: ro-eco +property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has agent" xsd:string +is_a: RO:0000057 ! has participant +is_obsolete: true + +[Typedef] +id: RO:0002222 +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002233 +name: has input +def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "consumes" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity +is_a: RO:0000057 ! has participant +inverse_of: RO:0002352 ! input of + +[Typedef] +id: RO:0002234 +name: has output +def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "produces" xsd:string +is_a: RO:0000057 ! has participant +inverse_of: RO:0002353 ! output of + +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 ! anatomical entity +range: CARO:0000000 ! anatomical entity +holds_over_chain: BFO:0000051 RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + +[Typedef] +id: RO:0002255 +name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +holds_over_chain: RO:0002203 BFO:0000050 +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002258 +name: developmentally preceded by +def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] +comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "false" xsd:boolean +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002324 ! developmentally related to +inverse_of: RO:0002286 ! developmentally succeeded by + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 RO:0002411 +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 RO:0002418 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002286 +name: developmentally succeeded by +def: "Inverse of developmentally preceded by" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +property_value: RO:0004049 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +property_value: RO:0004050 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: RO:0002314 +name: inheres in part of +def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." [] +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso "defining-property-chains-involving-reflexivity" +holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002502 ! depends on +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002320 +name: evolutionarily related to +def: "A relationship that holds via some environmental process" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string + +[Typedef] +id: RO:0002323 +name: mereotopologically related to +def: "A mereological relationship or a topological relationship" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0002324 +name: developmentally related to +def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string + +[Typedef] +id: RO:0002327 +name: enables +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "catalyzes" xsd:string +property_value: IAO:0000118 "executes" xsd:string +property_value: IAO:0000118 "has" xsd:string +property_value: IAO:0000118 "is catalyzing" xsd:string +property_value: IAO:0000118 "is executing" xsd:string +property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string +is_a: RO:0002215 ! capable of +inverse_of: RO:0002333 ! enabled by +transitive_over: BFO:0000051 ! has part +transitive_over: RO:0002017 ! has component activity + +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "false" xsd:boolean +holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: seeAlso Involved:in +holds_over_chain: RO:0002327 BFO:0000050 +is_a: RO:0002217 ! actively participates in +is_a: RO:0002431 ! involved in or involved in regulation of +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000057 ! has participant +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002334 +name: regulated by +def: "inverse of regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "regulated by (processual)" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002335 +name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002336 +name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000050 ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002353 +name: output of +def: "inverse of has output" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002354 +name: formed as result of +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002353 ! output of + +[Typedef] +id: RO:0002384 +name: has developmental potential involving +def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 ! anatomical entity +range: CARO:0000000 ! anatomical entity +is_a: RO:0002324 ! developmentally related to + +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002388 +name: has potential to directly develop into +def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002387 ! has potential to develop into + +[Typedef] +id: RO:0002404 +name: causally downstream of +def: "inverse of upstream of" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: BFO:0000062 ! preceded by +is_a: RO:0002427 ! causally downstream of or within +inverse_of: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002405 +name: immediately causally downstream of +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002087 ! immediately preceded by +is_a: RO:0002404 ! causally downstream of +inverse_of: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002410 +name: causally related to +def: "This relation groups causal relations between material entities and causal relations between processes" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string + +[Typedef] +id: RO:0002411 +name: causally upstream of +def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_transitive: true +is_a: BFO:0000063 ! precedes +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002412 +name: immediately causally upstream of +def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: RO:0002575 RO:0002411 +is_a: RO:0002090 ! immediately precedes +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002418 +name: causally upstream of or within +def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +synonym: "affects" RELATED [] +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "influences (processual)" xsd:string +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002427 +name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +holds_over_chain: RO:0002327 RO:0002211 +holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 RO:0002213 +holds_over_chain: RO:0002331 RO:0002213 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 RO:0002212 +holds_over_chain: RO:0002331 RO:0002212 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +name: involved in or involved in regulation of +def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002432 +name: is active in +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +synonym: "enables activity in" EXACT [] +property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "executes activity in" xsd:string +holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002131 ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002434 +name: interacts with +def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] +subset: ro-eco +synonym: "in pairwise interaction with" EXACT [] +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: seeAlso ECO:0000353 +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002447 +name: phosphorylates +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002448 +name: activity directly regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002449 +name: activity directly negatively regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "inhibits" xsd:string +is_a: RO:0002448 ! activity directly regulates activity of + +[Typedef] +id: RO:0002450 +name: activity directly positively regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "activates" xsd:string +is_a: RO:0002448 ! activity directly regulates activity of + +[Typedef] +id: RO:0002464 +name: helper property (not for use in curation) +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002479 +name: has part that occurs in +def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] +subset: ro-eco +property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} + +[Typedef] +id: RO:0002481 +name: is kinase activity +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002564 ! molecular interaction relation helper property + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: RO:0002608 ! process has causal agent + +[Typedef] +id: RO:0002501 +name: causal relation between processes +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002502 +name: depends on +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: seeAlso BFO:0000169 + +[Typedef] +id: RO:0002506 +name: causal relation between material entities +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002514 +name: sequentially related to +def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string +domain: RO:0002532 ! sequentially ordered entity +range: RO:0002532 ! sequentially ordered entity + +[Typedef] +id: RO:0002522 +name: bounds sequence of +def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_transitive: true +is_a: RO:0002514 ! sequentially related to +inverse_of: RO:0002523 ! is bound by sequence of + +[Typedef] +id: RO:0002523 +name: is bound by sequence of +def: "inverse of bounds sequence of" [] +subset: RO:0002259 +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_transitive: true +is_a: RO:0002514 ! sequentially related to + +[Typedef] +id: RO:0002524 +name: has subsequence +def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "contains" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +is_transitive: true +is_a: BFO:0000051 ! has part +is_a: RO:0002522 ! bounds sequence of +is_a: RO:0002526 ! overlaps sequence of +inverse_of: RO:0002525 ! is subsequence of + +[Typedef] +id: RO:0002525 +name: is subsequence of +def: "inverse of has subsequence" [] +subset: RO:0002259 +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "contained by" xsd:string +is_transitive: true +is_a: BFO:0000050 ! part of +is_a: RO:0002523 ! is bound by sequence of +is_a: RO:0002526 ! overlaps sequence of + +[Typedef] +id: RO:0002526 +name: overlaps sequence of +def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +holds_over_chain: RO:0002524 RO:0002525 +is_symmetric: true +is_a: RO:0002131 ! overlaps +is_a: RO:0002514 ! sequentially related to + +[Typedef] +id: RO:0002527 +name: does not overlap sequence of +def: "x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "disconnected from" xsd:string +is_symmetric: true +is_a: RO:0002514 ! sequentially related to + +[Typedef] +id: RO:0002528 +name: is upstream of sequence of +def: "inverse of downstream of sequence of" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_transitive: true +is_a: RO:0002527 ! does not overlap sequence of + +[Typedef] +id: RO:0002529 +name: is downstream of sequence of +def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_transitive: true +is_a: RO:0002527 ! does not overlap sequence of +inverse_of: RO:0002529 ! is downstream of sequence of + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (material entity to material entity)" xsd:string +is_a: RO:0002506 ! causal relation between material entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002563 +name: interaction relation helper property +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 +is_a: RO:0002464 ! helper property (not for use in curation) + +[Typedef] +id: RO:0002564 +name: molecular interaction relation helper property +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002563 ! interaction relation helper property + +[Typedef] +id: RO:0002566 +name: causally influences +def: "Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (material entity to material entity)" xsd:string +is_a: RO:0002506 ! causal relation between material entities + +[Typedef] +id: RO:0002578 +name: directly regulates +def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: RO:0002575 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002584 +name: has part structure that is capable of +def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +holds_over_chain: BFO:0000051 RO:0002215 +is_a: RO:0002328 ! functionally related to +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +name: causal relation between material entity and a process +def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002596 +name: capable of regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002211 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +name: capable of negatively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002212 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +name: capable of positively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002213 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002608 +name: process has causal agent +def: "Inverse of 'causal agent in process'" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002610 +name: correlated with +def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] +property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string + +[Typedef] +id: RO:0002615 +name: has model +def: "Inverse of is-model-of" [] +inverse_of: RO:0003301 ! is model of + +[Typedef] +id: RO:0002629 +name: directly positively regulates +def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string +property_value: RO:0004049 RO:0002578 +is_a: RO:0002213 ! positively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0002630 +name: directly negatively regulates +def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string +property_value: RO:0004050 RO:0002578 +is_a: RO:0002212 ! negatively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0003000 +name: produces +def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] +comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Melissa Haendel" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +inverse_of: RO:0003001 ! produced by + +[Typedef] +id: RO:0003001 +name: produced by +def: "a produced_by b iff some process that occurs_in b has_output a." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Melissa Haendel" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity + +[Typedef] +id: RO:0003301 +name: is model of +def: "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] +comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. +property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" xsd:string +property_value: IAO:0000117 "Matthew Brush" xsd:string +is_asymmetric: true + +[Typedef] +id: RO:0003302 +name: causes or contributes to condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. +property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." xsd:string +property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0003303 +name: causes condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003304 +name: contributes to condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003305 +name: contributes to severity of condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." [] +property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003306 +name: contributes to frequency of condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." [] +property_value: IAO:0000118 "contributes to penetrance of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003307 +name: ameliorates condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. +property_value: IAO:0000118 "is preventative for condition" xsd:string +is_a: RO:0003305 ! contributes to severity of condition + +[Typedef] +id: RO:0003308 +name: correlated with condition +def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] +is_a: RO:0002610 ! correlated with + +[Typedef] +id: RO:0004031 +name: enables subfunction +def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] +holds_over_chain: RO:0002327 BFO:0000051 +is_a: RO:0002328 ! functionally related to +created_by: cjm +creation_date: 2018-01-25T23:20:13Z + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 RO:0002304 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: cjm +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 RO:0002305 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: cjm +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: RO:0004050 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: RO:0004049 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:19Z + +[Typedef] +id: RO:0010001 +name: generically depends on +def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] +synonym: "g-depends on" EXACT [] +property_value: IAO:0000112 "Genetic information generically depend on molecules of DNA." xsd:string +property_value: IAO:0000112 "The novel *War and Peace* generically depends on this copy of the novel." xsd:string +property_value: IAO:0000112 "The pattern shared by chess boards generically depends on any chess board." xsd:string +property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string +property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0000052 RO:0000058 +inverse_of: RO:0010002 ! is carrier of + +[Typedef] +id: RO:0010002 +name: is carrier of +def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] +property_value: IAO:0000112 "Molecules of DNA are carriers of genetic information." xsd:string +property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string +property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000031 ! generically dependent continuant +holds_over_chain: RO:0000059 RO:0000053 + +[Typedef] +id: results_in_developmental_progression_of +name: results in developmental progression of +def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: seeAlso Ontology:extensions +domain: GO:0008150 ! biological_process +range: CARO:0000003 ! connected anatomical structure +is_a: RO:0002324 ! developmentally related to + +[Typedef] +id: results_in_formation_of +name: results in formation of +property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string +property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +is_a: results_in_developmental_progression_of ! results in developmental progression of +is_a: RO:0002234 ! has output +inverse_of: RO:0002354 ! formed as result of + diff --git a/imports/ro_import.owl b/imports/ro_import.owl new file mode 100644 index 0000000..831058a --- /dev/null +++ b/imports/ro_import.owl @@ -0,0 +1,4539 @@ + + + + + + + + + + + + + + + + + editor preferred term + + + + + + + + + example of usage + + + + + + + + has curation status + + + + + + + + + definition + definition + + + + + + + + + editor note + + + + + + + + + term editor + + + + + + + + + alternative term + + + + + + + + + definition source + + + + + + + + + + + + + + + curator note + + + + + + + + + imported from + + + + + + + + expand expression to + + + + + + + + expand assertion to + + + + + + + + An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + first order logic expression + + + + + + + + + OBO foundry unique label + + + + + + + + elucidation + + + + + + + + + + + + + + + + + + + + + + + + + + + + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + is a defining property chain axiom + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subset_property + + + + + + + + + + + + + + + + + + + + has_broad_synonym + + + + + + + + database_cross_reference + + + + + + + + has_exact_synonym + + + + + + + + has_related_synonym + + + + + + + + in_subset + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + + + + + + + + part of + + + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + has part + + + + + + + + + + + + + + + + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + + preceded by + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes + + + + + + + + + + + + + + + + + + + occurs in + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + occurs_in + unfolds in + unfolds_in + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs in + + + + + + + + site of + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + role of + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + disposition of + + + + + + + + + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + + derives from + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + + derives into + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. + dos + 2017-07-19T17:30:36Z + has ligand + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + directly negatively regulated by + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + directly positively regulated by + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + David Osumi-Sutherland + o + overlaps + + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + overlaps + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + Chris Mungall + Jennifer Deegan + + + + Connects a biological entity to its taxon of origin. + in taxon + + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + has component + + + + + + + + + + + + + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + Chris Mungall + + has phenotype + + + + + + + + + + + inverse of has phenotype + Chris Mungall + + + phenotype of + + + + + + + + + + + + + + x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + Chris Mungall + David Osumi-Sutherland + Melissa Haendel + Terry Meehan + This is the transitive form of the develops from relation + develops from + + + + + + + + + + + + + inverse of develops from + Chris Mungall + David Osumi-Sutherland + Terry Meehan + + develops into + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall + David Hill + Tanya Berardini + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + regulates + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + negatively regulates (process to process) + + negatively regulates + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + positively regulates (process to process) + + positively regulates + + + + + + + + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + Chris Mungall + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + + capable of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + Chris Mungall + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + capable of part of + + + + + + + + + + true + + + + + + + + + + x actively participates in y if and only if x participates in y and x realizes some active role + Chris Mungall + agent in + actively participates in + + + + + + + + + 'heart development' has active participant some Shh protein + + x has participant y if and only if x realizes some active role that inheres in y + This may be obsoleted and replaced by the original 'has agent' relation + Chris Mungall + has agent + + obsolete has active participant + true + + + + + + + + + + + Chris Mungall + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + Chris Mungall + consumes + + has input + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + Chris Mungall + produces + + has output + + + + + + + + + + + + + + + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] + + x has developmental contribution from y iff x has some part z such that z develops from y + Chris Mungall + has developmental contribution from + + + + + + + + + + + + + + + inverse of has developmental contribution from + Chris Mungall + + developmentally contributes to + + + + + + + + + + + + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + false + Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one + This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from + developmentally preceded by + + + + + + + + + + + + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of + + + + + + + + + + + + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + acts upstream of or within + + + + + + + + + + + Inverse of developmentally preceded by + Chris Mungall + developmentally succeeded by + + + + + + + + + + + + p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). + This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. + Chris Mungall + results_in_developmental_progression_of + results in developmental progression of + + + + + + + + + + + + an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. + every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + + Chris Mungall + GOC:mtg_berkeley_2013 + results_in_formation_of + results in formation of + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + + + + + + + + + + + + + + q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of inheres in part of + Chris Mungall + + + inheres in part of + + + + + + + + + + true + + + + + + + + A relationship that holds via some environmental process + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + evolutionarily related to + + + + + + + + A mereological relationship or a topological relationship + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + mereotopologically related to + + + + + + + + A relationship that holds between entities participating in some developmental process (GO:0032502) + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development + developmentally related to + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + Chris Mungall + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + Chris Mungall + false + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + Chris Mungall + actively involved in + enables part of + involved in + + + + + + + + + + + inverse of enables + Chris Mungall + enabled by + + + + + + + + + + + + inverse of regulates + Chris Mungall + regulated by (processual) + + regulated by + + + + + + + + + inverse of negatively regulates + Chris Mungall + + negatively regulated by + + + + + + + + + inverse of positively regulates + Chris Mungall + + positively regulated by + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + inverse of has input + Chris Mungall + + + input of + + + + + + + + + + inverse of has output + Chris Mungall + + + output of + + + + + + + + + Chris Mungall + formed as result of + + + + + + + + + + + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). + Chris Mungall + has developmental potential involving + + + + + + + + + + x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + Chris Mungall + has potential to developmentally contribute to + + + + + + + + + + x has the potential to develop into y iff x develops into y or if x is capable of developing into y + Chris Mungall + has potential to develop into + + + + + + + + + + x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + Chris Mungall + has potential to directly develop into + + + + + + + + + + + + inverse of upstream of + Chris Mungall + causally downstream of + + + + + + + + + + + + Chris Mungall + immediately causally downstream of + + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types. + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causally related to + + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + Chris Mungall + causally upstream of + + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + Chris Mungall + + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) + affects + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + Chris Mungall + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + Chris Mungall + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + Chris Mungall + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + Chris Mungall + + involved in negative regulation of + + + + + + + + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union + Chris Mungall + involved in or reguates + involved in or involved in regulation of + + + + + + + + + + + + + + A protein that enables activity in a cytosol. + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + Chris Mungall + executes activity in + enables activity in + + is active in + + + + + + + + + true + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + GOC:cjm + GOC:dos + + + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + Considering relabeling as 'pairwise interacts with' + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + Chris Mungall + binds + molecularly binds with + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + Axiomatization to GO to be added later + Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + phosphorylates + + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + Chris Mungall + molecularly controls + activity directly regulates activity of + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + Chris Mungall + inhibits + molecularly decreases activity of + activity directly negatively regulates activity of + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + Chris Mungall + activates + molecularly increases activity of + activity directly positively regulates activity of + + + + + + + + Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + helper property (not for use in curation) + + + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + Chris Mungall + + has part that occurs in + + + + + + + + + true + + + + + + + + + Chris Mungall + is kinase activity + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + causal agent in process + + + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + + + + + + + + Chris Mungall + depends on + + + + + + + + + + + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between material entities + + + + + + + + + + A relation that holds between two entities that have the property of being sequences or having sequences. + Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. + The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. + + sequentially related to + + + + + + + + + + + The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) + x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + Chris Mungall + + bounds sequence of + + + + + + + + + + inverse of bounds sequence of + Chris Mungall + + + is bound by sequence of + + + + + + + + + + + + + x has subsequence y iff all of the sequence parts of x are sequence parts of y + Chris Mungall + contains + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has subsequence + + + + + + + + + + + + inverse of has subsequence + Chris Mungall + contained by + + + is subsequence of + + + + + + + + + + + + + + + x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. + Chris Mungall + + overlaps sequence of + + + + + + + + + + x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + Chris Mungall + disconnected from + + does not overlap sequence of + + + + + + + + + + inverse of downstream of sequence of + Chris Mungall + + is upstream of sequence of + + + + + + + + + + + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + Chris Mungall + + is downstream of sequence of + + + + + + + + + + Chris Mungall + + causally influenced by (material entity to material entity) + causally influenced by + + + + + + + + + Chris Mungall + interaction relation helper property + + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + Chris Mungall + molecular interaction relation helper property + + + + + + + + + + + + + + + + + + + Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b + Chris Mungall + + causally influences (material entity to material entity) + causally influences + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + Chris Mungall + + directly regulates (processual) + + directly regulates + + + + + + + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + Chris Mungall + has part structure that is capable of + + + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + Chris Mungall + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + capable of negatively regulating + + + + + + + + + + + + + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + + process has causal agent + + + + + + + + A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + Groups both positive and negative correlation + correlated with + + + + + + + + + Inverse of is-model-of + has model + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + + directly positively regulates (process to process) + + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + directly negatively regulates (process to process) + + directly negatively regulates + + + + + + + + + + + + + + + + + + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + Melissa Haendel + + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + produces + + + + + + + + + + + a produced_by b iff some process that occurs_in b has_output a. + Melissa Haendel + + produced by + + + + + + + + + + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + Matthew Brush + The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + is model of + + + + + + + + + The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. + +An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + causes or contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. + causes condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. + contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. + contributes to expressivity of condition + contributes to severity of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. + contributes to penetrance of condition + contributes to frequency of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. + is preventative for condition + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + ameliorates condition + + + + + + + + + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + correlated with condition + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + enables subfunction + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:30Z + acts upstream of or within, positive effect + + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:51Z + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + cjm + 2018-01-26T23:53:14Z + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + cjm + 2018-01-26T23:53:22Z + acts upstream of, negative effect + + + + + + + + + + + cjm + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + + + + + + + + + + cjm + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + + + + + + + + + + + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + + + + + + + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + + disposition + + + + + + + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + + + + + + + + + + + + + + + quality + + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + + + + + + + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + generically dependent continuant + + + + + + + + + function + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + + anatomical entity + + + + + + + + + + connected anatomical structure + + + + + + + + + + + material anatomical entity + + + + + + + + + organism or virus or viroid + + + + + + + + + biological entity + + + + + + + + + + cell + + + + + + + + + environmental system + + + + + + + + + molecular process + molecular_function + + + + + + + + + catalytic activity + + + + + + + + + + + + + + + biological_process + + + + + + + + + + + + true + + + kinase activity + + + + + + + + + transferase activity + + + + + + + + + transferase activity, transferring phosphorus-containing groups + + + + + + + + + + + + + + + A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. + disease + + + + + + + + + quality (PATO) + quality + + + + + + + + + + + + + + Any entity that is ordered in discrete units along a linear axis. + Chris Mungall + sequentially ordered entity + + + + + + + + + Any individual unit of a collection of like units arranged in a linear order + Chris Mungall + An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. + sequence atomic unit + + + + + + + + + A material entity consisting of multiple components that are causally integrated. + May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 + Chris Mungall + http://www.jbiomedsem.com/content/4/1/43 + system + + + + + + + + + phenotype + + + + + + + + Obsolete Class + + + + + + + + + + + + + + ready for release + + + + + + + + + pending final vetting + + + + + + + + + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From ligand activity to has_ligand + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From has_ligand to ligand activity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/reports/geno-edit.owl-obo-report.tsv b/reports/geno-edit.owl-obo-report.tsv new file mode 100644 index 0000000..bf796e5 --- /dev/null +++ b/reports/geno-edit.owl-obo-report.tsv @@ -0,0 +1,330 @@ +Level Rule Name Subject Property Value +ERROR duplicate_definition GENO:0000847 IAO:0000115 A relation used to describe an environment contextualizing the identity of an entity. +ERROR duplicate_definition GENO:0000873 IAO:0000115 A relation used to describe an environment contextualizing the identity of an entity. +ERROR duplicate_definition GENO:0000846 IAO:0000115 A relation used to describe a process contextualizing the identity of an entity. +ERROR duplicate_definition GENO:0000874 IAO:0000115 A relation used to describe a process contextualizing the identity of an entity. +ERROR duplicate_definition GENO:0000719 IAO:0000115 A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. +ERROR duplicate_definition GENO:0000899 IAO:0000115 A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. +ERROR misused_obsolete_label GENO:0000019 rdfs:label obsolete_sequence feature collection +ERROR misused_obsolete_label GENO:0000022 rdfs:label obsolete_genomic feature collection +ERROR misused_obsolete_label GENO:0000029 rdfs:label obsolete_reference single locus complement +ERROR misused_obsolete_label GENO:0000037 rdfs:label obsolete_unspecified feature +ERROR misused_obsolete_label GENO:0000042 rdfs:label obsolete_reference junction +ERROR misused_obsolete_label GENO:0000060 rdfs:label obsolete_reference gene allele +ERROR misused_obsolete_label GENO:0000091 rdfs:label obsolete_experimental insertion +ERROR misused_obsolete_label GENO:0000125 rdfs:label obsolete_sequence feature collection attribute +ERROR misused_obsolete_label GENO:0000142 rdfs:label obsolete_dominant inheritance +ERROR misused_obsolete_label GENO:0000150 rdfs:label obsolete_autosomal recessive inheritance +ERROR misused_obsolete_label GENO:0000242 rdfs:label obsolete_specifies +ERROR misused_obsolete_label GENO:0000243 rdfs:label obsolete_approximates_sequence +ERROR misused_obsolete_label GENO:0000244 rdfs:label obsolete_resolves_to_sequence +ERROR misused_obsolete_label GENO:0000253 rdfs:label obsolete_is_specified_by +ERROR misused_obsolete_label GENO:0000324 rdfs:label obsolete_chromosome complement +ERROR misused_obsolete_label GENO:0000359 rdfs:label obsolete_is_phenotype_of_genotype +ERROR misused_obsolete_label GENO:0000368 rdfs:label obsolete_participates_in_inheritance_process +ERROR misused_obsolete_label GENO:0000410 rdfs:label obsolete_is_genetic_variant_of +ERROR misused_obsolete_label GENO:0000411 rdfs:label obsolete_has_genetic_variant +ERROR misused_obsolete_label GENO:0000415 rdfs:label obsolete_reagent sequence feature +ERROR misused_obsolete_label GENO:0000486 rdfs:label obsolete_is_variant_with@en +ERROR misused_obsolete_label GENO:0000488 rdfs:label obsolete_is_expression_variant_with@en +ERROR misused_obsolete_label GENO:0000491 rdfs:label obsolete_mutant allele +ERROR misused_obsolete_label GENO:0000680 rdfs:label obsolete_null feature@en +ERROR misused_obsolete_label GENO:0000712 rdfs:label ObsoleteDataProperty@en +ERROR misused_obsolete_label GENO:0000724 rdfs:label obsolete_biological sequence or collection@en +ERROR misused_obsolete_label GENO:0000725 rdfs:label obsolete_biological sequence collection@en +ERROR misused_obsolete_label GENO:0000741 rdfs:label obsolete_has_regulatory_part@en +ERROR misused_obsolete_label GENO:0000742 rdfs:label obsolete_is_alteration_within@en +ERROR misused_obsolete_label GENO:0000767 rdfs:label obsolete_has_position_component@en +ERROR misused_obsolete_label GENO:0000768 rdfs:label obsolete_genomic position +ERROR misused_obsolete_label GENO:0000772 rdfs:label obsolete_unspecified@en +ERROR misused_obsolete_label GENO:0000778 rdfs:label obsolete_sequence information entity@en +ERROR misused_obsolete_label GENO:0000848 rdfs:label obsolete_coding sequence alteration@en +ERROR misused_obsolete_label GENO:0000870 rdfs:label obsolete_sequence feature collection@en +ERROR misused_obsolete_label GENO:0000876 rdfs:label obsolete_genetic dosage@en +ERROR misused_obsolete_label GENO:0000883 rdfs:label obsolete_gametic@en +ERROR misused_obsolete_label GENO:0000890 rdfs:label obsolete_canonical allele +ERROR misused_obsolete_label GENO:0000891 rdfs:label obsolete_contextual allele +ERROR misused_obsolete_label GENO:0000901 rdfs:label obsolete_allele cellular context +ERROR misused_obsolete_label GENO:0000915 rdfs:label obsolete_haplotype@en +ERROR misused_obsolete_label GENO:0000916 rdfs:label obsolete_haplotype block@en +ERROR misused_obsolete_label GENO:0000923 rdfs:label obsolete_functional copy number complement +ERROR misused_obsolete_label GENO:0000924 rdfs:label obsolete_intrinsic sequence feature attribute@en +ERROR misused_obsolete_label GENO:0000925 rdfs:label obsolete_extrinsic sequence feature attribute@en +ERROR misused_obsolete_label GENO:0000955 rdfs:label obsolete_variant copy number complement +ERROR misused_obsolete_label GENO:0000956 rdfs:label obsolete_copy number complement@en +ERROR misused_obsolete_label PATO:0000016 rdfs:label obsolete_color brightness@en +ERROR misused_obsolete_label RO:0002354 rdfs:label obsolete_formed as result of@en +ERROR misused_obsolete_label SO:0000143 rdfs:label obsolete_assembly_component@en +ERROR misused_obsolete_label SO:0000149 rdfs:label obsolete_contig@en +ERROR misused_obsolete_label SO:0000637 rdfs:label obsolete_engineered_plasmid@en +ERROR misused_obsolete_label SO:0001410 rdfs:label obsolete_experimental_feature@en +ERROR duplicate_label http://biohackathon.org/resource/faldo#reference rdfs:label reference +ERROR duplicate_label GENO:0000152 rdfs:label reference +ERROR multiple_definitions BFO:0000020 IAO:0000115 b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])@en +ERROR multiple_definitions BFO:0000020 IAO:0000115 b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])@en +ERROR multiple_labels BFO:0000002 rdfs:label continuant +ERROR multiple_labels BFO:0000002 rdfs:label continuant@en +ERROR multiple_labels BFO:0000003 rdfs:label occurrent +ERROR multiple_labels BFO:0000003 rdfs:label occurrent@en +ERROR multiple_labels BFO:0000004 rdfs:label independent continuant +ERROR multiple_labels BFO:0000004 rdfs:label independent continuant@en +ERROR multiple_labels BFO:0000015 rdfs:label process +ERROR multiple_labels BFO:0000015 rdfs:label process@en +ERROR multiple_labels BFO:0000016 rdfs:label disposition +ERROR multiple_labels BFO:0000016 rdfs:label disposition@en +ERROR multiple_labels BFO:0000017 rdfs:label realizable entity +ERROR multiple_labels BFO:0000017 rdfs:label realizable entity@en +ERROR multiple_labels BFO:0000019 rdfs:label quality +ERROR multiple_labels BFO:0000019 rdfs:label quality@en +ERROR multiple_labels BFO:0000020 rdfs:label specifically dependent continuant +ERROR multiple_labels BFO:0000020 rdfs:label specifically dependent continuant@en +ERROR multiple_labels BFO:0000023 rdfs:label role +ERROR multiple_labels BFO:0000023 rdfs:label role@en +ERROR multiple_labels BFO:0000031 rdfs:label generically dependent continuant +ERROR multiple_labels BFO:0000031 rdfs:label generically dependent continuant@en +ERROR multiple_labels BFO:0000040 rdfs:label material entity +ERROR multiple_labels BFO:0000040 rdfs:label material entity@en +ERROR multiple_labels IAO:0000030 rdfs:label information content entity +ERROR multiple_labels IAO:0000030 rdfs:label information content entity@en +WARN duplicate_label_synonym GENO:0000017 IAO:0000118 reference sequence +WARN duplicate_label_synonym GENO:0000501 IAO:0000118 wild-type allele +WARN duplicate_label_synonym SO:0000667 IAO:0000118 insertion +WARN duplicate_label_synonym SO:0001744 IAO:0000118 UPD +WARN duplicate_label_synonym SO:1000036 IAO:0000118 inversion +WARN missing_definition http://biohackathon.org/resource/faldo#BothStrandsPosition IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#ForwardStrandPosition IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#ReverseStrandPosition IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#StrandedPosition IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#begin IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#end IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#location IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#position IAO:0000115 +WARN missing_definition BFO:0000050 IAO:0000115 +WARN missing_definition BFO:0000051 IAO:0000115 +WARN missing_definition CHEBI:23367 IAO:0000115 +WARN missing_definition CHEBI:33696 IAO:0000115 +WARN missing_definition CL:0000000 IAO:0000115 +WARN missing_definition ENVO:01000254 IAO:0000115 +WARN missing_definition GENO:0000091 IAO:0000115 +WARN missing_definition GENO:0000092 IAO:0000115 +WARN missing_definition GENO:0000113 IAO:0000115 +WARN missing_definition GENO:0000118 IAO:0000115 +WARN missing_definition GENO:0000119 IAO:0000115 +WARN missing_definition GENO:0000134 IAO:0000115 +WARN missing_definition GENO:0000135 IAO:0000115 +WARN missing_definition GENO:0000136 IAO:0000115 +WARN missing_definition GENO:0000137 IAO:0000115 +WARN missing_definition GENO:0000139 IAO:0000115 +WARN missing_definition GENO:0000140 IAO:0000115 +WARN missing_definition GENO:0000150 IAO:0000115 +WARN missing_definition GENO:0000160 IAO:0000115 +WARN missing_definition GENO:0000164 IAO:0000115 +WARN missing_definition GENO:0000165 IAO:0000115 +WARN missing_definition GENO:0000169 IAO:0000115 +WARN missing_definition GENO:0000170 IAO:0000115 +WARN missing_definition GENO:0000171 IAO:0000115 +WARN missing_definition GENO:0000172 IAO:0000115 +WARN missing_definition GENO:0000173 IAO:0000115 +WARN missing_definition GENO:0000174 IAO:0000115 +WARN missing_definition GENO:0000175 IAO:0000115 +WARN missing_definition GENO:0000220 IAO:0000115 +WARN missing_definition GENO:0000243 IAO:0000115 +WARN missing_definition GENO:0000244 IAO:0000115 +WARN missing_definition GENO:0000251 IAO:0000115 +WARN missing_definition GENO:0000252 IAO:0000115 +WARN missing_definition GENO:0000253 IAO:0000115 +WARN missing_definition GENO:0000351 IAO:0000115 +WARN missing_definition GENO:0000383 IAO:0000115 +WARN missing_definition GENO:0000387 IAO:0000115 +WARN missing_definition GENO:0000391 IAO:0000115 +WARN missing_definition GENO:0000392 IAO:0000115 +WARN missing_definition GENO:0000393 IAO:0000115 +WARN missing_definition GENO:0000394 IAO:0000115 +WARN missing_definition GENO:0000458 IAO:0000115 +WARN missing_definition GENO:0000495 IAO:0000115 +WARN missing_definition GENO:0000502 IAO:0000115 +WARN missing_definition GENO:0000533 IAO:0000115 +WARN missing_definition GENO:0000575 IAO:0000115 +WARN missing_definition GENO:0000604 IAO:0000115 +WARN missing_definition GENO:0000605 IAO:0000115 +WARN missing_definition GENO:0000606 IAO:0000115 +WARN missing_definition GENO:0000616 IAO:0000115 +WARN missing_definition GENO:0000618 IAO:0000115 +WARN missing_definition GENO:0000619 IAO:0000115 +WARN missing_definition GENO:0000620 IAO:0000115 +WARN missing_definition GENO:0000621 IAO:0000115 +WARN missing_definition GENO:0000622 IAO:0000115 +WARN missing_definition GENO:0000623 IAO:0000115 +WARN missing_definition GENO:0000624 IAO:0000115 +WARN missing_definition GENO:0000625 IAO:0000115 +WARN missing_definition GENO:0000626 IAO:0000115 +WARN missing_definition GENO:0000632 IAO:0000115 +WARN missing_definition GENO:0000633 IAO:0000115 +WARN missing_definition GENO:0000640 IAO:0000115 +WARN missing_definition GENO:0000650 IAO:0000115 +WARN missing_definition GENO:0000651 IAO:0000115 +WARN missing_definition GENO:0000655 IAO:0000115 +WARN missing_definition GENO:0000708 IAO:0000115 +WARN missing_definition GENO:0000712 IAO:0000115 +WARN missing_definition GENO:0000720 IAO:0000115 +WARN missing_definition GENO:0000721 IAO:0000115 +WARN missing_definition GENO:0000722 IAO:0000115 +WARN missing_definition GENO:0000724 IAO:0000115 +WARN missing_definition GENO:0000725 IAO:0000115 +WARN missing_definition GENO:0000740 IAO:0000115 +WARN missing_definition GENO:0000741 IAO:0000115 +WARN missing_definition GENO:0000743 IAO:0000115 +WARN missing_definition GENO:0000761 IAO:0000115 +WARN missing_definition GENO:0000770 IAO:0000115 +WARN missing_definition GENO:0000779 IAO:0000115 +WARN missing_definition GENO:0000780 IAO:0000115 +WARN missing_definition GENO:0000781 IAO:0000115 +WARN missing_definition GENO:0000782 IAO:0000115 +WARN missing_definition GENO:0000790 IAO:0000115 +WARN missing_definition GENO:0000791 IAO:0000115 +WARN missing_definition GENO:0000793 IAO:0000115 +WARN missing_definition GENO:0000794 IAO:0000115 +WARN missing_definition GENO:0000833 IAO:0000115 +WARN missing_definition GENO:0000839 IAO:0000115 +WARN missing_definition GENO:0000840 IAO:0000115 +WARN missing_definition GENO:0000841 IAO:0000115 +WARN missing_definition GENO:0000843 IAO:0000115 +WARN missing_definition GENO:0000844 IAO:0000115 +WARN missing_definition GENO:0000845 IAO:0000115 +WARN missing_definition GENO:0000849 IAO:0000115 +WARN missing_definition GENO:0000867 IAO:0000115 +WARN missing_definition GENO:0000876 IAO:0000115 +WARN missing_definition GENO:0000887 IAO:0000115 +WARN missing_definition GENO:0000905 IAO:0000115 +WARN missing_definition GENO:0000906 IAO:0000115 +WARN missing_definition GENO:0000909 IAO:0000115 +WARN missing_definition GENO:0000910 IAO:0000115 +WARN missing_definition GENO:0000911 IAO:0000115 +WARN missing_definition GENO:0000912 IAO:0000115 +WARN missing_definition GENO:0000964 IAO:0000115 +WARN missing_definition GO:0003674 IAO:0000115 +WARN missing_definition HP:0000118 IAO:0000115 +WARN missing_definition HsapDv:0000000 IAO:0000115 +WARN missing_definition IAO:0000102 IAO:0000115 +WARN missing_definition MP:0000001 IAO:0000115 +WARN missing_definition NCBITaxon:10090 IAO:0000115 +WARN missing_definition NCBITaxon:10239 IAO:0000115 +WARN missing_definition NCBITaxon:7955 IAO:0000115 +WARN missing_definition NCBITaxon:8090 IAO:0000115 +WARN missing_definition NCBITaxon:9606 IAO:0000115 +WARN missing_definition OBI:0000086 IAO:0000115 +WARN missing_definition OBI:0001149 IAO:0000115 +WARN missing_definition OBI:0100026 IAO:0000115 +WARN missing_definition PATO:0000016 IAO:0000115 +WARN missing_definition PATO:0000383 IAO:0000115 +WARN missing_definition PATO:0000384 IAO:0000115 +WARN missing_definition PATO:0001894 IAO:0000115 +WARN missing_definition RO:0000087 IAO:0000115 +WARN missing_definition RO:0001000 IAO:0000115 +WARN missing_definition RO:0002091 IAO:0000115 +WARN missing_definition RO:0002093 IAO:0000115 +WARN missing_definition RO:0002201 IAO:0000115 +WARN missing_definition RO:0002222 IAO:0000115 +WARN missing_definition RO:0002350 IAO:0000115 +WARN missing_definition RO:0002352 IAO:0000115 +WARN missing_definition RO:0002353 IAO:0000115 +WARN missing_definition RO:0002354 IAO:0000115 +WARN missing_definition RO:0002525 IAO:0000115 +WARN missing_definition SO:0000165 IAO:0000115 +WARN missing_definition SO:0000207 IAO:0000115 +WARN missing_definition SO:0000248 IAO:0000115 +WARN missing_definition SO:0000281 IAO:0000115 +WARN missing_definition SO:0000337 IAO:0000115 +WARN missing_definition SO:0000577 IAO:0000115 +WARN missing_definition SO:0000637 IAO:0000115 +WARN missing_definition SO:0000699 IAO:0000115 +WARN missing_definition SO:0000804 IAO:0000115 +WARN missing_definition SO:0001785 IAO:0000115 +WARN missing_definition SO:0005836 IAO:0000115 +WARN missing_definition SO:1000013 IAO:0000115 +WARN missing_definition SO:1000020 IAO:0000115 +WARN missing_definition UBERON:0000105 IAO:0000115 +WARN missing_definition UBERON:0001062 IAO:0000115 +WARN missing_definition UPHENO:0001001 IAO:0000115 +WARN missing_definition ZP:0000199 IAO:0000115 +WARN missing_definition ZP:0000386 IAO:0000115 +WARN missing_definition ZP:0000755 IAO:0000115 +WARN missing_definition ZP:0005531 IAO:0000115 +WARN missing_definition ZP:0005692 IAO:0000115 +WARN missing_definition http://purl.org/oban/association IAO:0000115 +WARN missing_definition http://purl.org/oban/association_has_object IAO:0000115 +WARN missing_definition http://purl.org/oban/association_has_predicate IAO:0000115 +WARN missing_definition http://purl.org/oban/association_has_subject IAO:0000115 +WARN missing_definition http://www.ncbi.nlm.nih.gov/gene/20423 IAO:0000115 +WARN missing_definition http://www.ncbi.nlm.nih.gov/gene/30269 IAO:0000115 +WARN missing_definition http://www.ncbi.nlm.nih.gov/gene/399483 IAO:0000115 +WARN missing_definition http://www.ncbi.nlm.nih.gov/gene/6469 IAO:0000115 +WARN invalid_xref GENO:0000010 oboInOwl:hasDbXref OBI:genetic population background information +WARN invalid_xref GENO:0000014 oboInOwl:hasDbXref http://purl.obolibrary.org/obo/SO_0001023 ! allele +WARN invalid_xref GENO:0000019 oboInOwl:hasDbXref perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one) +WARN invalid_xref GENO:0000033 oboInOwl:hasDbXref http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here) +WARN invalid_xref GENO:0000666 oboInOwl:hasDbXref SO:0000831 (gene member region) +WARN invalid_xref GENO:0000870 oboInOwl:hasDbXref http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection +INFO lowercase_definition BFO:0000004 IAO:0000115 b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])@en +INFO lowercase_definition BFO:0000015 IAO:0000115 p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])@en +INFO lowercase_definition BFO:0000016 IAO:0000600 b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])@en +INFO lowercase_definition BFO:0000019 IAO:0000600 a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])@en +INFO lowercase_definition BFO:0000020 IAO:0000115 b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])@en +INFO lowercase_definition BFO:0000020 IAO:0000115 b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])@en +INFO lowercase_definition BFO:0000023 IAO:0000600 b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])@en +INFO lowercase_definition BFO:0000031 IAO:0000115 b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])@en +INFO lowercase_definition GENO:0000019 IAO:0000115 a collection more than one sequence features (ie a collection of discontinuous sequence features) +INFO lowercase_definition GENO:0000111 IAO:0000115 a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role) +INFO lowercase_definition GENO:0000125 IAO:0000115 sequence attribute that can inhere only in a collection of more than one sequence features +INFO lowercase_definition GENO:0000142 IAO:0000115 disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes +INFO lowercase_definition GENO:0000166 IAO:0000115 a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). +INFO lowercase_definition GENO:0000359 IAO:0000115 shortcut relation used to link a phenotype directly to a genotype of an organism +INFO lowercase_definition GENO:0000513 IAO:0000115 a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation. +INFO lowercase_definition GENO:0000602 IAO:0000115 an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. +INFO lowercase_definition GENO:0000603 IAO:0000115 an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. +INFO lowercase_definition GENO:0000608 IAO:0000115 a relation to link a single locus complement to its zygosity. +INFO lowercase_definition GENO:0000634 IAO:0000115 relation between an molecular agent and its molecular target +INFO lowercase_definition GENO:0000883 IAO:0000115 a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells). +INFO lowercase_definition IAO:0000030 IAO:0000115 an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity@en +INFO lowercase_definition IAO:0000136 IAO:0000115 is_about is a (currently) primitive relation that relates an information artifact to an entity. +INFO lowercase_definition OBI:0000181 IAO:0000115 a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area +INFO lowercase_definition OBI:0600043 IAO:0000115 the introduction. alteration or integration of genetic material into a cell or organism +INFO lowercase_definition RO:0000052 IAO:0000115 a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence +INFO lowercase_definition RO:0000053 IAO:0000115 a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence +INFO lowercase_definition RO:0000056 IAO:0000115 a relation between a continuant and a process, in which the continuant is somehow involved in the process +INFO lowercase_definition RO:0000057 IAO:0000115 a relation between a process and a continuant, in which the continuant is somehow involved in the process +INFO lowercase_definition RO:0000086 IAO:0000115 a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence +INFO lowercase_definition RO:0000091 IAO:0000115 a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence +INFO lowercase_definition RO:0002131 IAO:0000115 x overlaps y if and only if there exists some z such that x has part z and z part of y +INFO lowercase_definition RO:0002162 IAO:0000115 x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. +INFO lowercase_definition RO:0002233 IAO:0000115 p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. +INFO lowercase_definition RO:0002234 IAO:0000115 p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. +INFO lowercase_definition RO:0002351 IAO:0000115 has member is a mereological relation between a collection and an item. +INFO lowercase_definition RO:0002522 IAO:0000115 x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y +INFO lowercase_definition RO:0002524 IAO:0000115 x has subsequence y iff all of the sequence parts of x are sequence parts of y +INFO lowercase_definition RO:0002526 IAO:0000115 x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. +INFO lowercase_definition RO:0002528 IAO:0000115 inverse of downstream of sequence of +INFO lowercase_definition RO:0002529 IAO:0000115 x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. +INFO missing_superclass BFO:0000001 rdfs:subClassOf +INFO missing_superclass GENO:0000009 rdfs:subClassOf +INFO missing_superclass GENO:0000017 rdfs:subClassOf +INFO missing_superclass GENO:0000030 rdfs:subClassOf +INFO missing_superclass GENO:0000036 rdfs:subClassOf +INFO missing_superclass GENO:0000047 rdfs:subClassOf +INFO missing_superclass GENO:0000054 rdfs:subClassOf +INFO missing_superclass GENO:0000057 rdfs:subClassOf +INFO missing_superclass GENO:0000460 rdfs:subClassOf +INFO missing_superclass GENO:0000494 rdfs:subClassOf +INFO missing_superclass GENO:0000512 rdfs:subClassOf +INFO missing_superclass GENO:0000666 rdfs:subClassOf +INFO missing_superclass GENO:0000720 rdfs:subClassOf +INFO missing_superclass GENO:0000721 rdfs:subClassOf +INFO missing_superclass GENO:0000722 rdfs:subClassOf +INFO missing_superclass GENO:0000777 rdfs:subClassOf +INFO missing_superclass GENO:0000779 rdfs:subClassOf +INFO missing_superclass GENO:0000823 rdfs:subClassOf +INFO missing_superclass GENO:0000885 rdfs:subClassOf +INFO missing_superclass SO:0000804 rdfs:subClassOf +INFO missing_superclass SO:0000830 rdfs:subClassOf +INFO missing_superclass SO:0001059 rdfs:subClassOf +INFO missing_superclass oboInOwl:ObsoleteClass rdfs:subClassOf diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 3e6e2aa..2b3493b 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -12,9 +12,7 @@ - - - + \ No newline at end of file diff --git a/src/ontology/geno-edit.owl b/src/ontology/geno-edit.owl index 3239bc6..215cbc3 100644 --- a/src/ontology/geno-edit.owl +++ b/src/ontology/geno-edit.owl @@ -18,7 +18,6 @@ Prefix(genotype_model:=) Ontology( Import() -Import() Annotation(dce:description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013") diff --git a/src/ontology/geno.Makefile b/src/ontology/geno.Makefile index e4e87b4..fba0af3 100644 --- a/src/ontology/geno.Makefile +++ b/src/ontology/geno.Makefile @@ -3,3 +3,5 @@ ## If you need to customize your Makefile, make ## changes here rather than in the main Makefile +json: + robot -vvv convert -I http://www.geneontology.org/formats/oboInOwl -f json -o out.json \ No newline at end of file diff --git a/src/ontology/imports/oboInOwl.owl b/src/ontology/imports/oboInOwl.owl index 2b8c2ae..7c6fa9b 100644 --- a/src/ontology/imports/oboInOwl.owl +++ b/src/ontology/imports/oboInOwl.owl @@ -33,19 +33,6 @@ - - - - - - - http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC - oboInOwl:GOC - - - This annotation property groups all subsets declared in the ontology - - subset_property @@ -54,19 +41,6 @@ - - - - - - - http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC - oboInOwl:GOC - - - This annotation property groups all synonym types declared in the ontology - - synonym_type_property @@ -82,19 +56,6 @@ oboFormat:consider - - - - - - - http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm - oboInOwl:cjm - - - Gives a term which may be an appropriate substitute for an obsolete term, but needs to be looked at carefully by a human expert before the replacement is done - - consider diff --git a/src/ontology/json.json b/src/ontology/json.json new file mode 100644 index 0000000..bd9605c --- /dev/null +++ b/src/ontology/json.json @@ -0,0 +1,26 @@ +{ + "graphs" : [ { + "nodes" : [ ], + "edges" : [ ], + "id" : "http://purl.obolibrary.org/obo/json", + "meta" : { + "subsets" : [ ], + "xrefs" : [ ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "\n This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi\n " + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "" + } ], + "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-09-09" + }, + "equivalentNodesSets" : [ ], + "logicalDefinitionAxioms" : [ ], + "domainRangeAxioms" : [ ], + "propertyChainAxioms" : [ ] + } ] +} \ No newline at end of file diff --git a/src/ontology/oboInOwl.owl b/src/ontology/oboInOwl.owl new file mode 100644 index 0000000..5349bd0 --- /dev/null +++ b/src/ontology/oboInOwl.owl @@ -0,0 +1,700 @@ + + + + + This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi + + OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties + + + + + + + + + + + + + + subset_property + + + + + + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + This annotation property groups all synonym types declared in the ontology + + + synonym_type_property + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_consider + oboFormat:consider + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + Gives a term which may be an appropriate substitute for an obsolete term, but needs to be looked at carefully by a human expert before the replacement is done + + + consider + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_alt_id + oboFormat:alt_id + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + An alternative identifier for this class; should follow ID syntax. These can result from class merges + + + has_alternative_id + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_broad_synonym + oboFormat:broad_synonym + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis + + + has_broad_synonym + + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_date + oboFormat:date + + + has_date + + + + + + + + database_cross_reference + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_default-namespace + oboFormat:default-namespace + + + has_default_namespace + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_def + oboFormat:def + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + a relation between a class and an instance of a oboInOwl:Definition + + + we are forced to use the n-ary relation pattern in OWL1.0. For OWL2 we may make this a direct axiom between a class and the string + has_definition + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_exact_synonym + oboFormat:exact_synonym + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle + + + has_exact_synonym + + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_narrow_synonym + oboFormat:narrow_synonym + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + An alias in which the alias is narrower than the primary class name. Example: pyrimidine-dimer repair by photolyase is a narrow synonym of photoreactive repair + + + has_narrow_synonym + + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_namespace + oboFormat:namespace + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + A relation between a class and an OBO namespace string. OBO namespaces are to be distinguished from IDspaces; for example, biological_process is a namespace, GO is an idspace. + + + has_obo_namespace + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_related_synonym + oboFormat:related_synonym + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + An alias in which the alias is related the primary class name, but not necessarily broader or narrower. Example: cytochrome bc1 complex is a related synonym of ubiquinol-cytochrome-c reductase activity; virulence is a related synonym of pathogenesis + + + has_related_synonym + + + + + + + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + relation between an ontology and a oboInOwl:Subset, indicating classes in the ontology belong to the subset + + + has_subset + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_synonym + oboFormat:synonym + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_GOC + oboInOwl:GOC + + + A relation between a class and an alias term. + + + Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL + has_synonym + + + + + + + + + + + http://www.geneontology.org/GO.usage.shtml#type + URL:http://www.geneontology.org/GO.usage.shtml#type + + + has_synonym_type + + + + + + + + has_URI + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_version + oboFormat:version + + + has_version + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_subset + oboFormat:subset + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + relation between a class and a oboInOwl:Subset, indicating the class belongs (is a member of) the subset + + + in_subset + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_is_cyclic + oboFormat:is_cyclic + + + + + + + + + is_cyclic + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_replaced_by + oboFormat:replaced_by + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + Gives a term which replaces an obsolete term. The value is the id of the replacement term. The value of this tag can safely be used to automatically reassign links to an obsolete term. The replaced_by tag may only be specified for obsolete terms. A single obsolete term may have more than one replaced_by tag. This tag can be used in conjunction with the consider tag. + + + replaced_by + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_saved_by + oboFormat:saved_by + + + saved_by + + + + + + + + + + + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + pseudo-property. in the oboInOwl translation, all obsolete relations are subProperties of this class + + + Note that this is not a metaclass + obsolete_property + + + + + + + + + + + + + database_cross_reference + + + + + + + + + + + http://www.obofoundry.org/wiki/index.php/Definitions + URL:http://www.obofoundry.org/wiki/index.php/Definitions + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + The textual definition of the current term. There must be zero or one instances of this tag per term description + + + we are forced to use the n-ary relation pattern in OWL1.0. For OWL2 we may make this a direct axiom between a class and the string + definition + + + + + + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + pseudo-class. in the oboInOwl translation, all obsolete classes are subclasses of this class. Note that this is not a metaclass + + + obsolete_class + + + + + + + + + + + http://purl.org/obo/owl/oboFormat#oboFormat_subsetdef + oboFormat:subsetdef + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + A grouping of terms from an ontology or ontologies. Note that this is not a metaclass - classes are linked to subsets via oboInOwl:inSubset + + + + + + slim + + + + + + GO-slim + + + + + + view + + + + + + partition + + + subset + + + + + + + + + + + + + + http://purl.org/obo/owl/oboInOwl#oboInOwl_cjm + oboInOwl:cjm + + + An instance of synonym usage. synonym instances are linked to classes via oboInOwl:has*Synonym properties + + + we are forced to use the n-ary relation pattern in OWL1.0. For OWL2 we may make this a direct axiom between a class and the string + synonym + + + + + + + + synonym_type + + + + http://purl.org/obo/owl/oboFormat#oboFormat_xref + oboFormat:xref + + + + + + + diff --git a/src/ontology/reports/geno-edit.owl-obo-report.tsv b/src/ontology/reports/geno-edit.owl-obo-report.tsv new file mode 100644 index 0000000..bf796e5 --- /dev/null +++ b/src/ontology/reports/geno-edit.owl-obo-report.tsv @@ -0,0 +1,330 @@ +Level Rule Name Subject Property Value +ERROR duplicate_definition GENO:0000847 IAO:0000115 A relation used to describe an environment contextualizing the identity of an entity. +ERROR duplicate_definition GENO:0000873 IAO:0000115 A relation used to describe an environment contextualizing the identity of an entity. +ERROR duplicate_definition GENO:0000846 IAO:0000115 A relation used to describe a process contextualizing the identity of an entity. +ERROR duplicate_definition GENO:0000874 IAO:0000115 A relation used to describe a process contextualizing the identity of an entity. +ERROR duplicate_definition GENO:0000719 IAO:0000115 A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. +ERROR duplicate_definition GENO:0000899 IAO:0000115 A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. +ERROR misused_obsolete_label GENO:0000019 rdfs:label obsolete_sequence feature collection +ERROR misused_obsolete_label GENO:0000022 rdfs:label obsolete_genomic feature collection +ERROR misused_obsolete_label GENO:0000029 rdfs:label obsolete_reference single locus complement +ERROR misused_obsolete_label GENO:0000037 rdfs:label obsolete_unspecified feature +ERROR misused_obsolete_label GENO:0000042 rdfs:label obsolete_reference junction +ERROR misused_obsolete_label GENO:0000060 rdfs:label obsolete_reference gene allele +ERROR misused_obsolete_label GENO:0000091 rdfs:label obsolete_experimental insertion +ERROR misused_obsolete_label GENO:0000125 rdfs:label obsolete_sequence feature collection attribute +ERROR misused_obsolete_label GENO:0000142 rdfs:label obsolete_dominant inheritance +ERROR misused_obsolete_label GENO:0000150 rdfs:label obsolete_autosomal recessive inheritance +ERROR misused_obsolete_label GENO:0000242 rdfs:label obsolete_specifies +ERROR misused_obsolete_label GENO:0000243 rdfs:label obsolete_approximates_sequence +ERROR misused_obsolete_label GENO:0000244 rdfs:label obsolete_resolves_to_sequence +ERROR misused_obsolete_label GENO:0000253 rdfs:label obsolete_is_specified_by +ERROR misused_obsolete_label GENO:0000324 rdfs:label obsolete_chromosome complement +ERROR misused_obsolete_label GENO:0000359 rdfs:label obsolete_is_phenotype_of_genotype +ERROR misused_obsolete_label GENO:0000368 rdfs:label obsolete_participates_in_inheritance_process +ERROR misused_obsolete_label GENO:0000410 rdfs:label obsolete_is_genetic_variant_of +ERROR misused_obsolete_label GENO:0000411 rdfs:label obsolete_has_genetic_variant +ERROR misused_obsolete_label GENO:0000415 rdfs:label obsolete_reagent sequence feature +ERROR misused_obsolete_label GENO:0000486 rdfs:label obsolete_is_variant_with@en +ERROR misused_obsolete_label GENO:0000488 rdfs:label obsolete_is_expression_variant_with@en +ERROR misused_obsolete_label GENO:0000491 rdfs:label obsolete_mutant allele +ERROR misused_obsolete_label GENO:0000680 rdfs:label obsolete_null feature@en +ERROR misused_obsolete_label GENO:0000712 rdfs:label ObsoleteDataProperty@en +ERROR misused_obsolete_label GENO:0000724 rdfs:label obsolete_biological sequence or collection@en +ERROR misused_obsolete_label GENO:0000725 rdfs:label obsolete_biological sequence collection@en +ERROR misused_obsolete_label GENO:0000741 rdfs:label obsolete_has_regulatory_part@en +ERROR misused_obsolete_label GENO:0000742 rdfs:label obsolete_is_alteration_within@en +ERROR misused_obsolete_label GENO:0000767 rdfs:label obsolete_has_position_component@en +ERROR misused_obsolete_label GENO:0000768 rdfs:label obsolete_genomic position +ERROR misused_obsolete_label GENO:0000772 rdfs:label obsolete_unspecified@en +ERROR misused_obsolete_label GENO:0000778 rdfs:label obsolete_sequence information entity@en +ERROR misused_obsolete_label GENO:0000848 rdfs:label obsolete_coding sequence alteration@en +ERROR misused_obsolete_label GENO:0000870 rdfs:label obsolete_sequence feature collection@en +ERROR misused_obsolete_label GENO:0000876 rdfs:label obsolete_genetic dosage@en +ERROR misused_obsolete_label GENO:0000883 rdfs:label obsolete_gametic@en +ERROR misused_obsolete_label GENO:0000890 rdfs:label obsolete_canonical allele +ERROR misused_obsolete_label GENO:0000891 rdfs:label obsolete_contextual allele +ERROR misused_obsolete_label GENO:0000901 rdfs:label obsolete_allele cellular context +ERROR misused_obsolete_label GENO:0000915 rdfs:label obsolete_haplotype@en +ERROR misused_obsolete_label GENO:0000916 rdfs:label obsolete_haplotype block@en +ERROR misused_obsolete_label GENO:0000923 rdfs:label obsolete_functional copy number complement +ERROR misused_obsolete_label GENO:0000924 rdfs:label obsolete_intrinsic sequence feature attribute@en +ERROR misused_obsolete_label GENO:0000925 rdfs:label obsolete_extrinsic sequence feature attribute@en +ERROR misused_obsolete_label GENO:0000955 rdfs:label obsolete_variant copy number complement +ERROR misused_obsolete_label GENO:0000956 rdfs:label obsolete_copy number complement@en +ERROR misused_obsolete_label PATO:0000016 rdfs:label obsolete_color brightness@en +ERROR misused_obsolete_label RO:0002354 rdfs:label obsolete_formed as result of@en +ERROR misused_obsolete_label SO:0000143 rdfs:label obsolete_assembly_component@en +ERROR misused_obsolete_label SO:0000149 rdfs:label obsolete_contig@en +ERROR misused_obsolete_label SO:0000637 rdfs:label obsolete_engineered_plasmid@en +ERROR misused_obsolete_label SO:0001410 rdfs:label obsolete_experimental_feature@en +ERROR duplicate_label http://biohackathon.org/resource/faldo#reference rdfs:label reference +ERROR duplicate_label GENO:0000152 rdfs:label reference +ERROR multiple_definitions BFO:0000020 IAO:0000115 b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])@en +ERROR multiple_definitions BFO:0000020 IAO:0000115 b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])@en +ERROR multiple_labels BFO:0000002 rdfs:label continuant +ERROR multiple_labels BFO:0000002 rdfs:label continuant@en +ERROR multiple_labels BFO:0000003 rdfs:label occurrent +ERROR multiple_labels BFO:0000003 rdfs:label occurrent@en +ERROR multiple_labels BFO:0000004 rdfs:label independent continuant +ERROR multiple_labels BFO:0000004 rdfs:label independent continuant@en +ERROR multiple_labels BFO:0000015 rdfs:label process +ERROR multiple_labels BFO:0000015 rdfs:label process@en +ERROR multiple_labels BFO:0000016 rdfs:label disposition +ERROR multiple_labels BFO:0000016 rdfs:label disposition@en +ERROR multiple_labels BFO:0000017 rdfs:label realizable entity +ERROR multiple_labels BFO:0000017 rdfs:label realizable entity@en +ERROR multiple_labels BFO:0000019 rdfs:label quality +ERROR multiple_labels BFO:0000019 rdfs:label quality@en +ERROR multiple_labels BFO:0000020 rdfs:label specifically dependent continuant +ERROR multiple_labels BFO:0000020 rdfs:label specifically dependent continuant@en +ERROR multiple_labels BFO:0000023 rdfs:label role +ERROR multiple_labels BFO:0000023 rdfs:label role@en +ERROR multiple_labels BFO:0000031 rdfs:label generically dependent continuant +ERROR multiple_labels BFO:0000031 rdfs:label generically dependent continuant@en +ERROR multiple_labels BFO:0000040 rdfs:label material entity +ERROR multiple_labels BFO:0000040 rdfs:label material entity@en +ERROR multiple_labels IAO:0000030 rdfs:label information content entity +ERROR multiple_labels IAO:0000030 rdfs:label information content entity@en +WARN duplicate_label_synonym GENO:0000017 IAO:0000118 reference sequence +WARN duplicate_label_synonym GENO:0000501 IAO:0000118 wild-type allele +WARN duplicate_label_synonym SO:0000667 IAO:0000118 insertion +WARN duplicate_label_synonym SO:0001744 IAO:0000118 UPD +WARN duplicate_label_synonym SO:1000036 IAO:0000118 inversion +WARN missing_definition http://biohackathon.org/resource/faldo#BothStrandsPosition IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#ForwardStrandPosition IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#ReverseStrandPosition IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#StrandedPosition IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#begin IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#end IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#location IAO:0000115 +WARN missing_definition http://biohackathon.org/resource/faldo#position IAO:0000115 +WARN missing_definition BFO:0000050 IAO:0000115 +WARN missing_definition BFO:0000051 IAO:0000115 +WARN missing_definition CHEBI:23367 IAO:0000115 +WARN missing_definition CHEBI:33696 IAO:0000115 +WARN missing_definition CL:0000000 IAO:0000115 +WARN missing_definition ENVO:01000254 IAO:0000115 +WARN missing_definition GENO:0000091 IAO:0000115 +WARN missing_definition GENO:0000092 IAO:0000115 +WARN missing_definition GENO:0000113 IAO:0000115 +WARN missing_definition GENO:0000118 IAO:0000115 +WARN missing_definition GENO:0000119 IAO:0000115 +WARN missing_definition GENO:0000134 IAO:0000115 +WARN missing_definition GENO:0000135 IAO:0000115 +WARN missing_definition GENO:0000136 IAO:0000115 +WARN missing_definition GENO:0000137 IAO:0000115 +WARN missing_definition GENO:0000139 IAO:0000115 +WARN missing_definition GENO:0000140 IAO:0000115 +WARN missing_definition GENO:0000150 IAO:0000115 +WARN missing_definition GENO:0000160 IAO:0000115 +WARN missing_definition GENO:0000164 IAO:0000115 +WARN missing_definition GENO:0000165 IAO:0000115 +WARN missing_definition GENO:0000169 IAO:0000115 +WARN missing_definition GENO:0000170 IAO:0000115 +WARN missing_definition GENO:0000171 IAO:0000115 +WARN missing_definition GENO:0000172 IAO:0000115 +WARN missing_definition GENO:0000173 IAO:0000115 +WARN missing_definition GENO:0000174 IAO:0000115 +WARN missing_definition GENO:0000175 IAO:0000115 +WARN missing_definition GENO:0000220 IAO:0000115 +WARN missing_definition GENO:0000243 IAO:0000115 +WARN missing_definition GENO:0000244 IAO:0000115 +WARN missing_definition GENO:0000251 IAO:0000115 +WARN missing_definition GENO:0000252 IAO:0000115 +WARN missing_definition GENO:0000253 IAO:0000115 +WARN missing_definition GENO:0000351 IAO:0000115 +WARN missing_definition GENO:0000383 IAO:0000115 +WARN missing_definition GENO:0000387 IAO:0000115 +WARN missing_definition GENO:0000391 IAO:0000115 +WARN missing_definition GENO:0000392 IAO:0000115 +WARN missing_definition GENO:0000393 IAO:0000115 +WARN missing_definition GENO:0000394 IAO:0000115 +WARN missing_definition GENO:0000458 IAO:0000115 +WARN missing_definition GENO:0000495 IAO:0000115 +WARN missing_definition GENO:0000502 IAO:0000115 +WARN missing_definition GENO:0000533 IAO:0000115 +WARN missing_definition GENO:0000575 IAO:0000115 +WARN missing_definition GENO:0000604 IAO:0000115 +WARN missing_definition GENO:0000605 IAO:0000115 +WARN missing_definition GENO:0000606 IAO:0000115 +WARN missing_definition GENO:0000616 IAO:0000115 +WARN missing_definition GENO:0000618 IAO:0000115 +WARN missing_definition GENO:0000619 IAO:0000115 +WARN missing_definition GENO:0000620 IAO:0000115 +WARN missing_definition GENO:0000621 IAO:0000115 +WARN missing_definition GENO:0000622 IAO:0000115 +WARN missing_definition GENO:0000623 IAO:0000115 +WARN missing_definition GENO:0000624 IAO:0000115 +WARN missing_definition GENO:0000625 IAO:0000115 +WARN missing_definition GENO:0000626 IAO:0000115 +WARN missing_definition GENO:0000632 IAO:0000115 +WARN missing_definition GENO:0000633 IAO:0000115 +WARN missing_definition GENO:0000640 IAO:0000115 +WARN missing_definition GENO:0000650 IAO:0000115 +WARN missing_definition GENO:0000651 IAO:0000115 +WARN missing_definition GENO:0000655 IAO:0000115 +WARN missing_definition GENO:0000708 IAO:0000115 +WARN missing_definition GENO:0000712 IAO:0000115 +WARN missing_definition GENO:0000720 IAO:0000115 +WARN missing_definition GENO:0000721 IAO:0000115 +WARN missing_definition GENO:0000722 IAO:0000115 +WARN missing_definition GENO:0000724 IAO:0000115 +WARN missing_definition GENO:0000725 IAO:0000115 +WARN missing_definition GENO:0000740 IAO:0000115 +WARN missing_definition GENO:0000741 IAO:0000115 +WARN missing_definition GENO:0000743 IAO:0000115 +WARN missing_definition GENO:0000761 IAO:0000115 +WARN missing_definition GENO:0000770 IAO:0000115 +WARN missing_definition GENO:0000779 IAO:0000115 +WARN missing_definition GENO:0000780 IAO:0000115 +WARN missing_definition GENO:0000781 IAO:0000115 +WARN missing_definition GENO:0000782 IAO:0000115 +WARN missing_definition GENO:0000790 IAO:0000115 +WARN missing_definition GENO:0000791 IAO:0000115 +WARN missing_definition GENO:0000793 IAO:0000115 +WARN missing_definition GENO:0000794 IAO:0000115 +WARN missing_definition GENO:0000833 IAO:0000115 +WARN missing_definition GENO:0000839 IAO:0000115 +WARN missing_definition GENO:0000840 IAO:0000115 +WARN missing_definition GENO:0000841 IAO:0000115 +WARN missing_definition GENO:0000843 IAO:0000115 +WARN missing_definition GENO:0000844 IAO:0000115 +WARN missing_definition GENO:0000845 IAO:0000115 +WARN missing_definition GENO:0000849 IAO:0000115 +WARN missing_definition GENO:0000867 IAO:0000115 +WARN missing_definition GENO:0000876 IAO:0000115 +WARN missing_definition GENO:0000887 IAO:0000115 +WARN missing_definition GENO:0000905 IAO:0000115 +WARN missing_definition GENO:0000906 IAO:0000115 +WARN missing_definition GENO:0000909 IAO:0000115 +WARN missing_definition GENO:0000910 IAO:0000115 +WARN missing_definition GENO:0000911 IAO:0000115 +WARN missing_definition GENO:0000912 IAO:0000115 +WARN missing_definition GENO:0000964 IAO:0000115 +WARN missing_definition GO:0003674 IAO:0000115 +WARN missing_definition HP:0000118 IAO:0000115 +WARN missing_definition HsapDv:0000000 IAO:0000115 +WARN missing_definition IAO:0000102 IAO:0000115 +WARN missing_definition MP:0000001 IAO:0000115 +WARN missing_definition NCBITaxon:10090 IAO:0000115 +WARN missing_definition NCBITaxon:10239 IAO:0000115 +WARN missing_definition NCBITaxon:7955 IAO:0000115 +WARN missing_definition NCBITaxon:8090 IAO:0000115 +WARN missing_definition NCBITaxon:9606 IAO:0000115 +WARN missing_definition OBI:0000086 IAO:0000115 +WARN missing_definition OBI:0001149 IAO:0000115 +WARN missing_definition OBI:0100026 IAO:0000115 +WARN missing_definition PATO:0000016 IAO:0000115 +WARN missing_definition PATO:0000383 IAO:0000115 +WARN missing_definition PATO:0000384 IAO:0000115 +WARN missing_definition PATO:0001894 IAO:0000115 +WARN missing_definition RO:0000087 IAO:0000115 +WARN missing_definition RO:0001000 IAO:0000115 +WARN missing_definition RO:0002091 IAO:0000115 +WARN missing_definition RO:0002093 IAO:0000115 +WARN missing_definition RO:0002201 IAO:0000115 +WARN missing_definition RO:0002222 IAO:0000115 +WARN missing_definition RO:0002350 IAO:0000115 +WARN missing_definition RO:0002352 IAO:0000115 +WARN missing_definition RO:0002353 IAO:0000115 +WARN missing_definition RO:0002354 IAO:0000115 +WARN missing_definition RO:0002525 IAO:0000115 +WARN missing_definition SO:0000165 IAO:0000115 +WARN missing_definition SO:0000207 IAO:0000115 +WARN missing_definition SO:0000248 IAO:0000115 +WARN missing_definition SO:0000281 IAO:0000115 +WARN missing_definition SO:0000337 IAO:0000115 +WARN missing_definition SO:0000577 IAO:0000115 +WARN missing_definition SO:0000637 IAO:0000115 +WARN missing_definition SO:0000699 IAO:0000115 +WARN missing_definition SO:0000804 IAO:0000115 +WARN missing_definition SO:0001785 IAO:0000115 +WARN missing_definition SO:0005836 IAO:0000115 +WARN missing_definition SO:1000013 IAO:0000115 +WARN missing_definition SO:1000020 IAO:0000115 +WARN missing_definition UBERON:0000105 IAO:0000115 +WARN missing_definition UBERON:0001062 IAO:0000115 +WARN missing_definition UPHENO:0001001 IAO:0000115 +WARN missing_definition ZP:0000199 IAO:0000115 +WARN missing_definition ZP:0000386 IAO:0000115 +WARN missing_definition ZP:0000755 IAO:0000115 +WARN missing_definition ZP:0005531 IAO:0000115 +WARN missing_definition ZP:0005692 IAO:0000115 +WARN missing_definition http://purl.org/oban/association IAO:0000115 +WARN missing_definition http://purl.org/oban/association_has_object IAO:0000115 +WARN missing_definition http://purl.org/oban/association_has_predicate IAO:0000115 +WARN missing_definition http://purl.org/oban/association_has_subject IAO:0000115 +WARN missing_definition http://www.ncbi.nlm.nih.gov/gene/20423 IAO:0000115 +WARN missing_definition http://www.ncbi.nlm.nih.gov/gene/30269 IAO:0000115 +WARN missing_definition http://www.ncbi.nlm.nih.gov/gene/399483 IAO:0000115 +WARN missing_definition http://www.ncbi.nlm.nih.gov/gene/6469 IAO:0000115 +WARN invalid_xref GENO:0000010 oboInOwl:hasDbXref OBI:genetic population background information +WARN invalid_xref GENO:0000014 oboInOwl:hasDbXref http://purl.obolibrary.org/obo/SO_0001023 ! allele +WARN invalid_xref GENO:0000019 oboInOwl:hasDbXref perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one) +WARN invalid_xref GENO:0000033 oboInOwl:hasDbXref http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here) +WARN invalid_xref GENO:0000666 oboInOwl:hasDbXref SO:0000831 (gene member region) +WARN invalid_xref GENO:0000870 oboInOwl:hasDbXref http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection +INFO lowercase_definition BFO:0000004 IAO:0000115 b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])@en +INFO lowercase_definition BFO:0000015 IAO:0000115 p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])@en +INFO lowercase_definition BFO:0000016 IAO:0000600 b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])@en +INFO lowercase_definition BFO:0000019 IAO:0000600 a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])@en +INFO lowercase_definition BFO:0000020 IAO:0000115 b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])@en +INFO lowercase_definition BFO:0000020 IAO:0000115 b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])@en +INFO lowercase_definition BFO:0000023 IAO:0000600 b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])@en +INFO lowercase_definition BFO:0000031 IAO:0000115 b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])@en +INFO lowercase_definition GENO:0000019 IAO:0000115 a collection more than one sequence features (ie a collection of discontinuous sequence features) +INFO lowercase_definition GENO:0000111 IAO:0000115 a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role) +INFO lowercase_definition GENO:0000125 IAO:0000115 sequence attribute that can inhere only in a collection of more than one sequence features +INFO lowercase_definition GENO:0000142 IAO:0000115 disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes +INFO lowercase_definition GENO:0000166 IAO:0000115 a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). +INFO lowercase_definition GENO:0000359 IAO:0000115 shortcut relation used to link a phenotype directly to a genotype of an organism +INFO lowercase_definition GENO:0000513 IAO:0000115 a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation. +INFO lowercase_definition GENO:0000602 IAO:0000115 an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. +INFO lowercase_definition GENO:0000603 IAO:0000115 an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. +INFO lowercase_definition GENO:0000608 IAO:0000115 a relation to link a single locus complement to its zygosity. +INFO lowercase_definition GENO:0000634 IAO:0000115 relation between an molecular agent and its molecular target +INFO lowercase_definition GENO:0000883 IAO:0000115 a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells). +INFO lowercase_definition IAO:0000030 IAO:0000115 an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity@en +INFO lowercase_definition IAO:0000136 IAO:0000115 is_about is a (currently) primitive relation that relates an information artifact to an entity. +INFO lowercase_definition OBI:0000181 IAO:0000115 a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area +INFO lowercase_definition OBI:0600043 IAO:0000115 the introduction. alteration or integration of genetic material into a cell or organism +INFO lowercase_definition RO:0000052 IAO:0000115 a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence +INFO lowercase_definition RO:0000053 IAO:0000115 a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence +INFO lowercase_definition RO:0000056 IAO:0000115 a relation between a continuant and a process, in which the continuant is somehow involved in the process +INFO lowercase_definition RO:0000057 IAO:0000115 a relation between a process and a continuant, in which the continuant is somehow involved in the process +INFO lowercase_definition RO:0000086 IAO:0000115 a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence +INFO lowercase_definition RO:0000091 IAO:0000115 a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence +INFO lowercase_definition RO:0002131 IAO:0000115 x overlaps y if and only if there exists some z such that x has part z and z part of y +INFO lowercase_definition RO:0002162 IAO:0000115 x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. +INFO lowercase_definition RO:0002233 IAO:0000115 p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. +INFO lowercase_definition RO:0002234 IAO:0000115 p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. +INFO lowercase_definition RO:0002351 IAO:0000115 has member is a mereological relation between a collection and an item. +INFO lowercase_definition RO:0002522 IAO:0000115 x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y +INFO lowercase_definition RO:0002524 IAO:0000115 x has subsequence y iff all of the sequence parts of x are sequence parts of y +INFO lowercase_definition RO:0002526 IAO:0000115 x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. +INFO lowercase_definition RO:0002528 IAO:0000115 inverse of downstream of sequence of +INFO lowercase_definition RO:0002529 IAO:0000115 x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. +INFO missing_superclass BFO:0000001 rdfs:subClassOf +INFO missing_superclass GENO:0000009 rdfs:subClassOf +INFO missing_superclass GENO:0000017 rdfs:subClassOf +INFO missing_superclass GENO:0000030 rdfs:subClassOf +INFO missing_superclass GENO:0000036 rdfs:subClassOf +INFO missing_superclass GENO:0000047 rdfs:subClassOf +INFO missing_superclass GENO:0000054 rdfs:subClassOf +INFO missing_superclass GENO:0000057 rdfs:subClassOf +INFO missing_superclass GENO:0000460 rdfs:subClassOf +INFO missing_superclass GENO:0000494 rdfs:subClassOf +INFO missing_superclass GENO:0000512 rdfs:subClassOf +INFO missing_superclass GENO:0000666 rdfs:subClassOf +INFO missing_superclass GENO:0000720 rdfs:subClassOf +INFO missing_superclass GENO:0000721 rdfs:subClassOf +INFO missing_superclass GENO:0000722 rdfs:subClassOf +INFO missing_superclass GENO:0000777 rdfs:subClassOf +INFO missing_superclass GENO:0000779 rdfs:subClassOf +INFO missing_superclass GENO:0000823 rdfs:subClassOf +INFO missing_superclass GENO:0000885 rdfs:subClassOf +INFO missing_superclass SO:0000804 rdfs:subClassOf +INFO missing_superclass SO:0000830 rdfs:subClassOf +INFO missing_superclass SO:0001059 rdfs:subClassOf +INFO missing_superclass oboInOwl:ObsoleteClass rdfs:subClassOf From 967f019ffb41d43d7436fc444789e2b0d19fb351 Mon Sep 17 00:00:00 2001 From: mbrush Date: Mon, 14 Oct 2019 14:53:59 -0700 Subject: [PATCH 06/11] - added GENO:0000968 (sequence role) object property to use in place of RO:has role when doamin is a sequence/GDC( and replaced usages of RO:has role in these contexts) - removed a handful of exploratory classes no longer needed: GENO: genetic modification technique hierarchy OBI: few genetic modification techniques, genotyping assay ERO: technique stem cell line embryonic stem cell line GO: molecular function --- src/ontology/geno-edit.owl | 182 ++++++------------------------------- 1 file changed, 27 insertions(+), 155 deletions(-) diff --git a/src/ontology/geno-edit.owl b/src/ontology/geno-edit.owl index 215cbc3..dfa56ca 100644 --- a/src/ontology/geno-edit.owl +++ b/src/ontology/geno-edit.owl @@ -42,16 +42,12 @@ Declaration(Class(obo:BFO_0000019)) Declaration(Class(obo:BFO_0000020)) Declaration(Class(obo:BFO_0000023)) Declaration(Class(obo:BFO_0000031)) -Declaration(Class(obo:BFO_0000034)) Declaration(Class(obo:BFO_0000040)) Declaration(Class(obo:CHEBI_23367)) Declaration(Class(obo:CHEBI_33696)) Declaration(Class(obo:CLO_0000031)) Declaration(Class(obo:CL_0000000)) Declaration(Class(obo:ENVO_01000254)) -Declaration(Class(obo:ERO_0000007)) -Declaration(Class(obo:ERO_0002002)) -Declaration(Class(obo:ERO_0002003)) Declaration(Class(obo:GENO_0000000)) Declaration(Class(obo:GENO_0000002)) Declaration(Class(obo:GENO_0000009)) @@ -103,16 +99,6 @@ Declaration(Class(obo:GENO_0000149)) Declaration(Class(obo:GENO_0000150)) Declaration(Class(obo:GENO_0000152)) Declaration(Class(obo:GENO_0000160)) -Declaration(Class(obo:GENO_0000164)) -Declaration(Class(obo:GENO_0000165)) -Declaration(Class(obo:GENO_0000166)) -Declaration(Class(obo:GENO_0000169)) -Declaration(Class(obo:GENO_0000170)) -Declaration(Class(obo:GENO_0000171)) -Declaration(Class(obo:GENO_0000172)) -Declaration(Class(obo:GENO_0000173)) -Declaration(Class(obo:GENO_0000174)) -Declaration(Class(obo:GENO_0000175)) Declaration(Class(obo:GENO_0000324)) Declaration(Class(obo:GENO_0000338)) Declaration(Class(obo:GENO_0000339)) @@ -309,7 +295,6 @@ Declaration(Class(obo:GENO_0000962)) Declaration(Class(obo:GENO_0000963)) Declaration(Class(obo:GENO_0000964)) Declaration(Class(obo:GENO_0000965)) -Declaration(Class(obo:GO_0003674)) Declaration(Class(obo:GO_0032502)) Declaration(Class(obo:HP_0000118)) Declaration(Class(obo:HsapDv_0000000)) @@ -324,11 +309,7 @@ Declaration(Class(obo:NCBITaxon_9606)) Declaration(Class(obo:OBI_0000011)) Declaration(Class(obo:OBI_0000086)) Declaration(Class(obo:OBI_0000181)) -Declaration(Class(obo:OBI_0000435)) -Declaration(Class(obo:OBI_0001148)) -Declaration(Class(obo:OBI_0001149)) Declaration(Class(obo:OBI_0100026)) -Declaration(Class(obo:OBI_0600043)) Declaration(Class(obo:PATO_0000016)) Declaration(Class(obo:PATO_0000383)) Declaration(Class(obo:PATO_0000384)) @@ -420,6 +401,7 @@ Declaration(Class(obo:ZP_0000755)) Declaration(Class(obo:ZP_0005531)) Declaration(Class(obo:ZP_0005692)) Declaration(Class()) +Declaration(Class(oboInOwl:ObsoleteClass)) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -506,6 +488,7 @@ Declaration(ObjectProperty(obo:GENO_0000958)) Declaration(ObjectProperty(obo:GENO_0000959)) Declaration(ObjectProperty(obo:GENO_0000966)) Declaration(ObjectProperty(obo:GENO_0000967)) +Declaration(ObjectProperty(obo:GENO_0000968)) Declaration(ObjectProperty(obo:IAO_0000136)) Declaration(ObjectProperty(obo:IAO_0000219)) Declaration(ObjectProperty(obo:OBI_0000293)) @@ -551,6 +534,7 @@ Declaration(ObjectProperty(obo:RO_0003308)) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty(oboInOwl:ObsoleteProperty)) Declaration(DataProperty()) Declaration(DataProperty(obo:GENO_0000678)) Declaration(DataProperty(obo:GENO_0000703)) @@ -576,6 +560,7 @@ Declaration(AnnotationProperty(dce:description)) Declaration(AnnotationProperty(dce:title)) Declaration(AnnotationProperty(dcterms:license)) Declaration(AnnotationProperty(dcterms:source)) +Declaration(AnnotationProperty(oboInOwl:hasDbXref)) ############################ # Annotation Properties ############################ @@ -1207,6 +1192,13 @@ ObjectPropertyDomain(obo:GENO_0000966 obo:GENO_0000815) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000967 "Relates a 'sequence feature location' to a sequence that it is anchored to.") AnnotationAssertion(rdfs:label obo:GENO_0000967 "has_reference_sequence") +# Object Property: obo:GENO_0000968 (sequence role) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000968 "A role assigned to a sequence feature, collection, or genotype, e.g. serving as a 'reference' against with other sequences are compared.") +AnnotationAssertion(rdfs:comment obo:GENO_0000968 "The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants.") +AnnotationAssertion(rdfs:label obo:GENO_0000968 "sequence role") +SubObjectPropertyOf(obo:GENO_0000968 obo:RO_0000053) + # Object Property: obo:IAO_0000136 (is about) AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000136 "is_about is a (currently) primitive relation that relates an information artifact to an entity.") @@ -1264,9 +1256,9 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0000086 "a relation between an indepe AnnotationAssertion(rdfs:label obo:RO_0000086 "has quality") SubObjectPropertyOf(obo:RO_0000086 obo:RO_0000053) -# Object Property: obo:RO_0000087 (has_role) +# Object Property: obo:RO_0000087 (has role) -AnnotationAssertion(rdfs:label obo:RO_0000087 "has_role") +AnnotationAssertion(rdfs:label obo:RO_0000087 "has role") SubObjectPropertyOf(obo:RO_0000087 obo:RO_0000053) # Object Property: obo:RO_0000091 (has disposition) @@ -1739,17 +1731,6 @@ AnnotationAssertion(rdfs:label obo:BFO_0000031 "generically dependent continuant AnnotationAssertion(rdfs:label obo:BFO_0000031 "generically dependent continuant"@en) SubClassOf(obo:BFO_0000031 obo:BFO_0000002) -# Class: obo:BFO_0000034 (function) - -AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000034 "the function of a hammer to drive in nails"@en) -AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000034 "the function of a heart pacemaker to regulate the beating of a heart through electricity"@en) -AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000034 "the function of amylase in saliva to break down starch into sugar"@en) -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000034 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc."@en) -AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000034 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])"@en) -AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000034 obo:bfo.owl) -AnnotationAssertion(rdfs:label obo:BFO_0000034 "function"@en) -SubClassOf(obo:BFO_0000034 obo:BFO_0000016) - # Class: obo:BFO_0000040 (material entity) AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000040 "a flame"@en) @@ -1806,24 +1787,6 @@ AnnotationAssertion(rdfs:comment obo:ENVO_01000254 "In ENVO's alignment with the AnnotationAssertion(rdfs:label obo:ENVO_01000254 "environmental system") SubClassOf(obo:ENVO_01000254 obo:BFO_0000040) -# Class: obo:ERO_0000007 (technique) - -AnnotationAssertion(obo:IAO_0000115 obo:ERO_0000007 "A technique is a planned process used to accomplish a specific activity or task.") -AnnotationAssertion(rdfs:label obo:ERO_0000007 "technique"@en) -SubClassOf(obo:ERO_0000007 obo:OBI_0000011) - -# Class: obo:ERO_0002002 (embryonic stem cell line) - -AnnotationAssertion(obo:IAO_0000115 obo:ERO_0002002 "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo.") -AnnotationAssertion(rdfs:label obo:ERO_0002002 "embryonic stem cell line"@en) -SubClassOf(obo:ERO_0002002 obo:ERO_0002003) - -# Class: obo:ERO_0002003 (stem cell line) - -AnnotationAssertion(obo:IAO_0000115 obo:ERO_0002003 "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types.") -AnnotationAssertion(rdfs:label obo:ERO_0002003 "stem cell line"@en) -SubClassOf(obo:ERO_0002003 obo:CLO_0000031) - # Class: obo:GENO_0000000 (genomic genotype (sex-agnostic)) AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000000 "Example zebrafish intrinsic genotype: @@ -1912,7 +1875,7 @@ AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000017 "The notion of a 'reference AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000017 "reference sequence") AnnotationAssertion(rdfs:comment obo:GENO_0000017 "A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence.") AnnotationAssertion(rdfs:label obo:GENO_0000017 "reference sequence") -EquivalentClasses(obo:GENO_0000017 ObjectIntersectionOf(obo:GENO_0000702 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000152))) +EquivalentClasses(obo:GENO_0000017 ObjectIntersectionOf(obo:GENO_0000702 ObjectSomeValuesFrom(obo:GENO_0000968 obo:GENO_0000152))) # Class: obo:GENO_0000019 (obsolete_sequence feature collection) @@ -1974,7 +1937,7 @@ AnnotationAssertion(rdfs:comment obo:GENO_0000036 "Being a 'reference allele' is In model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared.") AnnotationAssertion(rdfs:label obo:GENO_0000036 "reference allele") -EquivalentClasses(obo:GENO_0000036 ObjectIntersectionOf(obo:GENO_0000512 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000152))) +EquivalentClasses(obo:GENO_0000036 ObjectIntersectionOf(obo:GENO_0000512 ObjectSomeValuesFrom(obo:GENO_0000968 obo:GENO_0000152))) # Class: obo:GENO_0000037 (obsolete_unspecified feature) @@ -2056,7 +2019,6 @@ SubClassOf(obo:GENO_0000091 oboInOwl:ObsoleteClass) AnnotationAssertion(rdfs:label obo:GENO_0000092 "gene trap insertion") SubClassOf(obo:GENO_0000092 obo:SO_0000667) -SubClassOf(obo:GENO_0000092 ObjectSomeValuesFrom(obo:RO_0002353 obo:GENO_0000172)) # Class: obo:GENO_0000093 (integrated transgene) @@ -2080,8 +2042,6 @@ AnnotationAssertion(rdfs:comment obo:GENO_0000106 "1. Genomic material here is c 2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms.") AnnotationAssertion(rdfs:label obo:GENO_0000106 "genomic material") SubClassOf(obo:GENO_0000106 obo:GENO_0000482) -SubClassOf(obo:GENO_0000106 ObjectSomeValuesFrom(obo:BFO_0000050 obo:GENO_0000108)) -SubClassOf(obo:GENO_0000106 ObjectSomeValuesFrom(obo:GENO_0000248 ObjectUnionOf(obo:CL_0000000 obo:NCBITaxon_10239))) SubClassOf(obo:GENO_0000106 ObjectSomeValuesFrom(obo:RO_0000091 obo:GENO_0000139)) # Class: obo:GENO_0000108 (material genome) @@ -2287,66 +2247,6 @@ SubClassOf(obo:GENO_0000152 obo:GENO_0000773) AnnotationAssertion(rdfs:label obo:GENO_0000160 "unspecified life cycle stage") SubClassOf(obo:GENO_0000160 obo:UBERON_0000105) -# Class: obo:GENO_0000164 (genetic insertion technique) - -AnnotationAssertion(rdfs:comment obo:GENO_0000164 "objective is to insert some specified sequence into the genome of a cell or virus") -AnnotationAssertion(rdfs:label obo:GENO_0000164 "genetic insertion technique") -SubClassOf(obo:GENO_0000164 obo:OBI_0600043) - -# Class: obo:GENO_0000165 (mutagen treatment technique) - -AnnotationAssertion(rdfs:label obo:GENO_0000165 "mutagen treatment technique") -SubClassOf(obo:GENO_0000165 obo:OBI_0600043) - -# Class: obo:GENO_0000166 (targeted gene mutation technique) - -AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000166 "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping).") -AnnotationAssertion(rdfs:comment obo:GENO_0000166 "This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created.") -AnnotationAssertion(rdfs:label obo:GENO_0000166 "targeted gene mutation technique") -SubClassOf(obo:GENO_0000166 obo:OBI_0600043) -SubClassOf(obo:GENO_0000166 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) - -# Class: obo:GENO_0000169 (random genetic insertion technique) - -AnnotationAssertion(rdfs:comment obo:GENO_0000169 "Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination.") -AnnotationAssertion(rdfs:label obo:GENO_0000169 "random genetic insertion technique") -SubClassOf(obo:GENO_0000169 obo:GENO_0000164) - -# Class: obo:GENO_0000170 (targeted genetic insertion technique) - -AnnotationAssertion(rdfs:label obo:GENO_0000170 "targeted genetic insertion technique") -SubClassOf(obo:GENO_0000170 obo:GENO_0000164) -SubClassOf(obo:GENO_0000170 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) - -# Class: obo:GENO_0000171 (enhancer trapping technique) - -AnnotationAssertion(rdfs:label obo:GENO_0000171 "enhancer trapping technique") -SubClassOf(obo:GENO_0000171 obo:GENO_0000170) -SubClassOf(obo:GENO_0000171 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) - -# Class: obo:GENO_0000172 (gene trapping technique) - -AnnotationAssertion(rdfs:label obo:GENO_0000172 "gene trapping technique") -SubClassOf(obo:GENO_0000172 obo:GENO_0000170) -SubClassOf(obo:GENO_0000172 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) - -# Class: obo:GENO_0000173 (promoter trapping technique) - -AnnotationAssertion(rdfs:label obo:GENO_0000173 "promoter trapping technique") -SubClassOf(obo:GENO_0000173 obo:GENO_0000170) -SubClassOf(obo:GENO_0000173 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) - -# Class: obo:GENO_0000174 (targeted knock-in technique) - -AnnotationAssertion(rdfs:label obo:GENO_0000174 "targeted knock-in technique") -SubClassOf(obo:GENO_0000174 obo:GENO_0000170) -SubClassOf(obo:GENO_0000174 ObjectSomeValuesFrom(obo:OBI_0000299 obo:GENO_0000515)) - -# Class: obo:GENO_0000175 (random transgene insertion technique) - -AnnotationAssertion(rdfs:label obo:GENO_0000175 "random transgene insertion technique") -SubClassOf(obo:GENO_0000175 obo:GENO_0000169) - # Class: obo:GENO_0000324 (obsolete_chromosome complement) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000324 "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome") @@ -2833,7 +2733,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000611 "A genomic genotype that sp AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000611 "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it.") AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000611 "background genotype") AnnotationAssertion(rdfs:label obo:GENO_0000611 "genomic background"@en) -EquivalentClasses(obo:GENO_0000611 ObjectIntersectionOf(obo:GENO_0000899 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000152))) +EquivalentClasses(obo:GENO_0000611 ObjectIntersectionOf(obo:GENO_0000899 ObjectSomeValuesFrom(obo:GENO_0000968 obo:GENO_0000152))) SubClassOf(obo:GENO_0000611 ObjectSomeValuesFrom(obo:IAO_0000219 obo:GENO_0000010)) # Class: obo:GENO_0000614 (chromosomal region) @@ -2953,7 +2853,7 @@ SubClassOf(obo:GENO_0000640 obo:GENO_0000638) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000642 "A transgene whose product is used as a selectable marker.") AnnotationAssertion(rdfs:label obo:GENO_0000642 "selectable marker transgene"@en) -EquivalentClasses(obo:GENO_0000642 ObjectIntersectionOf(obo:SO_0000902 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000911))) +EquivalentClasses(obo:GENO_0000642 ObjectIntersectionOf(obo:SO_0000902 ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000911))) SubClassOf(obo:GENO_0000642 ObjectSomeValuesFrom(obo:GENO_0000207 obo:SO_0000783)) # Class: obo:GENO_0000644 (karyotype) @@ -3047,7 +2947,7 @@ EquivalentClasses(obo:GENO_0000666 ObjectIntersectionOf(obo:GENO_0000481 ObjectS AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000667 "A transgene that codes for a product used as a reporter of gene expression or activity.") AnnotationAssertion(rdfs:label obo:GENO_0000667 "reporter transgene"@en) -EquivalentClasses(obo:GENO_0000667 ObjectIntersectionOf(obo:SO_0000902 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000910))) +EquivalentClasses(obo:GENO_0000667 ObjectIntersectionOf(obo:SO_0000902 ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000910))) SubClassOf(obo:GENO_0000667 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GENO_0000640)) SubClassOf(obo:GENO_0000667 ObjectSomeValuesFrom(obo:GENO_0000207 obo:SO_0000783)) @@ -3215,6 +3115,7 @@ SubClassOf(obo:GENO_0000768 oboInOwl:ObsoleteClass) # Class: obo:GENO_0000770 (phenotypic inheritance process) +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000770 obo:GENO_0000484) AnnotationAssertion(rdfs:label obo:GENO_0000770 "phenotypic inheritance process"@en) SubClassOf(obo:GENO_0000770 obo:GENO_0000351) @@ -3635,6 +3536,7 @@ SubClassOf(obo:GENO_0000902 obo:GENO_0000815) # Class: obo:GENO_0000904 (organismal entity) AnnotationAssertion(obo:GENO_0000905 obo:GENO_0000904 "true"^^xsd:boolean) +AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000904 obo:GENO_0000484) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000904 "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc).") AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000904 "useful organizational term to collect entities that have genomes/genotypes.") AnnotationAssertion(rdfs:label obo:GENO_0000904 "organismal entity"@en) @@ -3647,15 +3549,15 @@ AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000907 "The molecular product resu AnnotationAssertion(rdfs:label obo:GENO_0000907 "gene product"@en) SubClassOf(obo:GENO_0000907 obo:SO_0000110) -# Class: obo:GENO_0000910 (reporter role) +# Class: obo:GENO_0000910 (reporter) -AnnotationAssertion(rdfs:label obo:GENO_0000910 "reporter role"@en) -SubClassOf(obo:GENO_0000910 obo:OBI_0000086) +AnnotationAssertion(rdfs:label obo:GENO_0000910 "reporter"@en) +SubClassOf(obo:GENO_0000910 obo:GENO_0000788) -# Class: obo:GENO_0000911 (selectable marker role) +# Class: obo:GENO_0000911 (selectable marker) -AnnotationAssertion(rdfs:label obo:GENO_0000911 "selectable marker role"@en) -SubClassOf(obo:GENO_0000911 obo:OBI_0000086) +AnnotationAssertion(rdfs:label obo:GENO_0000911 "selectable marker"@en) +SubClassOf(obo:GENO_0000911 obo:GENO_0000788) # Class: obo:GENO_0000912 (selectable marker region) @@ -4039,11 +3941,6 @@ AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000965 "A pair of integers represe AnnotationAssertion(rdfs:label obo:GENO_0000965 "sequence interval") SubClassOf(obo:GENO_0000965 obo:IAO_0000030) -# Class: obo:GO_0003674 (molecular function) - -AnnotationAssertion(rdfs:label obo:GO_0003674 "molecular function") -SubClassOf(obo:GO_0003674 obo:BFO_0000034) - # Class: obo:GO_0032502 (developmental process) AnnotationAssertion(obo:IAO_0000115 obo:GO_0032502 "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete]") @@ -4134,37 +4031,12 @@ AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000181 "a population is a collectio AnnotationAssertion(rdfs:label obo:OBI_0000181 "population"@en) SubClassOf(obo:OBI_0000181 obo:GENO_0000113) -# Class: obo:OBI_0000435 (genotyping assay) - -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000435 "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.") -AnnotationAssertion(rdfs:label obo:OBI_0000435 "genotyping assay") -SubClassOf(obo:OBI_0000435 obo:ERO_0000007) - -# Class: obo:OBI_0001148 (targeted gene knock-out technique) - -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001148 "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.") -AnnotationAssertion(rdfs:comment obo:OBI_0001148 "A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a \"targeted\" insertion.") -AnnotationAssertion(rdfs:label obo:OBI_0001148 "targeted gene knock-out technique") -SubClassOf(obo:OBI_0001148 obo:GENO_0000166) - -# Class: obo:OBI_0001149 (targeted gene knock-in technique) - -AnnotationAssertion(rdfs:label obo:OBI_0001149 "targeted gene knock-in technique"@en) -SubClassOf(obo:OBI_0001149 obo:GENO_0000166) - # Class: obo:OBI_0100026 (organism) AnnotationAssertion(obo:IAO_0000116 obo:OBI_0100026 "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy.") AnnotationAssertion(rdfs:label obo:OBI_0100026 "organism") SubClassOf(obo:OBI_0100026 obo:BFO_0000040) -# Class: obo:OBI_0600043 (genetic modification technique) - -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0600043 "the introduction. alteration or integration of genetic material into a cell or organism") -AnnotationAssertion(rdfs:label obo:OBI_0600043 "genetic modification technique") -SubClassOf(obo:OBI_0600043 obo:ERO_0000007) -SubClassOf(obo:OBI_0600043 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectIntersectionOf(obo:GENO_0000106 ObjectSomeValuesFrom(obo:GENO_0000211 obo:GENO_0000002)))) - # Class: obo:PATO_0000016 (obsolete_color brightness) AnnotationAssertion(obo:IAO_0000116 obo:PATO_0000016 "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html") @@ -4559,7 +4431,7 @@ AnnotationAssertion(obo:IAO_0000112 obo:SO_0001505 "'GRCh37.p10' (a human refere AnnotationAssertion(obo:IAO_0000115 obo:SO_0001505 "A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced.") AnnotationAssertion(rdfs:label obo:SO_0001505 "reference genome sequence") SubClassOf(obo:SO_0001505 obo:GENO_0000017) -SubClassOf(obo:SO_0001505 ObjectSomeValuesFrom(obo:RO_0000087 obo:GENO_0000152)) +SubClassOf(obo:SO_0001505 ObjectSomeValuesFrom(obo:GENO_0000968 obo:GENO_0000152)) # Class: obo:SO_0001742 (copy_number_gain) From 3a1bef7fd87ae011c3076fbd45733549883c0cf8 Mon Sep 17 00:00:00 2001 From: Matthew Brush Date: Fri, 6 Mar 2020 13:45:46 -0800 Subject: [PATCH 07/11] pushing files with changes due to odk pipeline - likely related to serialization differences, not content differences. --- docs/~$GENO_Overview(2017-02-24).pptx | Bin 0 -> 165 bytes geno-base.json | 556 +++++------------- geno-base.obo | 153 +---- geno-base.owl | 302 +--------- geno-full.json | 470 ++++----------- geno-full.obo | 157 +---- geno-full.owl | 292 +-------- geno.json | 472 ++++----------- geno.obo | 157 +---- geno.owl | 292 +-------- imports/iao_import.json | 54 +- imports/iao_import.obo | 16 +- imports/iao_import.owl | 32 +- imports/ro_import.json | 145 ++--- imports/ro_import.obo | 26 +- imports/ro_import.owl | 90 ++- reports/geno-edit.owl-obo-report.tsv | 13 - src/ontology/imports/iao_import.json | 54 +- src/ontology/imports/iao_import.obo | 16 +- src/ontology/imports/iao_import.owl | 32 +- src/ontology/imports/ro_import.json | 145 ++--- src/ontology/imports/ro_import.obo | 26 +- src/ontology/imports/ro_import.owl | 90 ++- .../reports/geno-edit.owl-obo-report.tsv | 13 - 24 files changed, 797 insertions(+), 2806 deletions(-) create mode 100644 docs/~$GENO_Overview(2017-02-24).pptx diff --git a/docs/~$GENO_Overview(2017-02-24).pptx b/docs/~$GENO_Overview(2017-02-24).pptx new file mode 100644 index 0000000000000000000000000000000000000000..51fad0301839295eb820c806bfc24db2e21e820b GIT binary patch literal 165 zcmd<}O)M$NNG(@zDk?3`U{D|u@G|%^Br=o$VFp7gLpg&2gA+p$Ln%Wskgq^>2mocB B6gL0> literal 0 HcmV?d00001 diff --git a/geno-base.json b/geno-base.json index 1fe9c25..5af9932 100644 --- a/geno-base.json +++ b/geno-base.json @@ -81,16 +81,6 @@ }, "type" : "CLASS", "lbl" : "mus musculus gene" - }, { - "id" : "http://purl.obolibrary.org/obo/ERO_0000007", - "meta" : { - "definition" : { - "val" : "A technique is a planned process used to accomplish a specific activity or task.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "technique" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000159", "meta" : { @@ -175,18 +165,6 @@ }, "type" : "CLASS", "lbl" : "SNV" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000173", - "type" : "CLASS", - "lbl" : "promoter trapping technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000172", - "type" : "CLASS", - "lbl" : "gene trapping technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000175", - "type" : "CLASS", - "lbl" : "random transgene insertion technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000054", "meta" : { @@ -197,10 +175,6 @@ }, "type" : "CLASS", "lbl" : "homo sapiens gene" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000174", - "type" : "CLASS", - "lbl" : "targeted knock-in technique" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000016", "meta" : { @@ -217,16 +191,6 @@ }, "type" : "CLASS", "lbl" : "obsolete_color brightness" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000435", - "meta" : { - "definition" : { - "val" : "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "genotyping assay" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002162", "meta" : { @@ -237,10 +201,6 @@ }, "type" : "PROPERTY", "lbl" : "in taxon" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000171", - "type" : "CLASS", - "lbl" : "enhancer trapping technique" }, { "id" : "http://www.ncbi.nlm.nih.gov/gene/6469", "meta" : { @@ -254,38 +214,6 @@ }, "type" : "CLASS", "lbl" : "homo sapiens SHH gene" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000170", - "type" : "CLASS", - "lbl" : "targeted genetic insertion technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000169", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination." - } ] - }, - "type" : "CLASS", - "lbl" : "random genetic insertion technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000166", - "meta" : { - "definition" : { - "val" : "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping).", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created." - } ] - }, - "type" : "CLASS", - "lbl" : "targeted gene mutation technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000165", - "type" : "CLASS", - "lbl" : "mutagen treatment technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000047", "meta" : { @@ -411,7 +339,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0000087", "type" : "PROPERTY", - "lbl" : "has_role" + "lbl" : "has role" }, { "id" : "http://purl.obolibrary.org/obo/RO_0000086", "meta" : { @@ -1022,11 +950,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000911", "type" : "CLASS", - "lbl" : "selectable marker role" + "lbl" : "selectable marker" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000910", "type" : "CLASS", - "lbl" : "reporter role" + "lbl" : "reporter" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000912", "type" : "CLASS", @@ -1075,24 +1003,6 @@ }, "type" : "PROPERTY", "lbl" : "has_specified_output" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0001148", - "meta" : { - "definition" : { - "val" : "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a \"targeted\" insertion." - } ] - }, - "type" : "CLASS", - "lbl" : "targeted gene knock-out technique" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0001149", - "type" : "CLASS", - "lbl" : "targeted gene knock-in technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000904", "meta" : { @@ -1106,6 +1016,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/GENO_0000905", "val" : "true" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" } ] }, "type" : "CLASS", @@ -2143,10 +2056,6 @@ }, "type" : "CLASS", "lbl" : "T_to_C_transition" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0003674", - "type" : "CLASS", - "lbl" : "molecular function" }, { "id" : "http://purl.obolibrary.org/obo/SO_1000019", "meta" : { @@ -2860,6 +2769,20 @@ "id" : "http://purl.obolibrary.org/obo/GENO_0000605", "type" : "CLASS", "lbl" : "hemizygous Y-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000968", + "meta" : { + "definition" : { + "val" : "A role assigned to a sequence feature, collection, or genotype, e.g. serving as a 'reference' against with other sequences are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants." + } ] + }, + "type" : "PROPERTY", + "lbl" : "sequence role" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000604", "type" : "CLASS", @@ -3852,6 +3775,12 @@ "lbl" : "has_sex_agnostic_part" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000770", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, "type" : "CLASS", "lbl" : "phenotypic inheritance process" }, { @@ -5486,16 +5415,6 @@ }, "type" : "CLASS", "lbl" : "genetic material" - }, { - "id" : "http://purl.obolibrary.org/obo/ERO_0002003", - "meta" : { - "definition" : { - "val" : "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "stem cell line" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000477", "meta" : { @@ -5604,16 +5523,6 @@ }, "type" : "CLASS", "lbl" : "strain or breed" - }, { - "id" : "http://purl.obolibrary.org/obo/ERO_0002002", - "meta" : { - "definition" : { - "val" : "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "embryonic stem cell line" }, { "id" : "http://purl.obolibrary.org/obo/UPHENO_0001001", "meta" : { @@ -5698,16 +5607,6 @@ }, "type" : "CLASS", "lbl" : "junction" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0600043", - "meta" : { - "definition" : { - "val" : "the introduction. alteration or integration of genetic material into a cell or organism", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "genetic modification technique" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000577", "type" : "CLASS", @@ -6828,16 +6727,6 @@ }, "type" : "CLASS", "lbl" : "obsolete_assembly_component" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000164", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "objective is to insert some specified sequence into the genome of a cell or virus" - } ] - }, - "type" : "CLASS", - "lbl" : "genetic insertion technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000042", "meta" : { @@ -6912,31 +6801,6 @@ }, "type" : "CLASS", "lbl" : "reference allele" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of a hammer to drive in nails" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of amylase in saliva to break down starch into sugar" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" - } ] - }, - "type" : "CLASS", - "lbl" : "function" }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", "meta" : { @@ -7322,14 +7186,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000477", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000773" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000926", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000623", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000619" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000926", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000010", "pred" : "is_a", @@ -7338,10 +7202,6 @@ "sub" : "http://purl.obolibrary.org/obo/UPHENO_0001001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000173", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000170" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000610", "pred" : "subPropertyOf", @@ -7402,10 +7262,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0032502", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000351" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000171", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000515" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000199", "pred" : "is_a", @@ -7422,10 +7278,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000861", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000902" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001149", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000166" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "inverseOf", @@ -7474,14 +7326,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000818", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000093", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/SO_0001218" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000492", "pred" : "http://purl.obolibrary.org/obo/GENO_0000683", "obj" : "http://purl.obolibrary.org/obo/GENO_0000501" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000093", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/SO_0001218" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000516", "pred" : "is_a", @@ -7534,10 +7386,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000898", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000481" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0000435", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ERO_0000007" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000920", "pred" : "http://purl.obolibrary.org/obo/GENO_0000726", @@ -7578,10 +7426,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000170", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000164" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000780", "pred" : "is_a", @@ -7634,18 +7478,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000741", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000166", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000515" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002234", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0600043", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ERO_0000007" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000002", "pred" : "is_a", @@ -7662,14 +7498,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002350", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002351" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000383", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001894" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000039", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000173" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000383", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001894" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000934", "pred" : "is_a", @@ -7734,22 +7570,22 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000133", "pred" : "http://purl.obolibrary.org/obo/RO_0000052", "obj" : "http://purl.obolibrary.org/obo/GENO_0000516" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000134", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000391" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000877", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000616", - "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000618" + "sub" : "http://purl.obolibrary.org/obo/GENO_0000134", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000391" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000383", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000655" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000616", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000618" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000408", "pred" : "subPropertyOf", @@ -7778,14 +7614,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000346", "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", "obj" : "http://purl.obolibrary.org/obo/GENO_0000513" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000501", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000512" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000680", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000501", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000512" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000146", "pred" : "is_a", @@ -7810,10 +7646,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000650", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000661" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000106", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000108" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000525", "pred" : "is_a", @@ -7922,10 +7754,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000174", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000170" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000022", "pred" : "is_a", @@ -7938,22 +7766,22 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000962", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000961" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000243", + "pred" : "subPropertyOf", + "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000637", "pred" : "http://purl.obolibrary.org/obo/RO_0002525", "obj" : "http://purl.obolibrary.org/obo/SO_0000902" }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000243", + "sub" : "http://purl.obolibrary.org/obo/GENO_0000414", "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" + "obj" : "http://purl.obolibrary.org/obo/GENO_0000418" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000889", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000414", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000418" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000931", "pred" : "is_a", @@ -7970,10 +7798,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000714", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000919" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000166", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0600043" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000701", "pred" : "is_a", @@ -7994,10 +7818,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000575", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UPHENO_0001001" - }, { - "sub" : "http://purl.obolibrary.org/obo/ERO_0000007", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/CHEBI_33696", "pred" : "is_a", @@ -8022,14 +7842,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000603", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000918" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001148", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000166" }, { "sub" : "http://biohackathon.org/resource/faldo#end", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000708" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000968", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000053" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000714", "pred" : "http://purl.obolibrary.org/obo/GENO_0000726", @@ -8038,10 +7858,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000633", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000619" - }, { - "sub" : "http://purl.obolibrary.org/obo/ERO_0002002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ERO_0002003" }, { "sub" : "http://biohackathon.org/resource/faldo#Position", "pred" : "is_a", @@ -8078,22 +7894,18 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000839", "pred" : "http://purl.obolibrary.org/obo/GENO_0000382", "obj" : "http://purl.obolibrary.org/obo/GENO_0000504" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000175", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000169" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000528", "pred" : "http://purl.obolibrary.org/obo/GENO_0000382", "obj" : "http://purl.obolibrary.org/obo/GENO_0000506" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000910", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000916", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000172", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000515" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000525", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -8130,10 +7942,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000629", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000105" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000910", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000086" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000392", "pred" : "is_a", @@ -8198,22 +8006,18 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000840", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003303" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000963", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000872" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000482", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CHEBI_33696" }, { - 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}, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000654", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002525", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000655" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000654", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000415", "pred" : "is_a", @@ -9438,10 +9202,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000137", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000169", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000164" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000159", "pred" : "is_a", @@ -9561,17 +9321,10 @@ "pred" : "http://purl.org/dc/terms/license", "val" : "Unspecified" } ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-09-09/geno-base.json" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-10-15/geno-base.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000611", - "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000899" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" - } ] - }, { "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000515", "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000014" ], "restrictions" : [ { @@ -9579,38 +9332,24 @@ "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000036" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000804", - "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000207", - "fillerId" : "http://purl.obolibrary.org/obo/SO_0000783" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000642", + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000667", "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000902" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000911" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000017", - "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000207", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000910" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000667", - "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000902" ], + "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000804", + "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000110" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000910" + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000207", + "fillerId" : "http://purl.obolibrary.org/obo/SO_0000783" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000036", "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000512" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000968", "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" } ] }, { @@ -9680,6 +9419,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_10090" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000642", + "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000902" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000207", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000911" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000460", "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000666" ], @@ -9729,6 +9475,20 @@ "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000219", "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000033" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000611", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000899" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000968", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000017", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000968", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" + } ] } ], "domainRangeAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002200", diff --git a/geno-base.obo b/geno-base.obo index d56018f..c7b6c40 100644 --- a/geno-base.obo +++ b/geno-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: geno/releases/2019-09-09/geno-base.owl +data-version: geno/releases/2019-10-15/geno-base.owl ontology: geno/geno-base property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string @@ -154,17 +154,6 @@ property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition -property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string -property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string -property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string -property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - [Term] id: BFO:0000040 name: material entity @@ -223,24 +212,6 @@ comment: In ENVO's alignment with the Basic Formal Ontology, this class is being is_a: BFO:0000040 ! material entity property_value: IAO:0000116 "1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions.\n\n2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity)." xsd:string -[Term] -id: ERO:0000007 -name: technique -def: "A technique is a planned process used to accomplish a specific activity or task." [] -is_a: OBI:0000011 ! planned process - -[Term] -id: ERO:0002002 -name: embryonic stem cell line -def: "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo." [] -is_a: ERO:0002003 ! stem cell line - -[Term] -id: ERO:0002003 -name: stem cell line -def: "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types." [] -is_a: CLO:0000031 ! cell line - [Term] id: ExactPosition name: Exact position @@ -312,7 +283,7 @@ name: reference sequence def: "A sequence that serves as a standard against which other sequences at the same location are compared." [] comment: A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence. intersection_of: GENO:0000702 ! biological sequence -intersection_of: RO:0000087 GENO:0000152 ! has_role reference +intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference property_value: IAO:0000116 "The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant." xsd:string property_value: IAO:0000118 "reference sequence" xsd:string @@ -366,7 +337,7 @@ name: reference allele def: "An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome." [] comment: Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.\n\nIn model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared. intersection_of: GENO:0000512 ! allele -intersection_of: RO:0000087 GENO:0000152 ! has_role reference +intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference [Term] id: GENO:0000037 @@ -427,7 +398,6 @@ is_a: ObsoleteClass id: GENO:0000092 name: gene trap insertion is_a: SO:0000667 ! insertion -relationship: RO:0002353 GENO:0000172 ! output of gene trapping technique [Term] id: GENO:0000093 @@ -443,7 +413,6 @@ name: genomic material def: "A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny." [] comment: 1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms. is_a: GENO:0000482 ! genetic material -relationship: BFO:0000050 GENO:0000108 ! is part of material genome relationship: RO:0000091 GENO:0000139 ! has disposition heritable property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000116 "1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way." xsd:string @@ -645,66 +614,6 @@ id: GENO:0000160 name: unspecified life cycle stage is_a: UBERON:0000105 ! life cycle stage -[Term] -id: GENO:0000164 -name: genetic insertion technique -comment: objective is to insert some specified sequence into the genome of a cell or virus -is_a: OBI:0600043 ! genetic modification technique - -[Term] -id: GENO:0000165 -name: mutagen treatment technique -is_a: OBI:0600043 ! genetic modification technique - -[Term] -id: GENO:0000166 -name: targeted gene mutation technique -def: "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping)." [] -comment: This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. -is_a: OBI:0600043 ! genetic modification technique -relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele - -[Term] -id: GENO:0000169 -name: random genetic insertion technique -comment: Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. -is_a: GENO:0000164 ! genetic insertion technique - -[Term] -id: GENO:0000170 -name: targeted genetic insertion technique -is_a: GENO:0000164 ! genetic insertion technique -relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele - -[Term] -id: GENO:0000171 -name: enhancer trapping technique -is_a: GENO:0000170 ! targeted genetic insertion technique -relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele - -[Term] -id: GENO:0000172 -name: gene trapping technique -is_a: GENO:0000170 ! targeted genetic insertion technique -relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele - -[Term] -id: GENO:0000173 -name: promoter trapping technique -is_a: GENO:0000170 ! targeted genetic insertion technique -relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele - -[Term] -id: GENO:0000174 -name: targeted knock-in technique -is_a: GENO:0000170 ! targeted genetic insertion technique -relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele - -[Term] -id: GENO:0000175 -name: random transgene insertion technique -is_a: GENO:0000169 ! random genetic insertion technique - [Term] id: GENO:0000324 name: obsolete_chromosome complement @@ -1118,7 +1027,7 @@ id: GENO:0000611 name: genomic background def: "A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations)." [] intersection_of: GENO:0000899 ! genomic genotype -intersection_of: RO:0000087 GENO:0000152 ! has_role reference +intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference relationship: IAO:0000219 GENO:0000010 ! denotes background genome property_value: IAO:0000116 "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it." xsd:string property_value: IAO:0000118 "background genotype" xsd:string @@ -1233,7 +1142,7 @@ id: GENO:0000642 name: selectable marker transgene def: "A transgene whose product is used as a selectable marker." [] intersection_of: SO:0000902 ! transgene -intersection_of: RO:0000087 GENO:0000911 ! has_role selectable marker role +intersection_of: GENO:0000207 GENO:0000911 ! has_sequence_attribute selectable marker relationship: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered [Term] @@ -1310,7 +1219,7 @@ id: GENO:0000667 name: reporter transgene def: "A transgene that codes for a product used as a reporter of gene expression or activity." [] intersection_of: SO:0000902 ! transgene -intersection_of: RO:0000087 GENO:0000910 ! has_role reporter role +intersection_of: GENO:0000207 GENO:0000910 ! has_sequence_attribute reporter relationship: BFO:0000051 GENO:0000640 ! has part reporter region relationship: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered @@ -1471,6 +1380,7 @@ property_value: IAO:0000231 "remodeling notion of sequence feature position arou id: GENO:0000770 name: phenotypic inheritance process is_a: GENO:0000351 ! biological process +property_value: IAO:0000114 GENO:0000484 [Term] id: GENO:0000772 @@ -1832,6 +1742,7 @@ name: organismal entity def: "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc)." [] is_a: BFO:0000040 ! material entity property_value: GENO:0000905 "true" xsd:boolean +property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000116 "useful organizational term to collect entities that have genomes/genotypes." xsd:string [Term] @@ -1842,13 +1753,13 @@ is_a: SO:0000110 ! sequence_feature [Term] id: GENO:0000910 -name: reporter role -is_a: OBI:0000086 ! reagent role +name: reporter +is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000911 -name: selectable marker role -is_a: OBI:0000086 ! reagent role +name: selectable marker +is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000912 @@ -2186,11 +2097,6 @@ name: sequence interval def: "A pair of integers representing start and end position of a location on a sequence coordinate system." [] is_a: IAO:0000030 ! information content entity -[Term] -id: GO:0003674 -name: molecular function -is_a: BFO:0000034 ! function - [Term] id: GO:0032502 name: developmental process @@ -2278,36 +2184,12 @@ name: population def: "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area" [] is_a: GENO:0000113 ! taxonomic group -[Term] -id: OBI:0000435 -name: genotyping assay -def: "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions." [] -is_a: ERO:0000007 ! technique - -[Term] -id: OBI:0001148 -name: targeted gene knock-out technique -def: "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods." [] -comment: A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. -is_a: GENO:0000166 ! targeted gene mutation technique - -[Term] -id: OBI:0001149 -name: targeted gene knock-in technique -is_a: GENO:0000166 ! targeted gene mutation technique - [Term] id: OBI:0100026 name: organism is_a: BFO:0000040 ! material entity property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy." xsd:string -[Term] -id: OBI:0600043 -name: genetic modification technique -def: "the introduction. alteration or integration of genetic material into a cell or organism" [] -is_a: ERO:0000007 ! technique - [Term] id: PATO:0000016 name: obsolete_color brightness @@ -2678,7 +2560,7 @@ id: SO:0001505 name: reference genome sequence def: "A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced." [] is_a: GENO:0000017 ! reference sequence -relationship: RO:0000087 GENO:0000152 ! has_role reference +relationship: GENO:0000968 GENO:0000152 ! sequence role reference property_value: IAO:0000112 "'GRCh37.p10' (a human reference genome build)" xsd:string [Term] @@ -3640,6 +3522,13 @@ id: GENO:0000967 name: has_reference_sequence def: "Relates a 'sequence feature location' to a sequence that it is anchored to." [] +[Typedef] +id: GENO:0000968 +name: sequence role +def: "A role assigned to a sequence feature, collection, or genotype, e.g. serving as a 'reference' against with other sequences are compared." [] +comment: The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants. +is_a: RO:0000053 ! bearer of + [Typedef] id: IAO:0000136 name: is about @@ -3699,7 +3588,7 @@ is_a: RO:0000053 ! bearer of [Typedef] id: RO:0000087 -name: has_role +name: has role is_a: RO:0000053 ! bearer of [Typedef] diff --git a/geno-base.owl b/geno-base.owl index 8750a6b..63b4691 100644 --- a/geno-base.owl +++ b/geno-base.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 @@ -1519,6 +1519,17 @@ For copy number complements, it is the sequence of this proxy feature on some re + + + + + A role assigned to a sequence feature, collection, or genotype, e.g. serving as a 'reference' against with other sequences are compared. + The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants. + sequence role + + + + @@ -1620,7 +1631,7 @@ For copy number complements, it is the sequence of this proxy feature on some re - has_role + has role @@ -2371,21 +2382,6 @@ Environments include natural environments or exposures, experimentally applied c - - - - - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - function - - - - @@ -2471,36 +2467,6 @@ Environments include natural environments or exposures, experimentally applied c - - - - - A technique is a planned process used to accomplish a specific activity or task. - technique - - - - - - - - - A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo. - embryonic stem cell line - - - - - - - - - A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types. - stem cell line - - - - @@ -2645,7 +2611,7 @@ A genomic feature being an allele_of a gene is based on its location in a host g - + @@ -2766,7 +2732,7 @@ Note that this class also covers cases where deviant numbers of genes or chromos - + @@ -2919,12 +2885,6 @@ In model organism datasets, 'reference' genes are typically the ' - - - - - - gene trap insertion @@ -2953,25 +2913,6 @@ An 'integrated transgene' differs from its parent 'transgene&apos - - - - - - - - - - - - - - - - - - - @@ -3342,136 +3283,6 @@ These genetic and environmental "interactions" of alleles play out at - - - - - objective is to insert some specified sequence into the genome of a cell or virus - genetic insertion technique - - - - - - - - - mutagen treatment technique - - - - - - - - - - - - - - - a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). - This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. - targeted gene mutation technique - - - - - - - - - Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. - random genetic insertion technique - - - - - - - - - - - - - - - targeted genetic insertion technique - - - - - - - - - - - - - - - enhancer trapping technique - - - - - - - - - - - - - - - gene trapping technique - - - - - - - - - - - - - - - promoter trapping technique - - - - - - - - - - - - - - - targeted knock-in technique - - - - - - - - - random transgene insertion technique - - - - @@ -4338,7 +4149,7 @@ This ontology does not have a root 'phenotype' class, however, and so - + @@ -4572,7 +4383,7 @@ chromosome > arm > band > sub-band > sub-sub-band - + @@ -4757,7 +4568,7 @@ The notion of a 'genomic feature set' differs from that of a 'gen - + @@ -5184,6 +4995,7 @@ A complements may contain 0, 1, or more than one members. For example, the compl + phenotypic inheritance process @@ -6051,6 +5863,7 @@ For example, we would define an 'HLA gene block' as a subclass of &ap true + A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc). useful organizational term to collect entities that have genomes/genotypes. organismal entity @@ -6071,8 +5884,8 @@ For example, we would define an 'HLA gene block' as a subclass of &ap - - reporter role + + reporter @@ -6080,8 +5893,8 @@ For example, we would define an 'HLA gene block' as a subclass of &ap - - selectable marker role + + selectable marker @@ -6672,15 +6485,6 @@ As we saw for 'copy number complement', the defining sequence here is - - - - - molecular function - - - - @@ -6827,36 +6631,6 @@ Previous. An information content entity is a non-realizable information entity t - - - - - An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. - genotyping assay - - - - - - - - - A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. - A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. - targeted gene knock-out technique - - - - - - - - - targeted gene knock-in technique - - - - @@ -6867,32 +6641,6 @@ Previous. An information content entity is a non-realizable information entity t - - - - - - - - - - - - - - - - - - - - - the introduction. alteration or integration of genetic material into a cell or organism - genetic modification technique - - - - @@ -7567,7 +7315,7 @@ For a particular instance of a sequence alteration, howver, we may in some cases - + diff --git a/geno-full.json b/geno-full.json index 3f48f2f..801f7ee 100644 --- a/geno-full.json +++ b/geno-full.json @@ -81,16 +81,6 @@ "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10090", "type" : "CLASS", "lbl" : "Mus musculus" - }, { - "id" : "http://purl.obolibrary.org/obo/ERO_0000007", - "meta" : { - "definition" : { - "val" : "A technique is a planned process used to accomplish a specific activity or task.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "technique" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000159", "meta" : { @@ -175,14 +165,6 @@ }, "type" : "CLASS", "lbl" : "SNV" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000173", - "type" : "CLASS", - "lbl" : "promoter trapping technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000172", - "type" : "CLASS", - "lbl" : "gene trapping technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000054", "meta" : { @@ -193,14 +175,6 @@ }, "type" : "CLASS", "lbl" : "homo sapiens gene" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000175", - "type" : "CLASS", - "lbl" : "random transgene insertion technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000174", - "type" : "CLASS", - "lbl" : "targeted knock-in technique" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000016", "meta" : { @@ -217,16 +191,6 @@ }, "type" : "CLASS", "lbl" : "obsolete_color brightness" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000435", - "meta" : { - "definition" : { - "val" : "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "genotyping assay" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002162", "meta" : { @@ -237,10 +201,6 @@ }, "type" : "PROPERTY", "lbl" : "in taxon" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000171", - "type" : "CLASS", - "lbl" : "enhancer trapping technique" }, { "id" : "http://www.ncbi.nlm.nih.gov/gene/6469", "meta" : { @@ -254,38 +214,6 @@ }, "type" : "CLASS", "lbl" : "homo sapiens SHH gene" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000170", - "type" : "CLASS", - "lbl" : "targeted genetic insertion technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000169", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination." - } ] - }, - "type" : "CLASS", - "lbl" : "random genetic insertion technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000166", - "meta" : { - "definition" : { - "val" : "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping).", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created." - } ] - }, - "type" : "CLASS", - "lbl" : "targeted gene mutation technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000165", - "type" : "CLASS", - "lbl" : "mutagen treatment technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000047", "meta" : { @@ -717,7 +645,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0000087", "type" : "PROPERTY", - "lbl" : "has_role" + "lbl" : "has role" }, { "id" : "http://purl.obolibrary.org/obo/RO_0000086", "meta" : { @@ -2209,11 +2137,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000911", "type" : "CLASS", - "lbl" : "selectable marker role" + "lbl" : "selectable marker" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000910", "type" : "CLASS", - "lbl" : "reporter role" + "lbl" : "reporter" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000912", "type" : "CLASS", @@ -2262,24 +2190,6 @@ }, "type" : "PROPERTY", "lbl" : "has_specified_output" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0001148", - "meta" : { - "definition" : { - "val" : "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a \"targeted\" insertion." - } ] - }, - "type" : "CLASS", - "lbl" : "targeted gene knock-out technique" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0001149", - "type" : "CLASS", - "lbl" : "targeted gene knock-in technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000904", "meta" : { @@ -2288,6 +2198,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "useful organizational term to collect entities that have genomes/genotypes." }, { @@ -3516,10 +3429,6 @@ }, "type" : "CLASS", "lbl" : "T_to_C_transition" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0003674", - "type" : "CLASS", - "lbl" : "molecular function" }, { "id" : "http://purl.obolibrary.org/obo/SO_1000019", "meta" : { @@ -4262,6 +4171,20 @@ "id" : "http://purl.obolibrary.org/obo/GENO_0000605", "type" : "CLASS", "lbl" : "hemizygous Y-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000968", + "meta" : { + "definition" : { + "val" : "A role assigned to a sequence feature, collection, or genotype, e.g. serving as a 'reference' against with other sequences are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants." + } ] + }, + "type" : "PROPERTY", + "lbl" : "sequence role" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000967", "meta" : { @@ -5254,6 +5177,12 @@ "lbl" : "has_sex_agnostic_part" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000770", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, "type" : "CLASS", "lbl" : "phenotypic inheritance process" }, { @@ -6735,12 +6664,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a tornado" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an aggregate of human beings." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the undetached arm of a human being" @@ -6891,16 +6820,6 @@ }, "type" : "CLASS", "lbl" : "genetic material" - }, { - "id" : "http://purl.obolibrary.org/obo/ERO_0002003", - "meta" : { - "definition" : { - "val" : "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "stem cell line" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000477", "meta" : { @@ -7009,16 +6928,6 @@ }, "type" : "CLASS", "lbl" : "strain or breed" - }, { - "id" : "http://purl.obolibrary.org/obo/ERO_0002002", - "meta" : { - "definition" : { - "val" : "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "embryonic stem cell line" }, { "id" : "http://purl.obolibrary.org/obo/UPHENO_0001001", "meta" : { @@ -7103,16 +7012,6 @@ }, "type" : "CLASS", "lbl" : "junction" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0600043", - "meta" : { - "definition" : { - "val" : "the introduction. alteration or integration of genetic material into a cell or organism", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "genetic modification technique" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000577", "type" : "CLASS", @@ -7812,10 +7711,10 @@ "val" : "the bottom right portion of a human torso" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an organism" + "val" : "a molecule" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a molecule" + "val" : "an organism" } ] }, "type" : "CLASS", @@ -8233,16 +8132,6 @@ }, "type" : "CLASS", "lbl" : "obsolete_assembly_component" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000164", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "objective is to insert some specified sequence into the genome of a cell or virus" - } ] - }, - "type" : "CLASS", - "lbl" : "genetic insertion technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000042", "meta" : { @@ -8317,31 +8206,6 @@ }, "type" : "CLASS", "lbl" : "reference allele" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of a hammer to drive in nails" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of amylase in saliva to break down starch into sugar" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" - } ] - }, - "type" : "CLASS", - "lbl" : "function" }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", "meta" : { @@ -8719,22 +8583,18 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000713", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000926", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000623", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000619" }, { - "sub" : "http://purl.obolibrary.org/obo/UPHENO_0001001", + "sub" : "http://purl.obolibrary.org/obo/GENO_0000926", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000173", + "sub" : "http://purl.obolibrary.org/obo/UPHENO_0001001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000170" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000610", "pred" : "subPropertyOf", @@ -8799,10 +8659,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000861", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000902" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001149", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000166" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "inverseOf", @@ -8827,14 +8683,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000818", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000492", - "pred" : "http://purl.obolibrary.org/obo/GENO_0000683", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000501" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000093", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/SO_0001218" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000492", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000683", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000501" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000035", "pred" : "is_a", @@ -8919,10 +8775,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000014", "pred" : "http://purl.obolibrary.org/obo/GENO_0000408", "obj" : "http://purl.obolibrary.org/obo/SO_0000704" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0600043", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ERO_0000007" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000383", "pred" : "is_a", @@ -8963,6 +8815,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000134", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000391" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000017", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000968", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000152" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000616", "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", @@ -9015,14 +8871,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000845", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000790" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_8000012", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_8000006" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000343", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_8000012", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_8000006" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000525", "pred" : "is_a", @@ -9103,10 +8959,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000174", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000170" }, { "sub" : "http://biohackathon.org/resource/faldo#begin", "pred" : "subPropertyOf", @@ -9159,14 +9011,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000575", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UPHENO_0001001" - }, { - "sub" : "http://purl.obolibrary.org/obo/ERO_0000007", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000611", - "pred" : "http://purl.obolibrary.org/obo/RO_0000087", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000152" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000882", "pred" : "is_a", @@ -9175,10 +9019,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000293", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002233" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001148", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000166" }, { "sub" : "http://biohackathon.org/resource/faldo#end", "pred" : "subPropertyOf", @@ -9188,9 +9028,9 @@ "pred" : "http://purl.obolibrary.org/obo/GENO_0000726", "obj" : "http://purl.obolibrary.org/obo/GENO_0000481" }, { - "sub" : "http://purl.obolibrary.org/obo/ERO_0002002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ERO_0002003" + "sub" : "http://purl.obolibrary.org/obo/GENO_0000968", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000053" }, { "sub" : "http://biohackathon.org/resource/faldo#Position", "pred" : "is_a", @@ -9207,10 +9047,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000023", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000017" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000175", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000169" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000009", "pred" : "is_a", @@ -9295,10 +9131,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000904", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0003674", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000034" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000502", "pred" : "is_a", @@ -9391,6 +9223,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000504", "pred" : "http://purl.obolibrary.org/obo/GENO_0000231", "obj" : "http://purl.obolibrary.org/obo/GENO_0000534" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000667", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000910" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000428", "pred" : "type", @@ -9611,10 +9447,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000148", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000934" - }, { - "sub" : "http://purl.obolibrary.org/obo/ERO_0002003", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CLO_0000031" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001784", "pred" : "is_a", @@ -9683,6 +9515,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000897", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000611", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000968", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000152" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000875", "pred" : "is_a", @@ -9735,10 +9571,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000108", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000642", - "pred" : "http://purl.obolibrary.org/obo/RO_0000087", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000911" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000777", "pred" : "http://purl.obolibrary.org/obo/IAO_0000219", @@ -10223,10 +10055,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_0000667", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0000435", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ERO_0000007" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000920", "pred" : "http://purl.obolibrary.org/obo/GENO_0000726", @@ -10259,10 +10087,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000125", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000170", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000164" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000780", "pred" : "is_a", @@ -10295,10 +10119,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000741", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000166", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000515" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002234", "pred" : "subPropertyOf", @@ -10359,10 +10179,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000133", "pred" : "http://purl.obolibrary.org/obo/RO_0000052", "obj" : "http://purl.obolibrary.org/obo/GENO_0000516" - 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}, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000166", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0600043" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000005", "pred" : "is_a", @@ -10499,10 +10307,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0003304", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003302" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000667", - "pred" : "http://purl.obolibrary.org/obo/RO_0000087", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000910" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000620", "pred" : "is_a", @@ -10547,6 +10351,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000528", "pred" : "http://purl.obolibrary.org/obo/GENO_0000382", "obj" : "http://purl.obolibrary.org/obo/GENO_0000506" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000910", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000525", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -10571,10 +10379,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000823", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000897" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000910", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000086" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000000", "pred" : "is_a", @@ -10683,10 +10487,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000639", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000092", - "pred" : "http://purl.obolibrary.org/obo/RO_0002353", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000172" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000047", "pred" : "is_a", @@ -10727,14 +10527,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000848", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_1000032", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0001059" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000955", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000956" + }, { + "sub" : "http://purl.obolibrary.org/obo/SO_1000032", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/SO_0001059" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000637", "pred" : "is_a", @@ -10779,18 +10579,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000847", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000580" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000165", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0600043" }, { "sub" : "http://purl.obolibrary.org/obo/ENVO_01000254", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000911", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000086" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000915", "pred" : "is_a", @@ -10815,10 +10607,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0003305", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000171", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000170" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000143", "pred" : "is_a", @@ -10891,6 +10679,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000036", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000968", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000152" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000843", "pred" : "subPropertyOf", @@ -10907,6 +10699,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000497", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000512" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000911", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000060", "pred" : "is_a", @@ -11007,10 +10803,6 @@ "sub" : "http://purl.obolibrary.org/obo/ZP_0000199", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000575" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000164", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0600043" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", "pred" : "is_a", @@ -11031,14 +10823,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000604", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000134" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_8000015", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_8000014" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000016", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_8000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_8000015", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_8000014" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000919", "pred" : "is_a", @@ -11067,10 +10859,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000091", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000053" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000172", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000170" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000901", "pred" : "is_a", @@ -11079,6 +10867,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000144", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000147" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000642", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000911" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000488", "pred" : "subPropertyOf", @@ -11095,10 +10887,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000534", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000170", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000515" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000008", "pred" : "is_a", @@ -11191,14 +10979,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000784", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000683" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000017", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000036", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000512" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000017", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000165", "pred" : "is_a", @@ -11235,10 +11023,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000495", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000856" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000034", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000016" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000341", "pred" : "is_a", @@ -11283,10 +11067,6 @@ "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_10239", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000169", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000164" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000159", "pred" : "is_a", @@ -11327,10 +11107,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_0001744", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000017", - "pred" : "http://purl.obolibrary.org/obo/RO_0000087", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000152" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001477", "pred" : "is_a", @@ -11362,21 +11138,21 @@ "pred" : "http://purl.org/dc/terms/license", "val" : "Unspecified" } ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-09-09/geno-full.json" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-10-15/geno-full.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000611", - "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000899" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000667", + "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000902" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000207", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000910" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000017", - "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000036", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000512" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000968", "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" } ] }, { @@ -11463,27 +11239,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000207", "fillerId" : "http://purl.obolibrary.org/obo/SO_0000783" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000642", - "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000902" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000911" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000667", - "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000902" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000910" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000036", - "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000512" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000009", "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000660" ], @@ -11509,6 +11264,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_10090" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000642", + "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000902" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000207", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000911" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000054", "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000704" ], @@ -11530,6 +11292,20 @@ "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000219", "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000033" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000611", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000899" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000968", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000017", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000968", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" + } ] } ], "domainRangeAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002200", @@ -11543,13 +11319,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000368", diff --git a/geno-full.obo b/geno-full.obo index f0b2a6a..2a793f6 100644 --- a/geno-full.obo +++ b/geno-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: geno/releases/2019-09-09/geno-full.owl +data-version: geno/releases/2019-10-15/geno-full.owl ontology: geno/geno-full property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string @@ -154,17 +154,6 @@ property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition -property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string -property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string -property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string -property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - [Term] id: BFO:0000040 name: material entity @@ -231,24 +220,6 @@ comment: In ENVO's alignment with the Basic Formal Ontology, this class is being is_a: BFO:0000040 ! material entity property_value: IAO:0000116 "1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions.\n\n2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity)." xsd:string -[Term] -id: ERO:0000007 -name: technique -def: "A technique is a planned process used to accomplish a specific activity or task." [] -is_a: OBI:0000011 ! planned process - -[Term] -id: ERO:0002002 -name: embryonic stem cell line -def: "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo." [] -is_a: ERO:0002003 ! stem cell line - -[Term] -id: ERO:0002003 -name: stem cell line -def: "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types." [] -is_a: CLO:0000031 ! cell line - [Term] id: ExactPosition name: Exact position @@ -325,8 +296,8 @@ def: "A sequence that serves as a standard against which other sequences at the comment: A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence. is_a: GENO:0000702 ! biological sequence intersection_of: GENO:0000702 ! biological sequence -intersection_of: RO:0000087 GENO:0000152 ! has_role reference -relationship: RO:0000087 GENO:0000152 ! has_role reference +intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference +relationship: GENO:0000968 GENO:0000152 ! sequence role reference property_value: IAO:0000116 "The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant." xsd:string property_value: IAO:0000118 "reference sequence" xsd:string @@ -385,8 +356,8 @@ def: "An allele whose sequence matches what is consdiered to be the reference se comment: Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.\n\nIn model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared. is_a: GENO:0000512 ! allele intersection_of: GENO:0000512 ! allele -intersection_of: RO:0000087 GENO:0000152 ! has_role reference -relationship: RO:0000087 GENO:0000152 ! has_role reference +intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference +relationship: GENO:0000968 GENO:0000152 ! sequence role reference [Term] id: GENO:0000037 @@ -453,7 +424,6 @@ is_a: ObsoleteClass id: GENO:0000092 name: gene trap insertion is_a: SO:0000667 ! insertion -relationship: RO:0002353 GENO:0000172 ! output of gene trapping technique [Term] id: GENO:0000093 @@ -469,7 +439,6 @@ name: genomic material def: "A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny." [] comment: 1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms. is_a: GENO:0000482 ! genetic material -relationship: BFO:0000050 GENO:0000108 ! is part of material genome relationship: RO:0000091 GENO:0000139 ! has disposition heritable property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000116 "1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way." xsd:string @@ -671,62 +640,6 @@ id: GENO:0000160 name: unspecified life cycle stage is_a: UBERON:0000105 ! life cycle stage -[Term] -id: GENO:0000164 -name: genetic insertion technique -comment: objective is to insert some specified sequence into the genome of a cell or virus -is_a: OBI:0600043 ! genetic modification technique - -[Term] -id: GENO:0000165 -name: mutagen treatment technique -is_a: OBI:0600043 ! genetic modification technique - -[Term] -id: GENO:0000166 -name: targeted gene mutation technique -def: "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping)." [] -comment: This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. -is_a: OBI:0600043 ! genetic modification technique -relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele - -[Term] -id: GENO:0000169 -name: random genetic insertion technique -comment: Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. -is_a: GENO:0000164 ! genetic insertion technique - -[Term] -id: GENO:0000170 -name: targeted genetic insertion technique -is_a: GENO:0000164 ! genetic insertion technique -relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele - -[Term] -id: GENO:0000171 -name: enhancer trapping technique -is_a: GENO:0000170 ! targeted genetic insertion technique - -[Term] -id: GENO:0000172 -name: gene trapping technique -is_a: GENO:0000170 ! targeted genetic insertion technique - -[Term] -id: GENO:0000173 -name: promoter trapping technique -is_a: GENO:0000170 ! targeted genetic insertion technique - -[Term] -id: GENO:0000174 -name: targeted knock-in technique -is_a: GENO:0000170 ! targeted genetic insertion technique - -[Term] -id: GENO:0000175 -name: random transgene insertion technique -is_a: GENO:0000169 ! random genetic insertion technique - [Term] id: GENO:0000324 name: obsolete_chromosome complement @@ -1150,9 +1063,9 @@ name: genomic background def: "A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations)." [] is_a: GENO:0000899 ! genomic genotype intersection_of: GENO:0000899 ! genomic genotype -intersection_of: RO:0000087 GENO:0000152 ! has_role reference +intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference +relationship: GENO:0000968 GENO:0000152 ! sequence role reference relationship: IAO:0000219 GENO:0000010 ! denotes background genome -relationship: RO:0000087 GENO:0000152 ! has_role reference property_value: IAO:0000116 "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it." xsd:string property_value: IAO:0000118 "background genotype" xsd:string @@ -1267,8 +1180,8 @@ def: "A transgene whose product is used as a selectable marker." [] is_a: SO:0000804 ! engineered_region is_a: SO:0000902 ! transgene intersection_of: SO:0000902 ! transgene -intersection_of: RO:0000087 GENO:0000911 ! has_role selectable marker role -relationship: RO:0000087 GENO:0000911 ! has_role selectable marker role +intersection_of: GENO:0000207 GENO:0000911 ! has_sequence_attribute selectable marker +relationship: GENO:0000207 GENO:0000911 ! has_sequence_attribute selectable marker [Term] id: GENO:0000644 @@ -1347,9 +1260,9 @@ def: "A transgene that codes for a product used as a reporter of gene expression is_a: SO:0000804 ! engineered_region is_a: SO:0000902 ! transgene intersection_of: SO:0000902 ! transgene -intersection_of: RO:0000087 GENO:0000910 ! has_role reporter role +intersection_of: GENO:0000207 GENO:0000910 ! has_sequence_attribute reporter relationship: BFO:0000051 GENO:0000640 ! has part reporter region -relationship: RO:0000087 GENO:0000910 ! has_role reporter role +relationship: GENO:0000207 GENO:0000910 ! has_sequence_attribute reporter [Term] id: GENO:0000680 @@ -1513,6 +1426,7 @@ property_value: IAO:0000231 "remodeling notion of sequence feature position arou id: GENO:0000770 name: phenotypic inheritance process is_a: GENO:0000351 ! biological process +property_value: IAO:0000114 GENO:0000484 [Term] id: GENO:0000772 @@ -1884,6 +1798,7 @@ name: organismal entity def: "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc)." [] is_a: BFO:0000040 ! material entity property_value: GENO:0000905 "true" xsd:boolean +property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000116 "useful organizational term to collect entities that have genomes/genotypes." xsd:string [Term] @@ -1894,13 +1809,13 @@ is_a: SO:0000110 ! sequence_feature [Term] id: GENO:0000910 -name: reporter role -is_a: OBI:0000086 ! reagent role +name: reporter +is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000911 -name: selectable marker role -is_a: OBI:0000086 ! reagent role +name: selectable marker +is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000912 @@ -2239,11 +2154,6 @@ name: sequence interval def: "A pair of integers representing start and end position of a location on a sequence coordinate system." [] is_a: IAO:0000030 ! information content entity -[Term] -id: GO:0003674 -name: molecular function -is_a: BFO:0000034 ! function - [Term] id: GO:0032502 name: developmental process @@ -2558,36 +2468,12 @@ name: population def: "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area" [] is_a: GENO:0000113 ! taxonomic group -[Term] -id: OBI:0000435 -name: genotyping assay -def: "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions." [] -is_a: ERO:0000007 ! technique - -[Term] -id: OBI:0001148 -name: targeted gene knock-out technique -def: "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods." [] -comment: A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. -is_a: GENO:0000166 ! targeted gene mutation technique - -[Term] -id: OBI:0001149 -name: targeted gene knock-in technique -is_a: GENO:0000166 ! targeted gene mutation technique - [Term] id: OBI:0100026 name: organism is_a: GENO:0000904 ! organismal entity property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy." xsd:string -[Term] -id: OBI:0600043 -name: genetic modification technique -def: "the introduction. alteration or integration of genetic material into a cell or organism" [] -is_a: ERO:0000007 ! technique - [Term] id: PATO:0000016 name: obsolete_color brightness @@ -3936,6 +3822,13 @@ id: GENO:0000967 name: has_reference_sequence def: "Relates a 'sequence feature location' to a sequence that it is anchored to." [] +[Typedef] +id: GENO:0000968 +name: sequence role +def: "A role assigned to a sequence feature, collection, or genotype, e.g. serving as a 'reference' against with other sequences are compared." [] +comment: The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants. +is_a: RO:0000053 ! bearer of + [Typedef] id: IAO:0000136 name: is about @@ -3995,7 +3888,7 @@ is_a: RO:0000053 ! bearer of [Typedef] id: RO:0000087 -name: has_role +name: has role is_a: RO:0000053 ! bearer of [Typedef] diff --git a/geno-full.owl b/geno-full.owl index 6bd98bb..efbf6af 100644 --- a/geno-full.owl +++ b/geno-full.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 @@ -1999,6 +1999,17 @@ For copy number complements, it is the sequence of this proxy feature on some re + + + + + A role assigned to a sequence feature, collection, or genotype, e.g. serving as a 'reference' against with other sequences are compared. + The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants. + sequence role + + + + @@ -2100,7 +2111,7 @@ For copy number complements, it is the sequence of this proxy feature on some re - has_role + has role @@ -2852,21 +2863,6 @@ Environments include natural environments or exposures, experimentally applied c - - - - - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - function - - - - @@ -2952,36 +2948,6 @@ Environments include natural environments or exposures, experimentally applied c - - - - - A technique is a planned process used to accomplish a specific activity or task. - technique - - - - - - - - - A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo. - embryonic stem cell line - - - - - - - - - A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types. - stem cell line - - - - @@ -3140,7 +3106,7 @@ A genomic feature being an allele_of a gene is based on its location in a host g - + @@ -3149,7 +3115,7 @@ A genomic feature being an allele_of a gene is based on its location in a host g - + @@ -3282,7 +3248,7 @@ Note that this class also covers cases where deviant numbers of genes or chromos - + @@ -3291,7 +3257,7 @@ Note that this class also covers cases where deviant numbers of genes or chromos - + @@ -3463,12 +3429,6 @@ In model organism datasets, 'reference' genes are typically the ' - - - - - - gene trap insertion @@ -3497,25 +3457,6 @@ An 'integrated transgene' differs from its parent 'transgene&apos - - - - - - - - - - - - - - - - - - - @@ -3886,112 +3827,6 @@ These genetic and environmental "interactions" of alleles play out at - - - - - objective is to insert some specified sequence into the genome of a cell or virus - genetic insertion technique - - - - - - - - - mutagen treatment technique - - - - - - - - - - - - - - - a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). - This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. - targeted gene mutation technique - - - - - - - - - Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. - random genetic insertion technique - - - - - - - - - - - - - - - targeted genetic insertion technique - - - - - - - - - enhancer trapping technique - - - - - - - - - gene trapping technique - - - - - - - - - promoter trapping technique - - - - - - - - - targeted knock-in technique - - - - - - - - - random transgene insertion technique - - - - @@ -4872,7 +4707,7 @@ This ontology does not have a root 'phenotype' class, however, and so - + @@ -4881,14 +4716,14 @@ This ontology does not have a root 'phenotype' class, however, and so - - + + - - + + A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). @@ -5102,7 +4937,7 @@ chromosome > arm > band > sub-band > sub-sub-band - + @@ -5112,7 +4947,7 @@ chromosome > arm > band > sub-band > sub-sub-band - + @@ -5285,7 +5120,7 @@ The notion of a 'genomic feature set' differs from that of a 'gen - + @@ -5301,7 +5136,7 @@ The notion of a 'genomic feature set' differs from that of a 'gen - + @@ -5714,6 +5549,7 @@ A complements may contain 0, 1, or more than one members. For example, the compl + phenotypic inheritance process @@ -6623,6 +6459,7 @@ For example, we would define an 'HLA gene block' as a subclass of &ap true + A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc). useful organizational term to collect entities that have genomes/genotypes. organismal entity @@ -6643,8 +6480,8 @@ For example, we would define an 'HLA gene block' as a subclass of &ap - - reporter role + + reporter @@ -6652,8 +6489,8 @@ For example, we would define an 'HLA gene block' as a subclass of &ap - - selectable marker role + + selectable marker @@ -7250,15 +7087,6 @@ As we saw for 'copy number complement', the defining sequence here is - - - - - molecular function - - - - @@ -7783,36 +7611,6 @@ No imports - - - - - An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. - genotyping assay - - - - - - - - - A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. - A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. - targeted gene knock-out technique - - - - - - - - - targeted gene knock-in technique - - - - @@ -7823,32 +7621,6 @@ No imports - - - - - - - - - - - - - - - - - - - - - the introduction. alteration or integration of genetic material into a cell or organism - genetic modification technique - - - - diff --git a/geno.json b/geno.json index 266763c..775a29a 100644 --- a/geno.json +++ b/geno.json @@ -81,16 +81,6 @@ "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10090", "type" : "CLASS", "lbl" : "Mus musculus" - }, { - "id" : "http://purl.obolibrary.org/obo/ERO_0000007", - "meta" : { - "definition" : { - "val" : "A technique is a planned process used to accomplish a specific activity or task.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "technique" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000159", "meta" : { @@ -175,14 +165,6 @@ }, "type" : "CLASS", "lbl" : "SNV" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000173", - "type" : "CLASS", - "lbl" : "promoter trapping technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000172", - "type" : "CLASS", - "lbl" : "gene trapping technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000054", "meta" : { @@ -193,14 +175,6 @@ }, "type" : "CLASS", "lbl" : "homo sapiens gene" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000175", - "type" : "CLASS", - "lbl" : "random transgene insertion technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000174", - "type" : "CLASS", - "lbl" : "targeted knock-in technique" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000016", "meta" : { @@ -217,16 +191,6 @@ }, "type" : "CLASS", "lbl" : "obsolete_color brightness" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000435", - "meta" : { - "definition" : { - "val" : "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "genotyping assay" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002162", "meta" : { @@ -237,10 +201,6 @@ }, "type" : "PROPERTY", "lbl" : "in taxon" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000171", - "type" : "CLASS", - "lbl" : "enhancer trapping technique" }, { "id" : "http://www.ncbi.nlm.nih.gov/gene/6469", "meta" : { @@ -254,38 +214,6 @@ }, "type" : "CLASS", "lbl" : "homo sapiens SHH gene" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000170", - "type" : "CLASS", - "lbl" : "targeted genetic insertion technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000169", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination." - } ] - }, - "type" : "CLASS", - "lbl" : "random genetic insertion technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000166", - "meta" : { - "definition" : { - "val" : "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping).", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created." - } ] - }, - "type" : "CLASS", - "lbl" : "targeted gene mutation technique" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000165", - "type" : "CLASS", - "lbl" : "mutagen treatment technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000047", "meta" : { @@ -717,7 +645,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0000087", "type" : "PROPERTY", - "lbl" : "has_role" + "lbl" : "has role" }, { "id" : "http://purl.obolibrary.org/obo/RO_0000086", "meta" : { @@ -2209,11 +2137,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000911", "type" : "CLASS", - "lbl" : "selectable marker role" + "lbl" : "selectable marker" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000910", "type" : "CLASS", - "lbl" : "reporter role" + "lbl" : "reporter" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000912", "type" : "CLASS", @@ -2262,24 +2190,6 @@ }, "type" : "PROPERTY", "lbl" : "has_specified_output" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0001148", - "meta" : { - "definition" : { - "val" : "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a \"targeted\" insertion." - } ] - }, - "type" : "CLASS", - "lbl" : "targeted gene knock-out technique" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0001149", - "type" : "CLASS", - "lbl" : "targeted gene knock-in technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000904", "meta" : { @@ -2288,6 +2198,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "useful organizational term to collect entities that have genomes/genotypes." }, { @@ -3516,10 +3429,6 @@ }, "type" : "CLASS", "lbl" : "T_to_C_transition" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0003674", - "type" : "CLASS", - "lbl" : "molecular function" }, { "id" : "http://purl.obolibrary.org/obo/SO_1000019", "meta" : { @@ -4262,6 +4171,20 @@ "id" : "http://purl.obolibrary.org/obo/GENO_0000605", "type" : "CLASS", "lbl" : "hemizygous Y-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000968", + "meta" : { + "definition" : { + "val" : "A role assigned to a sequence feature, collection, or genotype, e.g. serving as a 'reference' against with other sequences are compared.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants." + } ] + }, + "type" : "PROPERTY", + "lbl" : "sequence role" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000967", "meta" : { @@ -5254,6 +5177,12 @@ "lbl" : "has_sex_agnostic_part" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000770", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/GENO_0000484" + } ] + }, "type" : "CLASS", "lbl" : "phenotypic inheritance process" }, { @@ -6891,16 +6820,6 @@ }, "type" : "CLASS", "lbl" : "genetic material" - }, { - "id" : "http://purl.obolibrary.org/obo/ERO_0002003", - "meta" : { - "definition" : { - "val" : "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "stem cell line" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000477", "meta" : { @@ -7009,16 +6928,6 @@ }, "type" : "CLASS", "lbl" : "strain or breed" - }, { - "id" : "http://purl.obolibrary.org/obo/ERO_0002002", - "meta" : { - "definition" : { - "val" : "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "embryonic stem cell line" }, { "id" : "http://purl.obolibrary.org/obo/UPHENO_0001001", "meta" : { @@ -7103,16 +7012,6 @@ }, "type" : "CLASS", "lbl" : "junction" - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0600043", - "meta" : { - "definition" : { - "val" : "the introduction. alteration or integration of genetic material into a cell or organism", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "genetic modification technique" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000577", "type" : "CLASS", @@ -7812,10 +7711,10 @@ "val" : "the bottom right portion of a human torso" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an organism" + "val" : "a molecule" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a molecule" + "val" : "an organism" } ] }, "type" : "CLASS", @@ -8233,16 +8132,6 @@ }, "type" : "CLASS", "lbl" : "obsolete_assembly_component" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000164", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "objective is to insert some specified sequence into the genome of a cell or virus" - } ] - }, - "type" : "CLASS", - "lbl" : "genetic insertion technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000042", "meta" : { @@ -8317,31 +8206,6 @@ }, "type" : "CLASS", "lbl" : "reference allele" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of a hammer to drive in nails" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of amylase in saliva to break down starch into sugar" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" - } ] - }, - "type" : "CLASS", - "lbl" : "function" }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", "meta" : { @@ -8719,22 +8583,18 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000713", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000926", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000623", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000619" }, { - "sub" : "http://purl.obolibrary.org/obo/UPHENO_0001001", + "sub" : "http://purl.obolibrary.org/obo/GENO_0000926", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000173", + "sub" : "http://purl.obolibrary.org/obo/UPHENO_0001001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000170" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000610", "pred" : "subPropertyOf", @@ -8799,10 +8659,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000861", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000902" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001149", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000166" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "inverseOf", @@ -8827,14 +8683,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000818", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000492", - "pred" : "http://purl.obolibrary.org/obo/GENO_0000683", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000501" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000093", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/SO_0001218" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000492", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000683", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000501" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000035", "pred" : "is_a", @@ -8919,10 +8775,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000014", "pred" : "http://purl.obolibrary.org/obo/GENO_0000408", "obj" : "http://purl.obolibrary.org/obo/SO_0000704" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0600043", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ERO_0000007" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000383", "pred" : "is_a", @@ -8963,6 +8815,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000134", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000391" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000017", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000968", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000152" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000616", "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", @@ -9103,10 +8959,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000174", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000170" }, { "sub" : "http://biohackathon.org/resource/faldo#begin", "pred" : "subPropertyOf", @@ -9159,14 +9011,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000575", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UPHENO_0001001" - }, { - "sub" : "http://purl.obolibrary.org/obo/ERO_0000007", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000611", - "pred" : "http://purl.obolibrary.org/obo/RO_0000087", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000152" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000882", "pred" : "is_a", @@ -9175,10 +9019,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000293", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002233" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001148", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000166" }, { "sub" : "http://biohackathon.org/resource/faldo#end", "pred" : "subPropertyOf", @@ -9188,9 +9028,9 @@ "pred" : "http://purl.obolibrary.org/obo/GENO_0000726", "obj" : "http://purl.obolibrary.org/obo/GENO_0000481" }, { - "sub" : "http://purl.obolibrary.org/obo/ERO_0002002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/ERO_0002003" + "sub" : "http://purl.obolibrary.org/obo/GENO_0000968", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000053" }, { "sub" : "http://biohackathon.org/resource/faldo#Position", "pred" : "is_a", @@ -9207,10 +9047,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000023", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000017" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000175", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000169" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000009", "pred" : "is_a", @@ -9299,10 +9135,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000502", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000704" - 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}, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000165", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0600043" }, { "sub" : "http://purl.obolibrary.org/obo/ENVO_01000254", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000911", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000086" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000915", "pred" : "is_a", @@ -10815,10 +10607,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0003305", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000171", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000170" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000143", "pred" : "is_a", @@ -10891,6 +10679,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000036", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000968", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000152" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000843", "pred" : "subPropertyOf", @@ -10907,6 +10699,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000497", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000512" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000911", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000060", "pred" : "is_a", @@ -11007,10 +10803,6 @@ "sub" : "http://purl.obolibrary.org/obo/ZP_0000199", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000575" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000164", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0600043" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", "pred" : "is_a", @@ -11043,14 +10835,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000919", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000713" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000720", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000720", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001059", "pred" : "http://purl.obolibrary.org/obo/GENO_0000784", @@ -11071,14 +10863,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000901", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000172", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000170" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000144", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000147" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000642", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000911" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000488", "pred" : "subPropertyOf", @@ -11095,10 +10887,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000534", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000170", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000515" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000008", "pred" : "is_a", @@ -11191,14 +10979,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000784", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000683" - 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}, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000169", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000164" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000159", "pred" : "is_a", @@ -11327,10 +11107,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_0001744", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000017", - "pred" : "http://purl.obolibrary.org/obo/RO_0000087", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000152" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001477", "pred" : "is_a", @@ -11362,21 +11138,21 @@ "pred" : "http://purl.org/dc/terms/license", "val" : "Unspecified" } ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-09-09" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-10-15" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000611", - "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000899" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000667", + "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000902" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000207", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000910" } ] }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000017", - "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ], + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000036", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000512" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000968", "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" } ] }, { @@ -11463,27 +11239,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000207", "fillerId" : "http://purl.obolibrary.org/obo/SO_0000783" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000642", - "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000902" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000911" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000667", - "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000902" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000910" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000036", - "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000512" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", - "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000009", "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000660" ], @@ -11509,6 +11264,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_10090" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000642", + "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000902" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000207", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000911" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000054", "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000704" ], @@ -11530,6 +11292,20 @@ "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000219", "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000033" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000611", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000899" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000968", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GENO_0000017", + "genusIds" : [ "http://purl.obolibrary.org/obo/GENO_0000702" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/GENO_0000968", + "fillerId" : "http://purl.obolibrary.org/obo/GENO_0000152" + } ] } ], "domainRangeAxioms" : [ { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002200", @@ -11543,13 +11319,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000368", diff --git a/geno.obo b/geno.obo index 6225fe0..06fb48a 100644 --- a/geno.obo +++ b/geno.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2019-09-09 +data-version: releases/2019-10-15 ontology: geno property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string @@ -154,17 +154,6 @@ property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition -property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string -property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string -property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string -property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - [Term] id: BFO:0000040 name: material entity @@ -231,24 +220,6 @@ comment: In ENVO's alignment with the Basic Formal Ontology, this class is being is_a: BFO:0000040 ! material entity property_value: IAO:0000116 "1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions.\n\n2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity)." xsd:string -[Term] -id: ERO:0000007 -name: technique -def: "A technique is a planned process used to accomplish a specific activity or task." [] -is_a: OBI:0000011 ! planned process - -[Term] -id: ERO:0002002 -name: embryonic stem cell line -def: "A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo." [] -is_a: ERO:0002003 ! stem cell line - -[Term] -id: ERO:0002003 -name: stem cell line -def: "A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types." [] -is_a: CLO:0000031 ! cell line - [Term] id: ExactPosition name: Exact position @@ -325,8 +296,8 @@ def: "A sequence that serves as a standard against which other sequences at the comment: A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence. is_a: GENO:0000702 ! biological sequence intersection_of: GENO:0000702 ! biological sequence -intersection_of: RO:0000087 GENO:0000152 ! has_role reference -relationship: RO:0000087 GENO:0000152 ! has_role reference +intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference +relationship: GENO:0000968 GENO:0000152 ! sequence role reference property_value: IAO:0000116 "The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant." xsd:string property_value: IAO:0000118 "reference sequence" xsd:string @@ -385,8 +356,8 @@ def: "An allele whose sequence matches what is consdiered to be the reference se comment: Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.\n\nIn model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared. is_a: GENO:0000512 ! allele intersection_of: GENO:0000512 ! allele -intersection_of: RO:0000087 GENO:0000152 ! has_role reference -relationship: RO:0000087 GENO:0000152 ! has_role reference +intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference +relationship: GENO:0000968 GENO:0000152 ! sequence role reference [Term] id: GENO:0000037 @@ -453,7 +424,6 @@ is_a: ObsoleteClass id: GENO:0000092 name: gene trap insertion is_a: SO:0000667 ! insertion -relationship: RO:0002353 GENO:0000172 ! output of gene trapping technique [Term] id: GENO:0000093 @@ -469,7 +439,6 @@ name: genomic material def: "A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny." [] comment: 1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms. is_a: GENO:0000482 ! genetic material -relationship: BFO:0000050 GENO:0000108 ! is part of material genome relationship: RO:0000091 GENO:0000139 ! has disposition heritable property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000116 "1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way." xsd:string @@ -671,62 +640,6 @@ id: GENO:0000160 name: unspecified life cycle stage is_a: UBERON:0000105 ! life cycle stage -[Term] -id: GENO:0000164 -name: genetic insertion technique -comment: objective is to insert some specified sequence into the genome of a cell or virus -is_a: OBI:0600043 ! genetic modification technique - -[Term] -id: GENO:0000165 -name: mutagen treatment technique -is_a: OBI:0600043 ! genetic modification technique - -[Term] -id: GENO:0000166 -name: targeted gene mutation technique -def: "a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping)." [] -comment: This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. -is_a: OBI:0600043 ! genetic modification technique -relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele - -[Term] -id: GENO:0000169 -name: random genetic insertion technique -comment: Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. -is_a: GENO:0000164 ! genetic insertion technique - -[Term] -id: GENO:0000170 -name: targeted genetic insertion technique -is_a: GENO:0000164 ! genetic insertion technique -relationship: OBI:0000299 GENO:0000515 ! has_specified_output variant gene allele - -[Term] -id: GENO:0000171 -name: enhancer trapping technique -is_a: GENO:0000170 ! targeted genetic insertion technique - -[Term] -id: GENO:0000172 -name: gene trapping technique -is_a: GENO:0000170 ! targeted genetic insertion technique - -[Term] -id: GENO:0000173 -name: promoter trapping technique -is_a: GENO:0000170 ! targeted genetic insertion technique - -[Term] -id: GENO:0000174 -name: targeted knock-in technique -is_a: GENO:0000170 ! targeted genetic insertion technique - -[Term] -id: GENO:0000175 -name: random transgene insertion technique -is_a: GENO:0000169 ! random genetic insertion technique - [Term] id: GENO:0000324 name: obsolete_chromosome complement @@ -1150,9 +1063,9 @@ name: genomic background def: "A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations)." [] is_a: GENO:0000899 ! genomic genotype intersection_of: GENO:0000899 ! genomic genotype -intersection_of: RO:0000087 GENO:0000152 ! has_role reference +intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference +relationship: GENO:0000968 GENO:0000152 ! sequence role reference relationship: IAO:0000219 GENO:0000010 ! denotes background genome -relationship: RO:0000087 GENO:0000152 ! has_role reference property_value: IAO:0000116 "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it." xsd:string property_value: IAO:0000118 "background genotype" xsd:string @@ -1267,8 +1180,8 @@ def: "A transgene whose product is used as a selectable marker." [] is_a: SO:0000804 ! engineered_region is_a: SO:0000902 ! transgene intersection_of: SO:0000902 ! transgene -intersection_of: RO:0000087 GENO:0000911 ! has_role selectable marker role -relationship: RO:0000087 GENO:0000911 ! has_role selectable marker role +intersection_of: GENO:0000207 GENO:0000911 ! has_sequence_attribute selectable marker +relationship: GENO:0000207 GENO:0000911 ! has_sequence_attribute selectable marker [Term] id: GENO:0000644 @@ -1347,9 +1260,9 @@ def: "A transgene that codes for a product used as a reporter of gene expression is_a: SO:0000804 ! engineered_region is_a: SO:0000902 ! transgene intersection_of: SO:0000902 ! transgene -intersection_of: RO:0000087 GENO:0000910 ! has_role reporter role +intersection_of: GENO:0000207 GENO:0000910 ! has_sequence_attribute reporter relationship: BFO:0000051 GENO:0000640 ! has part reporter region -relationship: RO:0000087 GENO:0000910 ! has_role reporter role +relationship: GENO:0000207 GENO:0000910 ! has_sequence_attribute reporter [Term] id: GENO:0000680 @@ -1513,6 +1426,7 @@ property_value: IAO:0000231 "remodeling notion of sequence feature position arou id: GENO:0000770 name: phenotypic inheritance process is_a: GENO:0000351 ! biological process +property_value: IAO:0000114 GENO:0000484 [Term] id: GENO:0000772 @@ -1884,6 +1798,7 @@ name: organismal entity def: "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc)." [] is_a: BFO:0000040 ! material entity property_value: GENO:0000905 "true" xsd:boolean +property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000116 "useful organizational term to collect entities that have genomes/genotypes." xsd:string [Term] @@ -1894,13 +1809,13 @@ is_a: SO:0000110 ! sequence_feature [Term] id: GENO:0000910 -name: reporter role -is_a: OBI:0000086 ! reagent role +name: reporter +is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000911 -name: selectable marker role -is_a: OBI:0000086 ! reagent role +name: selectable marker +is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000912 @@ -2239,11 +2154,6 @@ name: sequence interval def: "A pair of integers representing start and end position of a location on a sequence coordinate system." [] is_a: IAO:0000030 ! information content entity -[Term] -id: GO:0003674 -name: molecular function -is_a: BFO:0000034 ! function - [Term] id: GO:0032502 name: developmental process @@ -2558,36 +2468,12 @@ name: population def: "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area" [] is_a: GENO:0000113 ! taxonomic group -[Term] -id: OBI:0000435 -name: genotyping assay -def: "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions." [] -is_a: ERO:0000007 ! technique - -[Term] -id: OBI:0001148 -name: targeted gene knock-out technique -def: "A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods." [] -comment: A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. -is_a: GENO:0000166 ! targeted gene mutation technique - -[Term] -id: OBI:0001149 -name: targeted gene knock-in technique -is_a: GENO:0000166 ! targeted gene mutation technique - [Term] id: OBI:0100026 name: organism is_a: GENO:0000904 ! organismal entity property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy." xsd:string -[Term] -id: OBI:0600043 -name: genetic modification technique -def: "the introduction. alteration or integration of genetic material into a cell or organism" [] -is_a: ERO:0000007 ! technique - [Term] id: PATO:0000016 name: obsolete_color brightness @@ -3936,6 +3822,13 @@ id: GENO:0000967 name: has_reference_sequence def: "Relates a 'sequence feature location' to a sequence that it is anchored to." [] +[Typedef] +id: GENO:0000968 +name: sequence role +def: "A role assigned to a sequence feature, collection, or genotype, e.g. serving as a 'reference' against with other sequences are compared." [] +comment: The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants. +is_a: RO:0000053 ! bearer of + [Typedef] id: IAO:0000136 name: is about @@ -3995,7 +3888,7 @@ is_a: RO:0000053 ! bearer of [Typedef] id: RO:0000087 -name: has_role +name: has role is_a: RO:0000053 ! bearer of [Typedef] diff --git a/geno.owl b/geno.owl index a70d2f3..cc5e55d 100644 --- a/geno.owl +++ b/geno.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 @@ -1999,6 +1999,17 @@ For copy number complements, it is the sequence of this proxy feature on some re + + + + + A role assigned to a sequence feature, collection, or genotype, e.g. serving as a 'reference' against with other sequences are compared. + The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants. + sequence role + + + + @@ -2100,7 +2111,7 @@ For copy number complements, it is the sequence of this proxy feature on some re - has_role + has role @@ -2852,21 +2863,6 @@ Environments include natural environments or exposures, experimentally applied c - - - - - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - function - - - - @@ -2952,36 +2948,6 @@ Environments include natural environments or exposures, experimentally applied c - - - - - A technique is a planned process used to accomplish a specific activity or task. - technique - - - - - - - - - A stem cell line comprised of embryonic stem cells, totipotent cells cultured from an early embryo. - embryonic stem cell line - - - - - - - - - A cell line comprised of stem cells,relatively undifferentiated cells that retain the ability to divide and proliferate provide progenitor cells that can differentiate into specialized cell types. - stem cell line - - - - @@ -3140,7 +3106,7 @@ A genomic feature being an allele_of a gene is based on its location in a host g - + @@ -3149,7 +3115,7 @@ A genomic feature being an allele_of a gene is based on its location in a host g - + @@ -3282,7 +3248,7 @@ Note that this class also covers cases where deviant numbers of genes or chromos - + @@ -3291,7 +3257,7 @@ Note that this class also covers cases where deviant numbers of genes or chromos - + @@ -3463,12 +3429,6 @@ In model organism datasets, 'reference' genes are typically the ' - - - - - - gene trap insertion @@ -3497,25 +3457,6 @@ An 'integrated transgene' differs from its parent 'transgene&apos - - - - - - - - - - - - - - - - - - - @@ -3886,112 +3827,6 @@ These genetic and environmental "interactions" of alleles play out at - - - - - objective is to insert some specified sequence into the genome of a cell or virus - genetic insertion technique - - - - - - - - - mutagen treatment technique - - - - - - - - - - - - - - - a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). - This is represented axiomatically by the requirement that a 'gene variant' (ie an allele/variant of a known gene) is the specified_output of this technique. This is contrasted to non-targted/random insertions/alterations where the altered locus is not known, and therefore no variant allele of a gene is created. - targeted gene mutation technique - - - - - - - - - Is considered to be 'non-targeted' in the sense that the insertion occurs randomly and not through homologous recombination. - random genetic insertion technique - - - - - - - - - - - - - - - targeted genetic insertion technique - - - - - - - - - enhancer trapping technique - - - - - - - - - gene trapping technique - - - - - - - - - promoter trapping technique - - - - - - - - - targeted knock-in technique - - - - - - - - - random transgene insertion technique - - - - @@ -4872,7 +4707,7 @@ This ontology does not have a root 'phenotype' class, however, and so - + @@ -4881,14 +4716,14 @@ This ontology does not have a root 'phenotype' class, however, and so - - + + - - + + A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations). @@ -5102,7 +4937,7 @@ chromosome > arm > band > sub-band > sub-sub-band - + @@ -5112,7 +4947,7 @@ chromosome > arm > band > sub-band > sub-sub-band - + @@ -5285,7 +5120,7 @@ The notion of a 'genomic feature set' differs from that of a 'gen - + @@ -5301,7 +5136,7 @@ The notion of a 'genomic feature set' differs from that of a 'gen - + @@ -5714,6 +5549,7 @@ A complements may contain 0, 1, or more than one members. For example, the compl + phenotypic inheritance process @@ -6623,6 +6459,7 @@ For example, we would define an 'HLA gene block' as a subclass of &ap true + A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc). useful organizational term to collect entities that have genomes/genotypes. organismal entity @@ -6643,8 +6480,8 @@ For example, we would define an 'HLA gene block' as a subclass of &ap - - reporter role + + reporter @@ -6652,8 +6489,8 @@ For example, we would define an 'HLA gene block' as a subclass of &ap - - selectable marker role + + selectable marker @@ -7250,15 +7087,6 @@ As we saw for 'copy number complement', the defining sequence here is - - - - - molecular function - - - - @@ -7783,36 +7611,6 @@ No imports - - - - - An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. - genotyping assay - - - - - - - - - A genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. - A genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. - targeted gene knock-out technique - - - - - - - - - targeted gene knock-in technique - - - - @@ -7823,32 +7621,6 @@ No imports - - - - - - - - - - - - - - - - - - - - - the introduction. alteration or integration of genetic material into a cell or organism - genetic modification technique - - - - diff --git a/imports/iao_import.json b/imports/iao_import.json index ee7a9ee..f675e57 100644 --- a/imports/iao_import.json +++ b/imports/iao_import.json @@ -744,12 +744,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an aggregate of human beings." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "MaterialEntity" @@ -2637,40 +2637,6 @@ }, "type" : "CLASS", "lbl" : "centrally registered identifier registry" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "function" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of a hammer to drive in nails" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of amylase in saliva to break down starch into sugar" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "Function" - } ] - }, - "type" : "CLASS", - "lbl" : "function" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000577", "meta" : { @@ -3353,14 +3319,14 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_8000000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000015", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_8000000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://www.geneontology.org/formats/oboInOwl#Synonym", "pred" : "is_a", @@ -3389,10 +3355,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000034", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000016" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000023", "pred" : "is_a", @@ -3479,7 +3441,7 @@ "subsets" : [ ], "xrefs" : [ ], "basicPropertyValues" : [ ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-09-09/imports/iao_import.owl" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-10-15/imports/iao_import.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { diff --git a/imports/iao_import.obo b/imports/iao_import.obo index bfff057..f0d568a 100644 --- a/imports/iao_import.obo +++ b/imports/iao_import.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: geno/releases/2019-09-09/imports/iao_import.owl +data-version: geno/releases/2019-10-15/imports/iao_import.owl ontology: geno/imports/iao_import owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (denotes)\n\nAnnotationAssertion(rdfs:comment \"\"@en)\n\n# Object Property: (has_specified_input)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (has_specified_output)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (is_specified_output_of)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (curation status specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (material information bearer)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))\n\n# Class: (obsolescence reason specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (denotator type)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (centrally registered identifier)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: ()\n\nEquivalentClasses( ObjectOneOf())\n\n\n############################\n# Named Individuals\n############################\n\n# Individual: (metadata complete)\n\n\n# Individual: (organizational term)\n\n\n# Individual: (ready for release)\n\n\n# Individual: (metadata incomplete)\n\n\n# Individual: (uncurated)\n\n\n# Individual: (pending final vetting)\n\n\n# Individual: (placeholder removed)\n\n\n# Individual: (terms merged)\n\n\n# Individual: (term imported)\n\n\n# Individual: (term split)\n\n\n# Individual: (to be replaced with external ontology term)\n\n\n# Individual: (requires discussion)\n\n\n\nDifferentIndividuals( )\nDifferentIndividuals( )\n) @@ -213,20 +213,6 @@ property_value: IAO:0000112 "the sequence of this protein molecule; the sequence property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition -property_value: BFO:0000179 "function" xsd:string -property_value: BFO:0000180 "Function" xsd:string -property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string -property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string -property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string -property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - [Term] id: BFO:0000040 name: material entity diff --git a/imports/iao_import.owl b/imports/iao_import.owl index 56b32ee..bb1af6d 100644 --- a/imports/iao_import.owl +++ b/imports/iao_import.owl @@ -11,7 +11,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -1609,36 +1609,6 @@ every c that is a concretization of g specifically denotes r - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - diff --git a/imports/ro_import.json b/imports/ro_import.json index 19e4750..918c29e 100644 --- a/imports/ro_import.json +++ b/imports/ro_import.json @@ -206,10 +206,6 @@ }, "type" : "PROPERTY", "lbl" : "in taxon" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", - "type" : "PROPERTY", - "lbl" : "has_related_synonym" }, { "id" : "http://purl.obolibrary.org/obo/RO_0000092", "meta" : { @@ -1176,12 +1172,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -1600,6 +1596,26 @@ }, "type" : "PROPERTY", "lbl" : "involved in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "meta" : { + "definition" : { + "val" : "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is used to study" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Brush" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has role in modeling" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", "meta" : { @@ -1668,26 +1684,6 @@ }, "type" : "PROPERTY", "lbl" : "derives into" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003301", - "meta" : { - "definition" : { - "val" : "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Matthew Brush" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is model of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002212", "meta" : { @@ -2454,7 +2450,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "cjm" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", @@ -2520,11 +2516,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002304", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "cjm" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002411" @@ -3124,10 +3120,6 @@ }, "type" : "PROPERTY", "lbl" : "bounds sequence of" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", - "type" : "PROPERTY", - "lbl" : "in_subset" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002523", "meta" : { @@ -3280,10 +3272,6 @@ }, "type" : "PROPERTY", "lbl" : "sequentially related to" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", - "type" : "PROPERTY", - "lbl" : "has_broad_synonym" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "meta" : { @@ -3304,10 +3292,6 @@ }, "type" : "CLASS", "lbl" : "occurrent" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", - "type" : "PROPERTY", - "lbl" : "has_exact_synonym" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "type" : "PROPERTY", @@ -3398,10 +3382,6 @@ }, "type" : "PROPERTY", "lbl" : "depends on" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "type" : "CLASS", - "lbl" : "function" }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", "type" : "CLASS", @@ -3511,10 +3491,6 @@ "id" : "http://purl.obolibrary.org/obo/GO_0016772", "type" : "CLASS", "lbl" : "transferase activity, transferring phosphorus-containing groups" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", - "type" : "PROPERTY", - "lbl" : "subset_property" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000020", "meta" : { @@ -3714,14 +3690,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002216", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002328" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002024", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002022" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0010001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0010002" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002024", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002022" }, { "sub" : "http://purl.obolibrary.org/obo/OGMS_0000031", "pred" : "is_a", @@ -4138,14 +4114,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002212", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000063", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002014", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002013" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000063", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002428", "pred" : "subPropertyOf", @@ -4250,14 +4226,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000091", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000092" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004032", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002264" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002212", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002335" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004032", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002264" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002528", "pred" : "subPropertyOf", @@ -4370,14 +4346,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002354", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002353" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002305", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004046" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002258", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002286" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002305", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004046" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002432", "pred" : "subPropertyOf", @@ -4398,10 +4374,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002213", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000034", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000016" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0003674", "pred" : "is_a", @@ -4464,7 +4436,7 @@ "subsets" : [ ], "xrefs" : [ ], "basicPropertyValues" : [ ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-09-09/imports/ro_import.owl" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-10-15/imports/ro_import.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], @@ -4514,6 +4486,14 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" @@ -4521,26 +4501,18 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002506", @@ -4640,11 +4612,11 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] } ], "propertyChainAxioms" : [ { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] - }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004035", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002305" ] @@ -4684,6 +4656,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002430", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002212" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004034", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002304" ] diff --git a/imports/ro_import.obo b/imports/ro_import.obo index d864e3b..d1d8928 100644 --- a/imports/ro_import.obo +++ b/imports/ro_import.obo @@ -1,9 +1,9 @@ format-version: 1.2 -data-version: geno/releases/2019-09-09/imports/ro_import.owl +data-version: geno/releases/2019-10-15/imports/ro_import.owl subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: geno/imports/ro_import -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (is model of)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 @@ -74,11 +74,6 @@ def: "A continuant that is dependent on one or other independent continuant bear is_a: BFO:0000002 ! continuant relationship: BFO:0000050 BFO:0000031 ! part of generically dependent continuant -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition - [Term] id: BFO:0000040 name: material entity @@ -628,6 +623,7 @@ holds_over_chain: BFO:0000050 BFO:0000050 holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_a: RO:0002323 ! mereotopologically related to +transitive_over: BFO:0000050 ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] @@ -817,7 +813,7 @@ id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra @@ -918,7 +914,7 @@ is_a: RO:0002384 ! has developmental potential involving id: RO:0002304 name: causally upstream of, positive effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y -property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004049 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -927,7 +923,7 @@ is_a: RO:0004047 ! causally upstream of or within, positive effect id: RO:0002305 name: causally upstream of, negative effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y -property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -1580,7 +1576,7 @@ property_value: IAO:0000232 "Groups both positive and negative correlation" xsd: id: RO:0002615 name: has model def: "Inverse of is-model-of" [] -inverse_of: RO:0003301 ! is model of +inverse_of: RO:0003301 ! has role in modeling [Typedef] id: RO:0002629 @@ -1626,11 +1622,11 @@ range: BFO:0000040 ! material entity [Typedef] id: RO:0003301 -name: is model of -def: "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] -comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. -property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" xsd:string +name: has role in modeling +def: "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] +comment: The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. property_value: IAO:0000117 "Matthew Brush" xsd:string +property_value: IAO:0000118 "is used to study" xsd:string is_asymmetric: true [Typedef] diff --git a/imports/ro_import.owl b/imports/ro_import.owl index 831058a..328cb8e 100644 --- a/imports/ro_import.owl +++ b/imports/ro_import.owl @@ -13,10 +13,11 @@ xmlns:swrl="http://www.w3.org/2003/11/swrl#" xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -103,12 +104,6 @@ - - - - - - @@ -245,12 +240,6 @@ - - - - - - @@ -269,6 +258,18 @@ + + + + + + + + + + + + @@ -283,9 +284,7 @@ - - subset_property - + @@ -301,14 +300,6 @@ - - - - has_broad_synonym - - - - @@ -319,25 +310,19 @@ - - has_exact_synonym - + - - has_related_synonym - + - - in_subset - + @@ -1005,6 +990,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) @@ -1317,7 +1306,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to @@ -1498,7 +1487,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - cjm + cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect @@ -1511,7 +1500,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - cjm + cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect @@ -2653,11 +2642,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. Matthew Brush - The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. - is model of + is used to study + The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. + has role in modeling @@ -3071,15 +3060,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - function - - - - @@ -4058,9 +4038,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -4069,9 +4049,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + diff --git a/reports/geno-edit.owl-obo-report.tsv b/reports/geno-edit.owl-obo-report.tsv index bf796e5..36fbb89 100644 --- a/reports/geno-edit.owl-obo-report.tsv +++ b/reports/geno-edit.owl-obo-report.tsv @@ -118,15 +118,6 @@ WARN missing_definition GENO:0000139 IAO:0000115 WARN missing_definition GENO:0000140 IAO:0000115 WARN missing_definition GENO:0000150 IAO:0000115 WARN missing_definition GENO:0000160 IAO:0000115 -WARN missing_definition GENO:0000164 IAO:0000115 -WARN missing_definition GENO:0000165 IAO:0000115 -WARN missing_definition GENO:0000169 IAO:0000115 -WARN missing_definition GENO:0000170 IAO:0000115 -WARN missing_definition GENO:0000171 IAO:0000115 -WARN missing_definition GENO:0000172 IAO:0000115 -WARN missing_definition GENO:0000173 IAO:0000115 -WARN missing_definition GENO:0000174 IAO:0000115 -WARN missing_definition GENO:0000175 IAO:0000115 WARN missing_definition GENO:0000220 IAO:0000115 WARN missing_definition GENO:0000243 IAO:0000115 WARN missing_definition GENO:0000244 IAO:0000115 @@ -202,7 +193,6 @@ WARN missing_definition GENO:0000910 IAO:0000115 WARN missing_definition GENO:0000911 IAO:0000115 WARN missing_definition GENO:0000912 IAO:0000115 WARN missing_definition GENO:0000964 IAO:0000115 -WARN missing_definition GO:0003674 IAO:0000115 WARN missing_definition HP:0000118 IAO:0000115 WARN missing_definition HsapDv:0000000 IAO:0000115 WARN missing_definition IAO:0000102 IAO:0000115 @@ -213,7 +203,6 @@ WARN missing_definition NCBITaxon:7955 IAO:0000115 WARN missing_definition NCBITaxon:8090 IAO:0000115 WARN missing_definition NCBITaxon:9606 IAO:0000115 WARN missing_definition OBI:0000086 IAO:0000115 -WARN missing_definition OBI:0001149 IAO:0000115 WARN missing_definition OBI:0100026 IAO:0000115 WARN missing_definition PATO:0000016 IAO:0000115 WARN missing_definition PATO:0000383 IAO:0000115 @@ -277,7 +266,6 @@ INFO lowercase_definition GENO:0000019 IAO:0000115 a collection more than one se INFO lowercase_definition GENO:0000111 IAO:0000115 a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role) INFO lowercase_definition GENO:0000125 IAO:0000115 sequence attribute that can inhere only in a collection of more than one sequence features INFO lowercase_definition GENO:0000142 IAO:0000115 disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes -INFO lowercase_definition GENO:0000166 IAO:0000115 a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). INFO lowercase_definition GENO:0000359 IAO:0000115 shortcut relation used to link a phenotype directly to a genotype of an organism INFO lowercase_definition GENO:0000513 IAO:0000115 a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation. INFO lowercase_definition GENO:0000602 IAO:0000115 an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. @@ -288,7 +276,6 @@ INFO lowercase_definition GENO:0000883 IAO:0000115 a quality inhering in a featu INFO lowercase_definition IAO:0000030 IAO:0000115 an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity@en INFO lowercase_definition IAO:0000136 IAO:0000115 is_about is a (currently) primitive relation that relates an information artifact to an entity. INFO lowercase_definition OBI:0000181 IAO:0000115 a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area -INFO lowercase_definition OBI:0600043 IAO:0000115 the introduction. alteration or integration of genetic material into a cell or organism INFO lowercase_definition RO:0000052 IAO:0000115 a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence INFO lowercase_definition RO:0000053 IAO:0000115 a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence INFO lowercase_definition RO:0000056 IAO:0000115 a relation between a continuant and a process, in which the continuant is somehow involved in the process diff --git a/src/ontology/imports/iao_import.json b/src/ontology/imports/iao_import.json index ee7a9ee..f675e57 100644 --- a/src/ontology/imports/iao_import.json +++ b/src/ontology/imports/iao_import.json @@ -744,12 +744,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an aggregate of human beings." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "MaterialEntity" @@ -2637,40 +2637,6 @@ }, "type" : "CLASS", "lbl" : "centrally registered identifier registry" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "function" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of a hammer to drive in nails" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of amylase in saliva to break down starch into sugar" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "Function" - } ] - }, - "type" : "CLASS", - "lbl" : "function" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000577", "meta" : { @@ -3353,14 +3319,14 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_8000000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000015", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_8000000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000102" }, { "sub" : "http://www.geneontology.org/formats/oboInOwl#Synonym", "pred" : "is_a", @@ -3389,10 +3355,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000034", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000016" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000023", "pred" : "is_a", @@ -3479,7 +3441,7 @@ "subsets" : [ ], "xrefs" : [ ], "basicPropertyValues" : [ ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-09-09/imports/iao_import.owl" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-10-15/imports/iao_import.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { diff --git a/src/ontology/imports/iao_import.obo b/src/ontology/imports/iao_import.obo index bfff057..f0d568a 100644 --- a/src/ontology/imports/iao_import.obo +++ b/src/ontology/imports/iao_import.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: geno/releases/2019-09-09/imports/iao_import.owl +data-version: geno/releases/2019-10-15/imports/iao_import.owl ontology: geno/imports/iao_import owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (denotes)\n\nAnnotationAssertion(rdfs:comment \"\"@en)\n\n# Object Property: (has_specified_input)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (has_specified_output)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (is_specified_output_of)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (curation status specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (material information bearer)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))\n\n# Class: (obsolescence reason specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (denotator type)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (centrally registered identifier)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: ()\n\nEquivalentClasses( ObjectOneOf())\n\n\n############################\n# Named Individuals\n############################\n\n# Individual: (metadata complete)\n\n\n# Individual: (organizational term)\n\n\n# Individual: (ready for release)\n\n\n# Individual: (metadata incomplete)\n\n\n# Individual: (uncurated)\n\n\n# Individual: (pending final vetting)\n\n\n# Individual: (placeholder removed)\n\n\n# Individual: (terms merged)\n\n\n# Individual: (term imported)\n\n\n# Individual: (term split)\n\n\n# Individual: (to be replaced with external ontology term)\n\n\n# Individual: (requires discussion)\n\n\n\nDifferentIndividuals( )\nDifferentIndividuals( )\n) @@ -213,20 +213,6 @@ property_value: IAO:0000112 "the sequence of this protein molecule; the sequence property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition -property_value: BFO:0000179 "function" xsd:string -property_value: BFO:0000180 "Function" xsd:string -property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string -property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string -property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string -property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - [Term] id: BFO:0000040 name: material entity diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index 56b32ee..bb1af6d 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -11,7 +11,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -1609,36 +1609,6 @@ every c that is a concretization of g specifically denotes r - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - diff --git a/src/ontology/imports/ro_import.json b/src/ontology/imports/ro_import.json index 19e4750..918c29e 100644 --- a/src/ontology/imports/ro_import.json +++ b/src/ontology/imports/ro_import.json @@ -206,10 +206,6 @@ }, "type" : "PROPERTY", "lbl" : "in taxon" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", - "type" : "PROPERTY", - "lbl" : "has_related_synonym" }, { "id" : "http://purl.obolibrary.org/obo/RO_0000092", "meta" : { @@ -1176,12 +1172,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -1600,6 +1596,26 @@ }, "type" : "PROPERTY", "lbl" : "involved in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "meta" : { + "definition" : { + "val" : "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is used to study" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Matthew Brush" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate." + } ] + }, + "type" : "PROPERTY", + "lbl" : "has role in modeling" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", "meta" : { @@ -1668,26 +1684,6 @@ }, "type" : "PROPERTY", "lbl" : "derives into" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003301", - "meta" : { - "definition" : { - "val" : "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Matthew Brush" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is model of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002212", "meta" : { @@ -2454,7 +2450,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "cjm" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", @@ -2520,11 +2516,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002304", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "cjm" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002411" @@ -3124,10 +3120,6 @@ }, "type" : "PROPERTY", "lbl" : "bounds sequence of" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", - "type" : "PROPERTY", - "lbl" : "in_subset" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002523", "meta" : { @@ -3280,10 +3272,6 @@ }, "type" : "PROPERTY", "lbl" : "sequentially related to" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", - "type" : "PROPERTY", - "lbl" : "has_broad_synonym" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "meta" : { @@ -3304,10 +3292,6 @@ }, "type" : "CLASS", "lbl" : "occurrent" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", - "type" : "PROPERTY", - "lbl" : "has_exact_synonym" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "type" : "PROPERTY", @@ -3398,10 +3382,6 @@ }, "type" : "PROPERTY", "lbl" : "depends on" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "type" : "CLASS", - "lbl" : "function" }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", "type" : "CLASS", @@ -3511,10 +3491,6 @@ "id" : "http://purl.obolibrary.org/obo/GO_0016772", "type" : "CLASS", "lbl" : "transferase activity, transferring phosphorus-containing groups" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", - "type" : "PROPERTY", - "lbl" : "subset_property" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000020", "meta" : { @@ -3714,14 +3690,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002216", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002328" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002024", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002022" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0010001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0010002" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002024", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002022" }, { "sub" : "http://purl.obolibrary.org/obo/OGMS_0000031", "pred" : "is_a", @@ -4138,14 +4114,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002212", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000063", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002014", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002013" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000063", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002222" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002428", "pred" : "subPropertyOf", @@ -4250,14 +4226,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000091", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000092" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004032", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002264" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002212", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002335" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004032", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002264" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002528", "pred" : "subPropertyOf", @@ -4370,14 +4346,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002354", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002353" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002305", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004046" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002258", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002286" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002305", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004046" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002432", "pred" : "subPropertyOf", @@ -4398,10 +4374,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002213", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000034", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000016" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0003674", "pred" : "is_a", @@ -4464,7 +4436,7 @@ "subsets" : [ ], "xrefs" : [ ], "basicPropertyValues" : [ ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-09-09/imports/ro_import.owl" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-10-15/imports/ro_import.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], @@ -4514,6 +4486,14 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" @@ -4521,26 +4501,18 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002506", @@ -4640,11 +4612,11 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] } ], "propertyChainAxioms" : [ { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] - }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004035", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002305" ] @@ -4684,6 +4656,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002430", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002212" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004034", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002304" ] diff --git a/src/ontology/imports/ro_import.obo b/src/ontology/imports/ro_import.obo index d864e3b..d1d8928 100644 --- a/src/ontology/imports/ro_import.obo +++ b/src/ontology/imports/ro_import.obo @@ -1,9 +1,9 @@ format-version: 1.2 -data-version: geno/releases/2019-09-09/imports/ro_import.owl +data-version: geno/releases/2019-10-15/imports/ro_import.owl subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: geno/imports/ro_import -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (is model of)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 @@ -74,11 +74,6 @@ def: "A continuant that is dependent on one or other independent continuant bear is_a: BFO:0000002 ! continuant relationship: BFO:0000050 BFO:0000031 ! part of generically dependent continuant -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition - [Term] id: BFO:0000040 name: material entity @@ -628,6 +623,7 @@ holds_over_chain: BFO:0000050 BFO:0000050 holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_a: RO:0002323 ! mereotopologically related to +transitive_over: BFO:0000050 ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] @@ -817,7 +813,7 @@ id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra @@ -918,7 +914,7 @@ is_a: RO:0002384 ! has developmental potential involving id: RO:0002304 name: causally upstream of, positive effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y -property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004049 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -927,7 +923,7 @@ is_a: RO:0004047 ! causally upstream of or within, positive effect id: RO:0002305 name: causally upstream of, negative effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y -property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: RO:0004050 RO:0002411 is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -1580,7 +1576,7 @@ property_value: IAO:0000232 "Groups both positive and negative correlation" xsd: id: RO:0002615 name: has model def: "Inverse of is-model-of" [] -inverse_of: RO:0003301 ! is model of +inverse_of: RO:0003301 ! has role in modeling [Typedef] id: RO:0002629 @@ -1626,11 +1622,11 @@ range: BFO:0000040 ! material entity [Typedef] id: RO:0003301 -name: is model of -def: "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] -comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. -property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" xsd:string +name: has role in modeling +def: "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] +comment: The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. property_value: IAO:0000117 "Matthew Brush" xsd:string +property_value: IAO:0000118 "is used to study" xsd:string is_asymmetric: true [Typedef] diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 831058a..328cb8e 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -13,10 +13,11 @@ xmlns:swrl="http://www.w3.org/2003/11/swrl#" xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -103,12 +104,6 @@ - - - - - - @@ -245,12 +240,6 @@ - - - - - - @@ -269,6 +258,18 @@ + + + + + + + + + + + + @@ -283,9 +284,7 @@ - - subset_property - + @@ -301,14 +300,6 @@ - - - - has_broad_synonym - - - - @@ -319,25 +310,19 @@ - - has_exact_synonym - + - - has_related_synonym - + - - in_subset - + @@ -1005,6 +990,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) @@ -1317,7 +1306,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to @@ -1498,7 +1487,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - cjm + cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect @@ -1511,7 +1500,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - cjm + cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect @@ -2653,11 +2642,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. Matthew Brush - The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. - is model of + is used to study + The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. + has role in modeling @@ -3071,15 +3060,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - function - - - - @@ -4058,9 +4038,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -4069,9 +4049,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + diff --git a/src/ontology/reports/geno-edit.owl-obo-report.tsv b/src/ontology/reports/geno-edit.owl-obo-report.tsv index bf796e5..36fbb89 100644 --- a/src/ontology/reports/geno-edit.owl-obo-report.tsv +++ b/src/ontology/reports/geno-edit.owl-obo-report.tsv @@ -118,15 +118,6 @@ WARN missing_definition GENO:0000139 IAO:0000115 WARN missing_definition GENO:0000140 IAO:0000115 WARN missing_definition GENO:0000150 IAO:0000115 WARN missing_definition GENO:0000160 IAO:0000115 -WARN missing_definition GENO:0000164 IAO:0000115 -WARN missing_definition GENO:0000165 IAO:0000115 -WARN missing_definition GENO:0000169 IAO:0000115 -WARN missing_definition GENO:0000170 IAO:0000115 -WARN missing_definition GENO:0000171 IAO:0000115 -WARN missing_definition GENO:0000172 IAO:0000115 -WARN missing_definition GENO:0000173 IAO:0000115 -WARN missing_definition GENO:0000174 IAO:0000115 -WARN missing_definition GENO:0000175 IAO:0000115 WARN missing_definition GENO:0000220 IAO:0000115 WARN missing_definition GENO:0000243 IAO:0000115 WARN missing_definition GENO:0000244 IAO:0000115 @@ -202,7 +193,6 @@ WARN missing_definition GENO:0000910 IAO:0000115 WARN missing_definition GENO:0000911 IAO:0000115 WARN missing_definition GENO:0000912 IAO:0000115 WARN missing_definition GENO:0000964 IAO:0000115 -WARN missing_definition GO:0003674 IAO:0000115 WARN missing_definition HP:0000118 IAO:0000115 WARN missing_definition HsapDv:0000000 IAO:0000115 WARN missing_definition IAO:0000102 IAO:0000115 @@ -213,7 +203,6 @@ WARN missing_definition NCBITaxon:7955 IAO:0000115 WARN missing_definition NCBITaxon:8090 IAO:0000115 WARN missing_definition NCBITaxon:9606 IAO:0000115 WARN missing_definition OBI:0000086 IAO:0000115 -WARN missing_definition OBI:0001149 IAO:0000115 WARN missing_definition OBI:0100026 IAO:0000115 WARN missing_definition PATO:0000016 IAO:0000115 WARN missing_definition PATO:0000383 IAO:0000115 @@ -277,7 +266,6 @@ INFO lowercase_definition GENO:0000019 IAO:0000115 a collection more than one se INFO lowercase_definition GENO:0000111 IAO:0000115 a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role) INFO lowercase_definition GENO:0000125 IAO:0000115 sequence attribute that can inhere only in a collection of more than one sequence features INFO lowercase_definition GENO:0000142 IAO:0000115 disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes -INFO lowercase_definition GENO:0000166 IAO:0000115 a genetic alteration technique that creates a variant/allele of a known gene - either by prospective targeting of a specific the gene through homologous recombination, or by retrospective sequence analysis to determine the insertion locus of a randomly integrated transgene (e.g. as done in gene trapping). INFO lowercase_definition GENO:0000359 IAO:0000115 shortcut relation used to link a phenotype directly to a genotype of an organism INFO lowercase_definition GENO:0000513 IAO:0000115 a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation. INFO lowercase_definition GENO:0000602 IAO:0000115 an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism. @@ -288,7 +276,6 @@ INFO lowercase_definition GENO:0000883 IAO:0000115 a quality inhering in a featu INFO lowercase_definition IAO:0000030 IAO:0000115 an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity@en INFO lowercase_definition IAO:0000136 IAO:0000115 is_about is a (currently) primitive relation that relates an information artifact to an entity. INFO lowercase_definition OBI:0000181 IAO:0000115 a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area -INFO lowercase_definition OBI:0600043 IAO:0000115 the introduction. alteration or integration of genetic material into a cell or organism INFO lowercase_definition RO:0000052 IAO:0000115 a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence INFO lowercase_definition RO:0000053 IAO:0000115 a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence INFO lowercase_definition RO:0000056 IAO:0000115 a relation between a continuant and a process, in which the continuant is somehow involved in the process From ba3a9e0f9a06e645c4a8ef9807e183f94929ac8f Mon Sep 17 00:00:00 2001 From: Matthew Brush Date: Fri, 6 Mar 2020 14:04:51 -0800 Subject: [PATCH 08/11] added four chromosomal inheritance terms per issue #50 --- src/ontology/geno-edit.owl | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/src/ontology/geno-edit.owl b/src/ontology/geno-edit.owl index dfa56ca..3aa66d1 100644 --- a/src/ontology/geno-edit.owl +++ b/src/ontology/geno-edit.owl @@ -295,6 +295,10 @@ Declaration(Class(obo:GENO_0000962)) Declaration(Class(obo:GENO_0000963)) Declaration(Class(obo:GENO_0000964)) Declaration(Class(obo:GENO_0000965)) +Declaration(Class(obo:GENO_0000969)) +Declaration(Class(obo:GENO_0000970)) +Declaration(Class(obo:GENO_0000971)) +Declaration(Class(obo:GENO_0000972)) Declaration(Class(obo:GO_0032502)) Declaration(Class(obo:HP_0000118)) Declaration(Class(obo:HsapDv_0000000)) @@ -3941,6 +3945,34 @@ AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000965 "A pair of integers represe AnnotationAssertion(rdfs:label obo:GENO_0000965 "sequence interval") SubClassOf(obo:GENO_0000965 obo:IAO_0000030) +# Class: obo:GENO_0000969 (chromosomal inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000969 "An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000969 "The Alliance of Genomic Resources") +AnnotationAssertion(rdfs:label obo:GENO_0000969 "chromosomal inheritance"@en) +SubClassOf(obo:GENO_0000969 obo:GENO_0000141) + +# Class: obo:GENO_0000970 (chromosomal deletion inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000970 "An inheritance pattern wherein the trait is determined by inheritance of missing sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000970 "Alliance of Genomic Resources") +AnnotationAssertion(rdfs:label obo:GENO_0000970 "chromosomal deletion inheritance"@en) +SubClassOf(obo:GENO_0000970 obo:GENO_0000969) + +# Class: obo:GENO_0000971 (chromosomal duplication inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000971 "An inheritance pattern wherein the trait is determined by inheritance of duplicated sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000971 "Alliance of Genomic Resources") +AnnotationAssertion(rdfs:label obo:GENO_0000971 "chromosomal duplication inheritance"@en) +SubClassOf(obo:GENO_0000971 obo:GENO_0000969) + +# Class: obo:GENO_0000972 (chromosomal rearrangement inheritance) + +AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000972 "An inheritance pattern wherein the trait is determined by inheritance of translocation or inversion of sections of one or more chromosomes, possibly together with environmental factors.") +AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000972 "Alliance of Genomic Resources") +AnnotationAssertion(rdfs:label obo:GENO_0000972 "chromosomal rearrangement inheritance"@en) +SubClassOf(obo:GENO_0000972 obo:GENO_0000969) + # Class: obo:GO_0032502 (developmental process) AnnotationAssertion(obo:IAO_0000115 obo:GO_0032502 "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete]") From 6f86a23517fe59cea3a8f011320503a0f67651fe Mon Sep 17 00:00:00 2001 From: matentzn Date: Sat, 7 Mar 2020 02:21:54 +0000 Subject: [PATCH 09/11] New release (ODK 1.2.22) --- .gitignore | 38 +- geno-base.json | 237 +- geno-base.obo | 31 +- geno-base.owl | 47 +- geno-full.json | 209 +- geno-full.obo | 30 +- geno-full.owl | 64 +- geno.json | 173 +- geno.obo | 30 +- geno.owl | 64 +- imports/obi_import.owl | 9486 ++++++++++++ imports/ro_import.owl | 308 +- reports/geno-edit.owl-obo-report.tsv | 1 - src/ontology/Makefile | 99 +- src/ontology/geno-odk.yaml | 30 + src/ontology/imports/faldo_import.owl | 14 + src/ontology/imports/faldo_terms.txt | 4 + src/ontology/imports/go_import.owl | 344 + src/ontology/imports/go_terms.txt | 2 + src/ontology/imports/hp_import.owl | 11363 ++++++++++++++ src/ontology/imports/hp_terms.txt | 4 + src/ontology/imports/hsapdv_import.owl | 143 + src/ontology/imports/hsapdv_terms.txt | 2 + src/ontology/imports/iao_import.owl | 687 +- src/ontology/imports/mp_import.owl | 12726 ++++++++++++++++ src/ontology/imports/mp_terms.txt | 4 + src/ontology/imports/ncbitaxon_import.owl | 1778 +++ src/ontology/imports/ncbitaxon_terms.txt | 2 + src/ontology/imports/oban_import.owl | 14 + src/ontology/imports/oban_terms.txt | 4 + src/ontology/imports/obi_import.owl | 9486 ++++++++++++ src/ontology/imports/obi_terms.txt | 2 + src/ontology/imports/pato_import.owl | 14 + src/ontology/imports/pato_terms.txt | 2 + src/ontology/imports/pco_import.owl | 14 + src/ontology/imports/pco_terms.txt | 4 + src/ontology/imports/ro_import.owl | 308 +- src/ontology/imports/uberon_import.owl | 14 + src/ontology/imports/uberon_terms.txt | 2 + .../reports/geno-edit.owl-obo-report.tsv | 1 - src/scripts/update_repo.sh | 22 + src/sparql/simple-seed.sparql | 2 + src/sparql/subsets-labeled.sparql | 2 +- 43 files changed, 46354 insertions(+), 1457 deletions(-) create mode 100644 imports/obi_import.owl create mode 100644 src/ontology/geno-odk.yaml create mode 100644 src/ontology/imports/faldo_import.owl create mode 100644 src/ontology/imports/faldo_terms.txt create mode 100644 src/ontology/imports/go_import.owl create mode 100644 src/ontology/imports/go_terms.txt create mode 100644 src/ontology/imports/hp_import.owl create mode 100644 src/ontology/imports/hp_terms.txt create mode 100644 src/ontology/imports/hsapdv_import.owl create mode 100644 src/ontology/imports/hsapdv_terms.txt create mode 100644 src/ontology/imports/mp_import.owl create mode 100644 src/ontology/imports/mp_terms.txt create mode 100644 src/ontology/imports/ncbitaxon_import.owl create mode 100644 src/ontology/imports/ncbitaxon_terms.txt create mode 100644 src/ontology/imports/oban_import.owl create mode 100644 src/ontology/imports/oban_terms.txt create mode 100644 src/ontology/imports/obi_import.owl create mode 100644 src/ontology/imports/obi_terms.txt create mode 100644 src/ontology/imports/pato_import.owl create mode 100644 src/ontology/imports/pato_terms.txt create mode 100644 src/ontology/imports/pco_import.owl create mode 100644 src/ontology/imports/pco_terms.txt create mode 100644 src/ontology/imports/uberon_import.owl create mode 100644 src/ontology/imports/uberon_terms.txt create mode 100644 src/scripts/update_repo.sh diff --git a/.gitignore b/.gitignore index 6af8efa..497ba37 100644 --- a/.gitignore +++ b/.gitignore @@ -1,22 +1,34 @@ .DS_Store *.tmp -src/ontology/mirror -src/ontology/mirror/* -src/ontology/geno.owl -src/ontology/geno.obo -src/ontology/geno.json +*.tmp.json +*.tmp.obo +*.tmp.owl +bin/ +semantic.cache +src/ontology/dosdp-tools.log +src/ontology/ed_definitions_merged.owl src/ontology/geno-base.* src/ontology/geno-basic.* src/ontology/geno-full.* -src/ontology/geno-simple.* src/ontology/geno-simple-non-classified.* -semantic.cache -bin/ +src/ontology/geno-simple.* +src/ontology/geno.json +src/ontology/geno.obo +src/ontology/geno.owl +src/ontology/imports/*_terms_combined.txt +src/ontology/merged-geno-edit.owl +src/ontology/mirror +src/ontology/mirror/* +src/ontology/ontologyterms.txt +src/ontology/patterns +src/ontology/patterns src/ontology/seed.txt +src/ontology/simple_seed.txt src/ontology/target/ -src/ontology/dosdp-tools.log +src/ontology/tmp/* +!src/ontology/tmp/README.md +src/patterns/all_pattern_terms.txt +src/patterns/data/**/*.ofn +src/patterns/data/**/*.txt src/patterns/imports/seed_sorted.txt -src/ontology/ed_definitions_merged.owl -src/ontology/patterns -*.tmp.obo -*.tmp.owl \ No newline at end of file +src/patterns/pattern_owl_seed.txt \ No newline at end of file diff --git a/geno-base.json b/geno-base.json index 5af9932..14b0532 100644 --- a/geno-base.json +++ b/geno-base.json @@ -2126,6 +2126,20 @@ }, "type" : "PROPERTY", "lbl" : "is_reference_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000972", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of translocation or inversion of sections of one or more chromosomes, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal rearrangement inheritance" }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "meta" : { @@ -2153,6 +2167,20 @@ }, "type" : "CLASS", "lbl" : "genomic background" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000971", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of duplicated sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal duplication inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000850", "meta" : { @@ -2163,6 +2191,20 @@ }, "type" : "CLASS", "lbl" : "P-element construct" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000970", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of missing sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal deletion inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000618", "meta" : { @@ -2602,6 +2644,20 @@ "id" : "http://purl.obolibrary.org/obo/GENO_0000606", "type" : "CLASS", "lbl" : "hemizygous insertion-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000969", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "The Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000608", "meta" : { @@ -5277,12 +5333,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a tornado" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an aggregate of human beings." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a photon" @@ -6306,10 +6362,10 @@ "val" : "a chair" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an organism" + "val" : "a molecule" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a molecule" + "val" : "an organism" } ] }, "type" : "CLASS", @@ -7318,14 +7374,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000231", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0000577", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0000830" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000818", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" + }, { + "sub" : "http://purl.obolibrary.org/obo/SO_0000577", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/SO_0000830" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000492", "pred" : "http://purl.obolibrary.org/obo/GENO_0000683", @@ -7426,6 +7482,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000970", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000969" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000780", "pred" : "is_a", @@ -7578,14 +7638,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000134", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000391" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000383", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000655" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000616", "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", "obj" : "http://purl.obolibrary.org/obo/GENO_0000618" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000383", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000655" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000408", "pred" : "subPropertyOf", @@ -7614,14 +7674,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000346", "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", "obj" : "http://purl.obolibrary.org/obo/GENO_0000513" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000680", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000501", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000512" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000680", + "pred" : "is_a", + "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000146", "pred" : "is_a", @@ -7718,6 +7778,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000873", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000874" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000969", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", "pred" : "is_a", @@ -7766,22 +7830,22 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000962", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000961" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000243", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000637", "pred" : "http://purl.obolibrary.org/obo/RO_0002525", "obj" : "http://purl.obolibrary.org/obo/SO_0000902" }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000414", + "sub" : "http://purl.obolibrary.org/obo/GENO_0000243", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000418" + "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000889", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000141" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000414", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000418" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000931", "pred" : "is_a", @@ -7846,14 +7910,14 @@ "sub" : "http://biohackathon.org/resource/faldo#end", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000708" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000968", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000053" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000714", "pred" : "http://purl.obolibrary.org/obo/GENO_0000726", "obj" : "http://purl.obolibrary.org/obo/GENO_0000481" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000968", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000053" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000633", "pred" : "is_a", @@ -7942,6 +8006,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000629", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000105" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000971", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000969" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000392", "pred" : "is_a", @@ -7970,14 +8038,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000740", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002200" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000105", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000351" }, { "sub" : "http://purl.obolibrary.org/obo/ZP_0005531", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000575" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000105", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000351" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000141", "pred" : "is_a", @@ -8166,14 +8234,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000641", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000408" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000608", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000207" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000667", "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", "obj" : "http://purl.obolibrary.org/obo/SO_0000783" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000608", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000207" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000504", "pred" : "http://purl.obolibrary.org/obo/GENO_0000231", @@ -8250,14 +8318,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000848", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000955", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000956" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000032", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000955", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000956" }, { "sub" : "http://purl.obolibrary.org/obo/PCO_0000020", "pred" : "is_a", @@ -8302,14 +8370,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000138", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000016" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000515", - "pred" : "http://purl.obolibrary.org/obo/GENO_0000382", - "obj" : "http://purl.obolibrary.org/obo/SO_0001059" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000029", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000515", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000382", + "obj" : "http://purl.obolibrary.org/obo/SO_0001059" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000847", "pred" : "subPropertyOf", @@ -8318,6 +8386,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000393", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000392" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000972", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000969" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000684", "pred" : "is_a", @@ -8331,11 +8403,11 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000870", + "sub" : "http://purl.obolibrary.org/obo/GENO_0000915", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000915", + "sub" : "http://purl.obolibrary.org/obo/GENO_0000870", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { @@ -8398,14 +8470,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000850", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000856" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000715", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000529", "pred" : "http://purl.obolibrary.org/obo/GENO_0000443", "obj" : "http://purl.obolibrary.org/obo/SO_0000704" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000715", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000920", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -8466,14 +8538,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000408", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000413" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000500", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000497" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001745", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001744" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000500", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000497" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000953", "pred" : "is_a", @@ -8754,14 +8826,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000527", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000715" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000891", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000112", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000113" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000891", + "pred" : "is_a", + "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000394", "pred" : "is_a", @@ -8794,14 +8866,14 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000244", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000244", + "pred" : "subPropertyOf", + "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000907", "pred" : "is_a", @@ -8878,14 +8950,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000534", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000791", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000790" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000008", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001483" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000791", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000790" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000086", "pred" : "is_a", @@ -9138,14 +9210,14 @@ "sub" : "http://purl.obolibrary.org/obo/SO_0000341", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000830" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000338", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000346" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000737", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000338", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000346" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000897", "pred" : "is_a", @@ -9158,22 +9230,22 @@ "sub" : "http://purl.obolibrary.org/obo/SO_0000110", "pred" : "http://purl.obolibrary.org/obo/GENO_0000239", "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002525", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000655" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000654", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000415", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" + "sub" : "http://purl.obolibrary.org/obo/RO_0002525", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000655" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000649", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000611" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000415", + "pred" : "is_a", + "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000086", "pred" : "subPropertyOf", @@ -9317,11 +9389,14 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/title", "val" : "GENO ontology" + }, { + "pred" : "http://purl.org/dc/elements/1.1/type", + "val" : "http://purl.obolibrary.org/obo/IAO_8000001" }, { "pred" : "http://purl.org/dc/terms/license", "val" : "Unspecified" } ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-10-15/geno-base.json" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2020-03-07/geno-base.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { @@ -9502,13 +9577,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000368", diff --git a/geno-base.obo b/geno-base.obo index c7b6c40..cbe9fbe 100644 --- a/geno-base.obo +++ b/geno-base.obo @@ -1,8 +1,9 @@ format-version: 1.2 -data-version: geno/releases/2019-10-15/geno-base.owl +data-version: geno/releases/2020-03-07/geno-base.owl ontology: geno/geno-base property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string +property_value: http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 xsd:string property_value: http://purl.org/dc/terms/license "Unspecified" xsd:string [Term] @@ -2097,6 +2098,34 @@ name: sequence interval def: "A pair of integers representing start and end position of a location on a sequence coordinate system." [] is_a: IAO:0000030 ! information content entity +[Term] +id: GENO:0000969 +name: chromosomal inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors." [] +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000119 "The Alliance of Genomic Resources" xsd:string + +[Term] +id: GENO:0000970 +name: chromosomal deletion inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of missing sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors." [] +is_a: GENO:0000969 ! chromosomal inheritance +property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string + +[Term] +id: GENO:0000971 +name: chromosomal duplication inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of duplicated sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors." [] +is_a: GENO:0000969 ! chromosomal inheritance +property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string + +[Term] +id: GENO:0000972 +name: chromosomal rearrangement inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of translocation or inversion of sections of one or more chromosomes, possibly together with environmental factors." [] +is_a: GENO:0000969 ! chromosomal inheritance +property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string + [Term] id: GO:0032502 name: developmental process diff --git a/geno-base.owl b/geno-base.owl index 63b4691..5b21b14 100644 --- a/geno-base.owl +++ b/geno-base.owl @@ -11,11 +11,12 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 GENO ontology + http://purl.obolibrary.org/obo/IAO_8000001 Unspecified @@ -6485,6 +6486,50 @@ As we saw for 'copy number complement', the defining sequence here is + + + + + An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors. + The Alliance of Genomic Resources + chromosomal inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by inheritance of missing sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors. + Alliance of Genomic Resources + chromosomal deletion inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by inheritance of duplicated sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors. + Alliance of Genomic Resources + chromosomal duplication inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by inheritance of translocation or inversion of sections of one or more chromosomes, possibly together with environmental factors. + Alliance of Genomic Resources + chromosomal rearrangement inheritance + + + + diff --git a/geno-full.json b/geno-full.json index 801f7ee..52c783f 100644 --- a/geno-full.json +++ b/geno-full.json @@ -1549,7 +1549,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" + "val" : "GROUP:OBI:" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" @@ -3499,6 +3499,20 @@ }, "type" : "PROPERTY", "lbl" : "is_reference_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000972", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of translocation or inversion of sections of one or more chromosomes, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal rearrangement inheritance" }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "meta" : { @@ -3526,6 +3540,20 @@ }, "type" : "CLASS", "lbl" : "genomic background" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000971", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of duplicated sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal duplication inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000850", "meta" : { @@ -3536,6 +3564,20 @@ }, "type" : "CLASS", "lbl" : "P-element construct" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000970", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of missing sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal deletion inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000618", "meta" : { @@ -4004,6 +4046,20 @@ "id" : "http://purl.obolibrary.org/obo/GENO_0000606", "type" : "CLASS", "lbl" : "hemizygous insertion-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000969", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "The Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000608", "meta" : { @@ -7223,6 +7279,23 @@ }, "type" : "CLASS", "lbl" : "aneusomic chromosomal part" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Nicolas Matentzoglu" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ontology root term" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ontology root term" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000207", "meta" : { @@ -7711,10 +7784,10 @@ "val" : "the bottom right portion of a human torso" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a molecule" + "val" : "an organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an organism" + "val" : "a molecule" } ] }, "type" : "CLASS", @@ -8683,14 +8756,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000818", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000093", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/SO_0001218" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000492", "pred" : "http://purl.obolibrary.org/obo/GENO_0000683", "obj" : "http://purl.obolibrary.org/obo/GENO_0000501" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000093", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/SO_0001218" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000035", "pred" : "is_a", @@ -8971,14 +9044,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000243", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000889", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000414", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000418" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000889", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000014", "pred" : "is_a", @@ -9023,14 +9096,14 @@ "sub" : "http://biohackathon.org/resource/faldo#end", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000708" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000714", - "pred" : "http://purl.obolibrary.org/obo/GENO_0000726", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000481" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000968", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000053" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000714", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000726", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000481" }, { "sub" : "http://biohackathon.org/resource/faldo#Position", "pred" : "is_a", @@ -9383,14 +9456,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000408", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000413" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000500", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000497" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001745", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001744" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000500", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000497" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000953", "pred" : "is_a", @@ -9607,14 +9680,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000688", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000110" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_1000012", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_1000011" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000244", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" + }, { + "sub" : "http://purl.obolibrary.org/obo/SO_1000012", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/SO_1000011" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000907", "pred" : "is_a", @@ -9824,17 +9897,13 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002200" }, { - "sub" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass", + "sub" : "http://purl.obolibrary.org/obo/GENO_0000737", "pred" : "is_a", - "obj" : "http://www.w3.org/2002/07/owl#Thing" + "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000338", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000346" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000737", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000110", "pred" : "http://purl.obolibrary.org/obo/GENO_0000239", @@ -10087,6 +10156,10 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000125", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000970", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000969" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000780", "pred" : "is_a", @@ -10192,17 +10265,13 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000655" }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000001", + "sub" : "http://purl.obolibrary.org/obo/GENO_0000777", "pred" : "is_a", - "obj" : "http://www.w3.org/2002/07/owl#Thing" + "obj" : "http://purl.obolibrary.org/obo/GENO_0000899" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000680", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000777", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000899" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000650", "pred" : "inverseOf", @@ -10235,14 +10304,14 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000016", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000014" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000344", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000343" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000057", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_10090" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000344", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000343" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000614", "pred" : "is_a", @@ -10251,18 +10320,22 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000873", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000874" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000969", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000956", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000721", - "pred" : "http://purl.obolibrary.org/obo/GENO_0000783", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000781" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0100026", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000904" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000721", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000783", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000781" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000525", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -10327,14 +10400,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000846", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000580" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000781", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000779" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001742", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001019" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000781", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000779" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000481", "pred" : "is_a", @@ -10375,6 +10448,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000411", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000971", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000969" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000823", "pred" : "is_a", @@ -10527,14 +10604,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000848", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000955", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000956" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000032", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000955", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000956" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000637", "pred" : "is_a", @@ -10579,6 +10656,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000847", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000580" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000972", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000969" }, { "sub" : "http://purl.obolibrary.org/obo/ENVO_01000254", "pred" : "is_a", @@ -10835,14 +10916,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000919", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000713" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000720", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000720", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001059", "pred" : "http://purl.obolibrary.org/obo/GENO_0000784", @@ -10887,14 +10968,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000534", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000737" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_1000008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0001483" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000791", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000790" + }, { + "sub" : "http://purl.obolibrary.org/obo/SO_1000008", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/SO_0001483" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000086", "pred" : "is_a", @@ -11138,7 +11219,7 @@ "pred" : "http://purl.org/dc/terms/license", "val" : "Unspecified" } ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-10-15/geno-full.json" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2020-03-07/geno-full.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { @@ -11319,13 +11400,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" - }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000368", diff --git a/geno-full.obo b/geno-full.obo index 2a793f6..37b050d 100644 --- a/geno-full.obo +++ b/geno-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: geno/releases/2019-10-15/geno-full.owl +data-version: geno/releases/2020-03-07/geno-full.owl ontology: geno/geno-full property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string @@ -2154,6 +2154,34 @@ name: sequence interval def: "A pair of integers representing start and end position of a location on a sequence coordinate system." [] is_a: IAO:0000030 ! information content entity +[Term] +id: GENO:0000969 +name: chromosomal inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors." [] +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000119 "The Alliance of Genomic Resources" xsd:string + +[Term] +id: GENO:0000970 +name: chromosomal deletion inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of missing sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors." [] +is_a: GENO:0000969 ! chromosomal inheritance +property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string + +[Term] +id: GENO:0000971 +name: chromosomal duplication inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of duplicated sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors." [] +is_a: GENO:0000969 ! chromosomal inheritance +property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string + +[Term] +id: GENO:0000972 +name: chromosomal rearrangement inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of translocation or inversion of sections of one or more chromosomes, possibly together with environmental factors." [] +is_a: GENO:0000969 ! chromosomal inheritance +property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string + [Term] id: GO:0032502 name: developmental process diff --git a/geno-full.owl b/geno-full.owl index efbf6af..76a3d66 100644 --- a/geno-full.owl +++ b/geno-full.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 @@ -166,7 +166,7 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober - GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note @@ -470,6 +470,17 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + + + + @@ -2662,7 +2673,6 @@ Environments include natural environments or exposures, experimentally applied c - Julius Caesar Verdi’s Requiem the Second World War @@ -7087,6 +7097,50 @@ As we saw for 'copy number complement', the defining sequence here is + + + + + An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors. + The Alliance of Genomic Resources + chromosomal inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by inheritance of missing sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors. + Alliance of Genomic Resources + chromosomal deletion inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by inheritance of duplicated sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors. + Alliance of Genomic Resources + chromosomal duplication inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by inheritance of translocation or inversion of sections of one or more chromosomes, possibly together with environmental factors. + Alliance of Genomic Resources + chromosomal rearrangement inheritance + + + + @@ -8930,9 +8984,7 @@ For a particular instance of a sequence alteration, howver, we may in some cases - - - + diff --git a/geno.json b/geno.json index 775a29a..17c0383 100644 --- a/geno.json +++ b/geno.json @@ -1549,7 +1549,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" + "val" : "GROUP:OBI:" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" @@ -3499,6 +3499,20 @@ }, "type" : "PROPERTY", "lbl" : "is_reference_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000972", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of translocation or inversion of sections of one or more chromosomes, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal rearrangement inheritance" }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "meta" : { @@ -3526,6 +3540,20 @@ }, "type" : "CLASS", "lbl" : "genomic background" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000971", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of duplicated sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal duplication inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000850", "meta" : { @@ -3536,6 +3564,20 @@ }, "type" : "CLASS", "lbl" : "P-element construct" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000970", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of missing sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal deletion inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000618", "meta" : { @@ -4004,6 +4046,20 @@ "id" : "http://purl.obolibrary.org/obo/GENO_0000606", "type" : "CLASS", "lbl" : "hemizygous insertion-linked" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000969", + "meta" : { + "definition" : { + "val" : "An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "The Alliance of Genomic Resources" + } ] + }, + "type" : "CLASS", + "lbl" : "chromosomal inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000608", "meta" : { @@ -7223,6 +7279,23 @@ }, "type" : "CLASS", "lbl" : "aneusomic chromosomal part" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Nicolas Matentzoglu" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has ontology root term" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has ontology root term" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000207", "meta" : { @@ -8583,14 +8656,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000713", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000623", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000619" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000926", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000623", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000619" }, { "sub" : "http://purl.obolibrary.org/obo/UPHENO_0001001", "pred" : "is_a", @@ -8683,14 +8756,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000818", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000093", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/SO_0001218" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000492", "pred" : "http://purl.obolibrary.org/obo/GENO_0000683", "obj" : "http://purl.obolibrary.org/obo/GENO_0000501" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000093", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/SO_0001218" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000035", "pred" : "is_a", @@ -9179,14 +9252,14 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000036", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000121", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0000121", + "pred" : "type", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000626", "pred" : "subPropertyOf", @@ -9823,10 +9896,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000743", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002200" - }, { - "sub" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass", - "pred" : "is_a", - "obj" : "http://www.w3.org/2002/07/owl#Thing" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000338", "pred" : "is_a", @@ -10087,6 +10156,10 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000125", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000970", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000969" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000780", "pred" : "is_a", @@ -10191,10 +10264,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000383", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000655" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000001", - "pred" : "is_a", - "obj" : "http://www.w3.org/2002/07/owl#Thing" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000680", "pred" : "is_a", @@ -10235,14 +10304,14 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000016", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000014" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000344", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000343" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000057", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_10090" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000344", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000343" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000614", "pred" : "is_a", @@ -10251,6 +10320,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000873", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000874" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000969", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000956", "pred" : "is_a", @@ -10327,14 +10400,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000846", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000580" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0001742", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0001019" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000781", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000779" + }, { + "sub" : "http://purl.obolibrary.org/obo/SO_0001742", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/SO_0001019" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000481", "pred" : "is_a", @@ -10375,6 +10448,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000411", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000971", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000969" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000823", "pred" : "is_a", @@ -10527,14 +10604,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000848", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_1000032", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0001059" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000955", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000956" + }, { + "sub" : "http://purl.obolibrary.org/obo/SO_1000032", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/SO_0001059" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000637", "pred" : "is_a", @@ -10579,6 +10656,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000847", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000580" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000972", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000969" }, { "sub" : "http://purl.obolibrary.org/obo/ENVO_01000254", "pred" : "is_a", @@ -10835,14 +10916,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000919", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000713" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000720", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001059", "pred" : "http://purl.obolibrary.org/obo/GENO_0000784", @@ -10979,14 +11060,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000784", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000683" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000036", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000512" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000017", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000036", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000512" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000165", "pred" : "is_a", @@ -11138,7 +11219,7 @@ "pred" : "http://purl.org/dc/terms/license", "val" : "Unspecified" } ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2019-10-15" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2020-03-07/geno.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { @@ -11319,13 +11400,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" - }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000368", diff --git a/geno.obo b/geno.obo index 06fb48a..3b47a98 100644 --- a/geno.obo +++ b/geno.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2019-10-15 +data-version: releases/2020-03-07 ontology: geno property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string @@ -2154,6 +2154,34 @@ name: sequence interval def: "A pair of integers representing start and end position of a location on a sequence coordinate system." [] is_a: IAO:0000030 ! information content entity +[Term] +id: GENO:0000969 +name: chromosomal inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors." [] +is_a: GENO:0000141 ! inheritance pattern +property_value: IAO:0000119 "The Alliance of Genomic Resources" xsd:string + +[Term] +id: GENO:0000970 +name: chromosomal deletion inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of missing sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors." [] +is_a: GENO:0000969 ! chromosomal inheritance +property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string + +[Term] +id: GENO:0000971 +name: chromosomal duplication inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of duplicated sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors." [] +is_a: GENO:0000969 ! chromosomal inheritance +property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string + +[Term] +id: GENO:0000972 +name: chromosomal rearrangement inheritance +def: "An inheritance pattern wherein the trait is determined by inheritance of translocation or inversion of sections of one or more chromosomes, possibly together with environmental factors." [] +is_a: GENO:0000969 ! chromosomal inheritance +property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string + [Term] id: GO:0032502 name: developmental process diff --git a/geno.owl b/geno.owl index cc5e55d..8064b49 100644 --- a/geno.owl +++ b/geno.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 @@ -166,7 +166,7 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober - GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note @@ -470,6 +470,17 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + + + + @@ -2662,7 +2673,6 @@ Environments include natural environments or exposures, experimentally applied c - Julius Caesar Verdi’s Requiem the Second World War @@ -7087,6 +7097,50 @@ As we saw for 'copy number complement', the defining sequence here is + + + + + An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors. + The Alliance of Genomic Resources + chromosomal inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by inheritance of missing sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors. + Alliance of Genomic Resources + chromosomal deletion inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by inheritance of duplicated sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors. + Alliance of Genomic Resources + chromosomal duplication inheritance + + + + + + + + + An inheritance pattern wherein the trait is determined by inheritance of translocation or inversion of sections of one or more chromosomes, possibly together with environmental factors. + Alliance of Genomic Resources + chromosomal rearrangement inheritance + + + + @@ -8930,9 +8984,7 @@ For a particular instance of a sequence alteration, howver, we may in some cases - - - + diff --git a/imports/obi_import.owl b/imports/obi_import.owl new file mode 100644 index 0000000..26bc5d0 --- /dev/null +++ b/imports/obi_import.owl @@ -0,0 +1,9486 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + + + + + + + example + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + + + + + + + + definition + definition + textual definition + + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + textual definition + + + + + + + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + + editor note + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + alternative term + + + + + + + + definition source + + formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + + + + + + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + imported from + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + + elucidation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Description may include but is not limited to: an abstract, + table of contents, reference to a graphical representation + of content or a free-text account of the content. + An account of the content of the resource. + + Description + Description + + + + + + + + + + + + + + + Typically, a Title will be a name by which the resource is + formally known. + + A name given to the resource. + + Title + Title + + + + + + + + Mark Miller + 2018-05-11T13:47:29Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + has part + + + + + + + + + + + + + + + + realized in + this disease is realized in this disease course + this fragility is realized in this shattering + this investigator role is realized in this investigation + is realized by + realized_in + [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + + + + + + + + + + + + + + + realizes + this disease course realizes this disease + this investigation realizes this investigator role + this shattering realizes this fragility + to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + + + + + + + + + This document is about information artifacts and their representations + + is_about is a (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + + + A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. + denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically + 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. +g denotes r =def +r is a portion of reality +there is some c that is a concretization of g +every c that is a concretization of g specifically denotes r + person:Alan Ruttenberg + Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan + + denotes + + + + + + + + + + + + + + + + has_specified_input + has_specified_input + see is_input_of example_of_usage + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot + + has_specified_input + + + + + + + + + + + + + + + is_specified_input_of + some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters + is_specified_input_of + + + + + + + + + + + + + + + + has_specified_output + has_specified_output + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot + + has_specified_output + + + + + + + + + + + + + + + is_specified_output_of + is_specified_output_of + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters + + is_specified_output_of + + + + + + + + + + + achieves_planned_objective + A cell sorting process achieves the objective specification 'material separation objective' + + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. + BP, AR, PPPB branch + PPPB branch derived + modified according to email thread from 1/23/09 in accordince with DT and PPPB branch + achieves_planned_objective + + + + + + + + + has grain + + the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. + Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form + PERSON: Alan Ruttenberg + PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 + has grain + + + + + + + + + + objective_achieved_by + + This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. + OBI + OBI + objective_achieved_by + + + + + + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + + + + + + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as + + + + + + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + quality of + + + + + + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + role of + + + + + + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + + + + + + disposition of + + + + + + + + + + + + + + + + + derives from + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + + derives from + + + + + + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + derives into + + + + + + + + + + move to BFO? + Allen + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporal relation + + + + + + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + + + + + + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + continuant + Continuant + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + + + + + occurrent + Occurrent + An entity that has temporal parts and that happens, unfolds or develops through time. + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + + + + + + + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process + + + + + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + + + + + + + + + + disposition + Disposition + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocytosis and exocytosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + disposition + + + + + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + + + + + + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + + + + + + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + + + + + + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + + + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + + + + + + + + + quality + Quality + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + quality + + + + + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + + + + + + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + + + + + + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + + + + + + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] + + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + + + + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + + + + + + + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant + + + + + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + + + + + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + + + + + molecular entity + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. + We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well + + molecular entity + + + + + + + + + nucleic acid + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + + nucleic acid + + + + + + + + + macromolecule + A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. + polymer + + macromolecule + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell line cell + A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture + A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture + + + cell line cell + + + + + + + + + + + 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. + + + + + + + + + + + + + + + + + + + + + cell line + A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). + A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). + + + cell line + + + + + + + + + cell + cell + PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + + cell + cell + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + primary cultured cell + A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. + + primary cultured cell + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured cell + A cell in vitro that is or has been maintained or propagated as part of a cell culture. + + cultured cell + + + + + + + + + B cell + A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. + + B cell + + + + + + + + + lymphocyte + A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. + + lymphocyte + + + + + + + + + + + + + + + + experimentally modified cell in vitro + A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. + + experimentally modified cell in vitro + + + + + + + + + mononuclear cell + A leukocyte with a single non-segmented nucleus in the mature form. + + mononuclear cell + + + + + + + + + + biological_process + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + + biological_process + + + + + + + + + measurement unit label + Examples of measurement unit labels are liters, inches, weight per volume. + + A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. + 2009-03-16: provenance: a term measurement unit was +proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and +Cristian Cocos, and subsequently moved to IAO where the objective for +which the original term was defined was satisfied with the definition +of this, different, term. + 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + measurement unit label + + + + + + + + + objective specification + In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. + + a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. + 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." + 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. + Answers the question, why did you do this experiment? + PERSON: Alan Ruttenberg + PERSON: Barry Smith + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + goal specification + OBI Plan and Planned Process/Roles Branch + OBI_0000217 + objective specification + + + + + + + + + Pour the contents of flask 1 into flask 2 + + a directive information entity that describes an action the bearer will take + Alan Ruttenberg + OBI Plan and Planned Process branch + action specification + + + + + + + + + datum label + + A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label + http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n + GROUP: IAO + 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. + + datum label + + + + + + + + + software + + Software is a plan specification composed of a series of instructions that can be +interpreted by or directly executed by a processing unit. + see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert + PERSON: Melanie Courtot + GROUP: OBI + software + + + + + + + + + + + + + + + + + + + + information carrier + In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. + + A quality of an information bearer that imparts the information content + 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. + 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. + PERSON: Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + information carrier + + + + + + + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item + + + + + + + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + A generically dependent continuant that is about some thing. + 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + + + + + + + + + + + + + + + + An information content entity whose concretizations indicate to their bearer how to realize them in a process. + 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. + 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO + Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + directive information entity + + + + + + + + + dot plot + Dot plot of SSC-H and FSC-H. + + A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000123 + group:OBI + dot plot + + + + + + + + + graph + + A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. + PERSON: Lawrence Hunter + person:Alan Ruttenberg + person:Allyson Lister + OBI_0000240 + group:OBI + graph + + + + + + + + + algorithm + PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. + + A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. + Philippe Rocca-Serra + PlanAndPlannedProcess Branch + OBI_0000270 + adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) + algorithm + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data format specification + + A data format specification is the information content borne by the document published defining the specification. +Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file + 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes +information. Example: The ISO document specifying what encompasses an +XML document; The instructions in a XSD file" + PERSON: Alan Ruttenberg + PlanAndPlannedProcess Branch + OBI branch derived + OBI_0000187 + data format specification + + + + + + + + + data set + Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). + + A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. + 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type + 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000042 + group:OBI + data set + + + + + + + + + image + + An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. + person:Alan Ruttenberg + person:Allyson + person:Chris Stoeckert + OBI_0000030 + group:OBI + image + + + + + + + + + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part + + + + + + + + + + + + + + + + + + + + + plan specification + PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. + + A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. + 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2014-03-31: A plan specification can have other parts, such as conditional specifications. + Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved + Alan Ruttenberg + OBI Plan and Planned Process branch + OBI_0000344 + 2/3/2009 Comment from OBI review. + +Action specification not well enough specified. +Conditional specification not well enough specified. +Question whether all plan specifications have objective specifications. + +Request that IAO either clarify these or change definitions not to use them + plan specification + + + + + + + + + + + + + + + + + + + + + + + + + material information bearer + A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. + a brain + a hard drive + + A material entity in which a concretization of an information content entity inheres. + GROUP: IAO + material information bearer + + + + + + + + + histogram + + A histogram is a report graph which is a statistical description of a +distribution in terms of occurrence frequencies of different event classes. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + GROUP:OBI + histogram + + + + + + + + + heatmap + + A heatmap is a report graph which is a graphical representation of data +where the values taken by a variable(s) are shown as colors in a +two-dimensional map. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + GROUP:OBI + heatmap + + + + + + + + + dendrogram + Dendrograms are often used in computational biology to +illustrate the clustering of genes. + + A dendrogram is a report graph which is a tree diagram +frequently used to illustrate the arrangement of the clusters produced by a +clustering algorithm. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + WEB: http://en.wikipedia.org/wiki/Dendrogram + dendrogram + + + + + + + + + scatter plot + Comparison of gene expression values in two samples can be displayed in a scatter plot + + A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + scattergraph + WEB: http://en.wikipedia.org/wiki/Scatterplot + scatter plot + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification + + + + + + + + + figure + Any picture, diagram or table + + An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. + PERSON: Lawrence Hunter + figure + + + + + + + + + diagram + A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. + + A figure that expresses one or more propositions + PERSON: Lawrence Hunter + diagram + + + + + + + + + document + A journal article, patent application, laboratory notebook, or a book + + A collection of information content entities intended to be understood together as a whole + PERSON: Lawrence Hunter + document + + + + + + + + + + + + + + + + + + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + + + + + + + Mus musculus + house mouse + mouse + + Mus musculus + + + + + + + + + Viruses + + Viruses + + + + + + + + + Euteleostomi + bony vertebrates + + Euteleostomi + + + + + + + + + Bacteria + eubacteria + + Bacteria + + + + + + + + + Archaea + + Archaea + + + + + + + + + Eukaryota + eucaryotes + eukaryotes + + Eukaryota + + + + + + + + + Euarchontoglires + + Euarchontoglires + + + + + + + + + Tetrapoda + tetrapods + + Tetrapoda + + + + + + + + + Amniota + amniotes + + Amniota + + + + + + + + + Opisthokonta + + Opisthokonta + + + + + + + + + Bilateria + + Bilateria + + + + + + + + + Murinae + + Murinae + + + + + + + + + Mammalia + mammals + + Mammalia + + + + + + + + + Vertebrata <Metazoa> + Vertebrata + vertebrates + + Vertebrata <Metazoa> + + + + + + + + + Danio rerio + leopard danio + zebra danio + zebra fish + zebrafish + + Danio rerio + + + + + + + + + Homo sapiens + human + human being + man + + Homo sapiens + + + + + + + + + Rodentia + rodent + + Rodentia + + + + + + + + + + + + + + + + + + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy + + A processual entity that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + planned process + + + + + + + + + regulator role + Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 + + a regulatory role involved with making and/or enforcing relevant legislation and governmental orders + Person:Jennifer Fostel + regulator + OBI + regulator role + + + + + + + + + regulatory role + Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 + + a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. + GROUP: Role branch + OBI, CDISC + govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent + regulatory role + + + + + + + + + material supplier role + Jackson Labs is an organization which provide mice as experimental material + + a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. + Supplier role is a special kind of service, e.g. biobank + PERSON:Jennifer Fostel + material provider role + supplier + material supplier role + + + + + + + + + + + + + + + classified data set + + A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. + PERSON: James Malone + PERSON: Monnie McGee + data set with assigned class labels + classified data set + + + + + + + + + + + + + + + + + + + + processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + Is a material entity that is created or changed during material processing. + PERSON: Alan Ruttenberg + processed material + + + + + + + + + culture medium + A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 + + a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. + changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 +Modification made by JZ. + Person: Jennifer Fostel, Jie Zheng + OBI + culture medium + + + + + + + + + reagent role + Buffer, dye, a catalyst, a solvating agent. + + A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. + PERSON:Matthew Brush + reagent + PERSON:Matthew Brush + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + +May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. + + (copied from ReO) +Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. + +Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. + +In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). + reagent role + + + + + + + + + + + + + + + + + + + + + + + + + + + material processing + A cell lysis, production of a cloning vector, creating a buffer. + + A planned process which results in physical changes in a specified input material + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca Serra + material transformation + OBI branch derived + material processing + + + + + + + + + + + + + + + + + + + + + + + + + specimen role + liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. + + a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + blood taken from animal: animal continues in study, whereas blood has role specimen. +something taken from study subject, leaves the study and becomes the specimen. + parasite example +- when parasite in people we study people, people are subjects and parasites are specimen +- when parasite extracted, they become subject in the following study +specimen can later be subject. + GROUP: Role Branch + OBI + specimen role + + + + + + + + + population + PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. + + a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area + 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: +http://code.google.com/p/popcomm-ontology/ + PERSON: Philippe Rocca-Serra + adapted from Oxford English Dictionnary + rem1: collection somehow always involve a selection process + population + + + + + + + + + organization + PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. + + An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. + BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: + +1) there are organization_member_roles (president, treasurer, branch +editor), with individual persons as bearers + +2) there are organization_roles (employer, owner, vendor, patent holder) + +3) an organization has a charter / rules / bylaws, which specify what roles +there are, how they should be realized, and how to modify the +charter/rules/bylaws themselves. + +It is debatable what the organization itself is (some kind of dependent +continuant or an aggregate of people). This also determines who/what the +bearer of organization_roles' are. My personal favorite is still to define +organization as a kind of 'legal entity', but thinking it through leads to +all kinds of questions that are clearly outside the scope of OBI. + +Interestingly enough, it does not seem to matter much where we place +organization itself, as long as we can subclass it (University, Corporation, +Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, +W3C, University of Oklahoma), and have it play roles. + +This leads to my proposal: We define organization through the statements 1 - +3 above, but without an 'is a' statement for now. We can leave it in its +current place in the is_a hierarchy (material entity) or move it up to +'continuant'. We leave further clarifications to BFO, and close this issue +for now. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra + PERSON: Susanna Sansone + GROUP: OBI + organization + + + + + + + + + + + + + + + + + + + + regulatory agency + The US Environmental Protection Agency + + A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. + GROUP: OBI Biomaterial Branch + WEB: en.wikipedia.org/wiki/Regulator + regulatory agency + + + + + + + + + material transformation objective + The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. + + an objective specifiction that creates an specific output object from input materials. + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + artifact creation objective + GROUP: OBI PlanAndPlannedProcess Branch + material transformation objective + + + + + + + + + + + + + + + + + + + + + + + + + + + manufacturing + + Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process + Manufacturing implies reproducibility and responsibility AR + This includes a single scientist making a processed material for personal use. + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + GROUP: OBI PlanAndPlannedProcess Branch + manufacturing + + + + + + + + + manufacturing objective + + is the objective to manufacture a material of a certain function (device) + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + GROUP: OBI PlanAndPlannedProcess Branch + manufacturing objective + + + + + + + + + + + + + + + + + + + + + + + + + + + + manufacturer role + With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. + + Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. + GROUP: Role Branch + OBI + manufacturer role + + + + + + + + + + + + + + + + + material separation objective + The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. + + is an objective to transform a material entity into spatially separated components. + PPPB branch + PPPB branch + material separation objective + + + + + + + + + + + + + + + clustered data set + A clustered data set is the output of a K means clustering data transformation + + A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. + PERSON: James Malone + PERSON: Monnie McGee + data set with assigned discovered class labels + AR thinks could be a data item instead + clustered data set + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + specimen collection process + drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation + + A planned process with the objective of collecting a specimen. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. + Philly2013: The specimen_role for the specimen is created during the specimen collection process. + label changed to 'specimen collection process' on 10/27/2014, details see tracker: +http://sourceforge.net/p/obi/obi-terms/716/ + Bjoern Peters + specimen collection + 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession + 6/9/09: used at workshop + specimen collection process + + + + + + + + + + + + + + + + + + + + + + + class prediction data transformation + + A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. + James Malone + supervised classification data transformation + PERSON: James Malone + class prediction data transformation + + + + + + + + + + portioning objective + The objective to obtain multiple aliquots of an enzyme preparation. + + A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. + portioning objective + + + + + + + + + separation into different composition objective + The objective to obtain cells contained in a sample of blood. + + A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). + We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives + separation into different composition objective + + + + + + + + + specimen collection objective + The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. + + A objective specification to obtain a material entity for potential use as an input during an investigation. + Bjoern Peters + Bjoern Peters + specimen collection objective + + + + + + + + + + + + + + + support vector machine + + A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. + James Malone + Ryan Brinkman + SVM + PERSON: Ryan Brinkman + support vector machine + + + + + + + + + decision tree induction objective + + A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. + James Malone + decision tree induction objective + + + + + + + + + + + + + + + decision tree building data transformation + + A decision tree building data transformation is a data transformation that has objective decision tree induction. + James Malone + PERSON: James Malone + decision tree building data transformation + + + + + + + + + GenePattern software + + a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. + James Malone + Person:Helen Parkinson + WEB: http://www.broadinstitute.org/cancer/software/genepattern/ + GenePattern software + + + + + + + + + peak matching + + Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold + James Malone + Ryan Brinkman + PERSON: Ryan Brinkman + peak matching + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k-nearest neighbors + + A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. + James Malone + k-NN + PERSON: James Malone + k-nearest neighbors + + + + + + + + + + + + + + + CART + + A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. + James Malone + classification and regression trees + BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. + CART + + + + + + + + + + + + + + + statistical model validation + Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia + + A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. + Helen Parkinson + http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 + statistical model validation + + + + + + + + + material maintenance objective + + An objective specification maintains some or all of the qualities of a material over time. + PERSON: Bjoern Peters + PERSON: Bjoern Peters + material maintenance objective + + + + + + + + + + + + + + + + + + + + + + + + + manufacturer + + A person or organization that has a manufacturer role + manufacturer + + + + + + + + + + + + + + + material maintenance + + a process with that achieves the objective to maintain some or all of the characteristics of an input material over time + material maintenance + + + + + + + + + + + + + + + + + + + + + + + + + + + + service provider role + Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. + + is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person + PERSON:Helen Parkinson + service provider role + + + + + + + + + + + + + + + + + + processed specimen + A tissue sample that has been sliced and stained for a histology study. +A blood specimen that has been centrifuged to obtain the white blood cells. + + A specimen that has been intentionally physically modified. + Bjoern Peters + Bjoern Peters + A tissue sample that has been sliced and stained for a histology study. + processed specimen + + + + + + + + + categorical label + The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. + + A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. + Bjoern Peters + Bjoern Peters + categorical label + + + + + + + + + questionnaire + + A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. + JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. +JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. + Need to clarify if this is a document or a directive information entity (or what their connection is)) + PERSON: Jessica Turner + Merriam-Webster + questionnaire + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + secondary cultured cell + + A cultured cell that has been passaged or derives from a cell that has been passaged in culture. + The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. + Person: Matthew Brush + PERSON: Matthew Brush + A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. + secondary cultured cell + + + + + + + + + + + + + + + establishing cell line + + a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). + 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. + Person: Matthew Brush + PERSON:Matthew Brush + establishing cell line + + + + + + + + + + + + + + + + + + + + + + + + + + reagent + + A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. + 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device. + PERSON:Matthew Brush + PERSON:Matthew Brush + (copied from ReO) +Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. + +Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. + +In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). + reagent + + + + + + + + + + + + + + + + + + + + + + + + + + + secondary cultured cell population + + A cultured cell population that is derived through one or more passages in culture. + The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. + PERSON:Matthew Brush + secondary cell culture sample + PERSON:Matthew Brush + The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally. + secondary cultured cell population + + + + + + + + + cell freezing medium + + A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. + PERSON: Matthew Brush + cell freezing medium + + + + + + + + + categorical value specification + + A value specification that is specifies one category out of a fixed number of nominal categories + PERSON:Bjoern Peters + categorical value specification + + + + + + + + + value specification + The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. + + An information content entity that specifies a value within a classification scheme or on a quantitative scale. + This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. + PERSON:Bjoern Peters + value specification + + + + + + + + + + + + + + + + + + + + collection of specimens + Blood cells collected from multiple donors over the course of a study. + + A material entity that has two or more specimens as its parts. + Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ + Person: Chris Stoeckert, Jie Zheng + OBIB, OBI + Biobank + collection of specimens + + + + + + + + + histologic grade according to AJCC 7th edition + G4: Undifferentiated + G1:Well differentiated + + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade according to AJCC 7th edition + + + + + + + + + histologic grade according to the Fuhrman Nuclear Grading System + + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. + Chris Stoeckert, Helena Ellis + Histologic Grade (Fuhrman Nuclear Grading System) + NCI BBRB, OBI + NCI BBRB + histologic grade according to the Fuhrman Nuclear Grading System + + + + + + + + + histologic grade for ovarian tumor + + A categorical value specification that is a histologic grade assigned to a ovarian tumor. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade for ovarian tumor + + + + + + + + + histologic grade for ovarian tumor according to a two-tier grading system + + A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade for ovarian tumor according to a two-tier grading system + + + + + + + + + histologic grade for ovarian tumor according to the World Health Organization + + A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade for ovarian tumor according to the World Health Organization + + + + + + + + + pathologic primary tumor stage for colon and rectum according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for colon and rectum according to AJCC 7th edition + + + + + + + + + pathologic primary tumor stage for lung according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread lung primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for lung according to AJCC 7th edition + + + + + + + + + pathologic primary tumor stage for kidney according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for kidney according to AJCC 7th edition + + + + + + + + + pathologic primary tumor stage for ovary according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for ovary according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for colon and rectum according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for colon and rectum according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for lung according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for lung according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for kidney according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for kidney according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for ovary according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for ovary according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for colon according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: colon distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for colon according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for lung according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: lung distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for lung according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for kidney according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: kidney distant Metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for kidney according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for ovary according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: ovarian distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for ovary according to AJCC 7th edition + + + + + + + + + clinical tumor stage group according to AJCC 7th edition + + A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. + Chris Stoeckert, Helena Ellis + Clinical tumor stage group (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + clinical tumor stage group according to AJCC 7th edition + + + + + + + + + International Federation of Gynecology and Obstetrics cervical cancer stage value specification + + A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. + Chris Stoeckert, Helena Ellis + Clinical FIGO stage + NCI BBRB, OBI + NCI BBRB + International Federation of Gynecology and Obstetrics cervical cancer stage value specification + + + + + + + + + International Federation of Gynecology and Obstetrics ovarian cancer stage value specification + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. + Chris Stoeckert, Helena Ellis + Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) + NCI BBRB, OBI + NCI BBRB + International Federation of Gynecology and Obstetrics ovarian cancer stage value specification + + + + + + + + + performance status value specification + + A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). + Chris Stoeckert, Helena Ellis + Performance Status Scale + https://en.wikipedia.org/wiki/Performance_status + NCI BBRB + performance status value specification + + + + + + + + + Eastern Cooperative Oncology Group score value specification + + A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. + Chris Stoeckert, Helena Ellis + ECOG score + NCI BBRB, OBI + NCI BBRB + Eastern Cooperative Oncology Group score value specification + + + + + + + + + Karnofsky score vaue specification + + A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. + Chris Stoeckert, Helena Ellis + Karnofsky Score + NCI BBRB, OBI + NCI BBRB + Karnofsky score vaue specification + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Epstein Barr virus transformed B cell + PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. + + A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity + PERSON: Susanna Sansone + GROUP: OBI Biomaterial Branch + Epstein Barr virus transformed B cell + + + + + + + + + + + + + + + + + + + organism + animal + fungus + plant + virus + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI. + GROUP: OBI Biomaterial Branch + WEB: http://en.wikipedia.org/wiki/Organism + organism + + + + + + + + + + + + + + + + + + + + specimen + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + + A material entity that has the specimen role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + PERSON: James Malone + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch + specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured cell population + A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). + +A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). + + A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. + 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. + PERSON:Matthew Brush + cell culture sample + PERSON:Matthew Brush + The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. + cultured cell population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + data transformation + The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. + + A planned process that produces output data from input data. + Elisabetta Manduchi + Helen Parkinson + James Malone + Melanie Courtot + Philippe Rocca-Serra + Richard Scheuermann + Ryan Brinkman + Tina Hernandez-Boussard + data analysis + data processing + Branch editors + data transformation + + + + + + + + + + + + + + + leave one out cross validation method + The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 + + is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data + 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 + Person:Helen Parkinson + leave one out cross validation method + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k-means clustering + + A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). + Elisabetta Manduchi + James Malone + Philippe Rocca-Serra + WEB: http://en.wikipedia.org/wiki/K-means + k-means clustering + + + + + + + + + + + + + + + + + + + + + + + hierarchical clustering + + A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). + James Malone + WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering + hierarchical clustering + + + + + + + + + + + + + + + + + + + + + + + dimensionality reduction + + A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. + Elisabetta Manduchi + James Malone + Melanie Courtot + Philippe Rocca-Serra + data projection + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + dimensionality reduction + + + + + + + + + principal components analysis dimensionality reduction + + A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. + Elisabetta Manduchi + James Malone + Melanie Courtot + Philippe Rocca-Serra + pca data reduction + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + principal components analysis dimensionality reduction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + data visualization + Generation of a heatmap from a microarray dataset + + An planned process that creates images, diagrams or animations from the input data. + Elisabetta Manduchi + James Malone + Melanie Courtot + Tina Boussard + data encoding as image + visualization + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + PERSON: Tina Boussard + Possible future hierarchy might include this: +information_encoding +>data_encoding +>>image_encoding + data visualization + + + + + + + + + data transformation objective + normalize objective + + An objective specification to transformation input data into output data + Modified definition in 2013 Philly OBI workshop + James Malone + PERSON: James Malone + data transformation objective + + + + + + + + + + + + + + + partitioning data transformation + + A partitioning data transformation is a data transformation that has objective partitioning. + James Malone + PERSON: James Malone + partitioning data transformation + + + + + + + + + partitioning objective + A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. + + A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. + Elisabetta Manduchi + James Malone + PERSON: Elisabetta Manduchi + partitioning objective + + + + + + + + + + + + + + + + + + + + + + + class discovery data transformation + + A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. + James Malone + clustering data transformation + unsupervised classification data transformation + PERSON: James Malone + class discovery data transformation + + + + + + + + + class discovery objective + + A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. + James Malone + clustering objective + discriminant analysis objective + unsupervised classification objective + PERSON: Elisabetta Manduchi + PERSON: James Malone + class discovery objective + + + + + + + + + class prediction objective + + A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and +class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. + James Malone + classification objective + supervised classification objective + PERSON: Elisabetta Manduchi + PERSON: James Malone + class prediction objective + + + + + + + + + cross validation objective + + A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. + James Malone + rotation estimation objective + WEB: http://en.wikipedia.org/wiki/Cross_validation + cross validation objective + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + clustered data visualization + + A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. + James Malone + clustered data visualization + + + + + + + + + + + + + + + + + + + + + + + + + + + material component separation + Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification + + a material processing in which components of an input material become segregated in space + Bjoern Peters + IEDB + material component separation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + maintaining cell culture + When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture + + a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing + PlanAndPlannedProcess Branch + OBI branch derived + maintaining cell culture + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'establishing cell culture' + + a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). + PERSON:Matthew Brush + PERSON:Matthew Brush + A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. + establishing cell culture + + + + + + + + + + + + + + + + + + + + + + + + + + + cell culture splitting + The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. + + The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing + PlanAndPlannedProcess Branch + cell culture passaging + OBI branch derived + An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone. + cell culture splitting + + + + + + + + + biological sex + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. + + biological sex + + + + + + + + + behavioral quality + An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. + + behavioral quality + + + + + + + + + female + A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. + + female + + + + + + + + + male + A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. + + male + + + + + + + + + physical object quality + A quality which inheres in a continuant. + + physical object quality + + + + + + + + + phenotypic sex + An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. + + phenotypic sex + + + + + + + + + organismal quality + A quality that inheres in an entire organism or part of an organism. + + organismal quality + + + + + + + + + handedness + A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. + + handedness + + + + + + + + + left handedness + Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. + + left handedness + + + + + + + + + right handedness + Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. + + right handedness + + + + + + + + + ambidextrous handedness + Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. + + ambidextrous handedness + + + + + + + + + region + A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. + primary structure of sequence macromolecule + sequence + + region + + + + + + + + + contig + A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. + + contig + + + + + + + + + sequence_assembly + A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. + + sequence_assembly + + + + + + + + + assembly + A region of the genome of known length that is composed by ordering and aligning two or more different regions. + + assembly + + + + + + + + + experimental_feature + A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. + + experimental_feature + + + + + + + + + life cycle stage + A spatiotemporal region encompassing some part of the life cycle of an organism. + + life cycle stage + + + + + + + + + length unit + A unit which is a standard measure of the distance between two points. + + length unit + + + + + + + + + mass unit + A unit which is a standard measure of the amount of matter/energy of a physical object. + + mass unit + + + + + + + + + time unit + A unit which is a standard measure of the dimension in which events occur in sequence. + + time unit + + + + + + + + + temperature unit + A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. + + temperature unit + + + + + + + + + substance unit + A unit which is a standardised quantity of an element or compound with uniform composition. + + substance unit + + + + + + + + + concentration unit + A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. + + concentration unit + + + + + + + + + volume unit + A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. + + volume unit + + + + + + + + + frequency unit + A unit which is a standard measure of the number of repetitive actions in a particular time. + + frequency unit + + + + + + + + + volumetric flow rate unit + A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . + + volumetric flow rate unit + + + + + + + + + rate unit + A unit which represents a standard measurement occurrence of a process per unit time. + + rate unit + + + + + + + + Obsolete Class + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + PERSON:Alan Ruttenberg + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + core + + + + + + + + + placeholder removed + + + + + + + + + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + + This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. + We expect to be able to mine these new reasons and add instances as required. + other + true + + + + + + + + + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + Transformation-ML + Transformation-ML file describing parameter transformations used in a GvHD experiment. + + Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) + person:Jennifer Fostel + web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf + Transformation-ML + + + + + + + + + ACS + d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment. + + ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) + person:Jennifer Fostel + web-page:http://www.isac-net.org/content/view/607/150/ + ACS + + + + + + + + + XML + RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document + + XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) + person:Jennifer Fostel + web-page:http://www.w3.org/XML/ + XML + + + + + + + + + RDF + A FOAF file, a SKOS file, an OWL file. + + RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) + person:Jennifer Fostel + web-page:http://www.w3.org/RDF/ + RDF + + + + + + + + + zip + MagicDraw MDZIP archive, Java JAR file. + + zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) + person:Jennifer Fostel + web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ + zip + + + + + + + + + tar + Example.tar file. + + tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) + person:Jennifer Fostel + web-page:http://www.gnu.org/software/tar/manual/ + tar + + + + + + + + + FCS + d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment. + + FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) + person:Jennifer Fostel + web-page:http://www.fcspress.com/ + FCS + + + + + + + + + Compensation-ML + compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment + + Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) + person:Jennifer Fostel + web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf + Compensation-ML + + + + + + + + + Gating-ML + foogate.xml, Gating-ML file describing gates used in a GvHD experiment. + + Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) + person:Jennifer Fostel + web-page:http://www.flowcyt.org/gating/ + Gating-ML + + + + + + + + + OWL + OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file. + + OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) + person:Jennifer Fostel + web-page:http://www.w3.org/2004/OWL/ + OWL + + + + + + + + + + + + + + + + + + + + + Affymetrix + Affymetrix supplied microarray + + An organization which supplies technology, tools and protocols for use in high throughput applications + Affymetrix + + + + + + + + + + + + + + + Thermo + + Philippe Rocca-Serra + Thermo + + + + + + + + + + + + + + + Waters + + Philippe Rocca-Serra + Waters + + + + + + + + + + + + + + + BIO-RAD + + Philippe Rocca-Serra + BIO-RAD + + + + + + + + + GenePattern hierarchical clustering + + James Malone + GenePattern hierarchical clustering + + + + + + + + + + + + + + + Ambion + + Philippe Rocca-Serra + Ambion + + + + + + + + + + + + + + + Helicos + + Philippe Rocca-Serra + Helicos + + + + + + + + + + + + + + + Roche + + Philippe Rocca-Serra + Roche + + + + + + + + + + + + + + + Illumina + + Philippe Rocca-Serra + Illumina + + + + + + + + + GenePattern PCA + + GenePattern PCA + + + + + + + + + + GenePattern module SVM + + GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. + James Malone + Ryan Brinkman + GenePattern module SVM + + + + + + + + + GenePattern k-nearest neighbors + + James Malone + GenePattern k-nearest neighbors + + + + + + + + + GenePattern LOOCV + + GenePattern LOOCV + + + + + + + + + GenePattern k-means clustering + + James Malone + GenePattern k-means clustering + + + + + + + + + + + + + + + Agilent + + Philippe Rocca-Serra + Agilent + + + + + + + + + + GenePattern module KMeansClustering + + GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. + James Malone + PERSON: James Malone + GenePattern module KMeansClustering + + + + + + + + + GenePattern CART + + James Malone + GenePattern CART + + + + + + + + + + + GenePattern module CARTXValidation + + GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. + GenePattern module CARTXValidation + + + + + + + + + + + + + + + Li-Cor + + Philippe Rocca-Serra + Li-Cor + + + + + + + + + + + + + + + Bruker Corporation + + Philippe Rocca-Serra + Bruker Corporation + + + + + + + + + GenePattern module KNNXValidation + + GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. + James Malone + PERSON: James Malone + GenePattern module KNNXValidation + + + + + + + + + + GenePattern module PeakMatch + + GenePattern module PeakMatch + + + + + + + + + + GenePattern module KNN + + GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. + James Malone + GenePattern module KNN + + + + + + + + + + GenePattern module HierarchicalClustering + + GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. + James Malone + PERSON: James Malone + GenePattern module HierarchicalClustering + + + + + + + + + GenePattern SVM + + James Malone + GenePattern SVM + + + + + + + + + + + + + + + Applied Biosystems + + Philippe Rocca-Serra + Applied Biosystems + + + + + + + + + + GenePattern module PCA + + GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. + James Malone + PERSON: James Malone + GenePattern module PCA + + + + + + + + + GenePattern peak matching + + James Malone + Ryan Brinkman + GenePattern peak matching + + + + + + + + + + + + + + + Bruker Daltonics + + Philippe Rocca-Serra + Bruker Daltonics + + + + + + + + + GenePattern HeatMapViewer data visualization + + The GenePattern process of generating Heat Maps from clustered data. + James Malone + GenePattern HeatMapViewer data visualization + + + + + + + + + GenePattern HierarchicalClusteringViewer data visualization + + The GenePattern process of generating hierarchical clustering visualization from clustered data. + James Malone + GenePattern HierarchicalClusteringViewer data visualization + + + + + + + + + + GenePattern module HeatMapViewer + + A GenePattern software module which is used to generate a heatmap view of data. + James Malone + GenePattern module HeatMapViewer + + + + + + + + + + GenePattern module HierarchicalClusteringViewer + + A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. + James Malone + GenePattern module HierarchicalClusteringViewer + + + + + + + + + + + + + + + Sysmex Corporation, Kobe, Japan + + WEB:http://www.sysmex.com/@2009/08/06 + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + Sysmex Corporation, Kobe, Japan + + + + + + + + + + + + + + + U.S. Food and Drug Administration + + FDA + U.S. Food and Drug Administration + + + + + + + + + + + + + + + right handed + + right handed + + + + + + + + + + + + + + + ambidexterous + + ambidexterous + + + + + + + + + + + + + + + left handed + + left handed + + + + + + + + + Edingburgh handedness inventory + + The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. + PERSON:Alan Ruttenberg + PERSON:Jessica Turner + PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 + WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html + Edingburgh handedness inventory + + + + + + + + + + + + + + + eBioscience + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.ebioscience.com/@2011/04/11 + eBioscience + + + + + + + + + + + + + + + Cytopeia + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.cytopeia.com/@2011/04/11 + Cytopeia + + + + + + + + + + + + + + + Exalpha Biological + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.exalpha.com/@2011/04/11 + Exalpha Biological + + + + + + + + + + + + + + + Apogee Flow Systems + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.apogeeflow.com/@2011/04/11 + Apogee Flow Systems + + + + + + + + + + + + + + + Exbio Antibodies + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.exbio.cz/@2011/04/11 + Exbio Antibodies + + + + + + + + + + + + + + + Becton Dickinson (BD Biosciences) + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.bdbiosciences.com/@2011/04/11 + Becton Dickinson (BD Biosciences) + + + + + + + + + + + + + + + Dako Cytomation + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.dakousa.com/@2011/04/11 + Dako Cytomation + + + + + + + + + + + + + + + Millipore + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.guavatechnologies.com/@2011/04/11 + Millipore + + + + + + + + + + + + + + + Antigenix + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.antigenix.com/@2011/04/11 + Antigenix + + + + + + + + + + + + + + + Partec + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.partec.de/@2011/04/11 + Partec + + + + + + + + + + + + + + + Beckman Coulter + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.beckmancoulter.com/@2011/04/11 + Beckman Coulter + + + + + + + + + + + + + + + Advanced Instruments Inc. (AI Companies) + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.aicompanies.com/@2011/04/11 + Advanced Instruments Inc. (AI Companies) + + + + + + + + + + + + + + + Miltenyi Biotec + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.miltenyibiotec.com/@2011/04/11 + Miltenyi Biotec + + + + + + + + + + + + + + + AES Chemunex + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.aeschemunex.com/@2011/04/11 + AES Chemunex + + + + + + + + + + + + + + + Bentley Instruments + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://bentleyinstruments.com/@2011/04/11 + Bentley Instruments + + + + + + + + + + + + + + + Invitrogen + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.invitrogen.com/@2011/04/11 + Invitrogen + + + + + + + + + + + + + + + Luminex + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.luminexcorp.com/@2011/04/11 + Luminex + + + + + + + + + + + + + + + CytoBuoy + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.cytobuoy.com/@2011/04/11 + CytoBuoy + + + + + + + + + + + + + + + Nimblegen + + An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. + Person: Jie Zheng + Nimblegen + + + + + + + + + + + + + + + Pacific Biosciences + + An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. + Person: Jie Zheng + Pacific Biosciences + + + + + + + + + + + + + + + NanoString Technologies + + An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. + NanoString Technologies + + + + + + + + + Thermo Fisher Scientific + + An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific + NCI BBRB + Thermo Fisher Scientific + + + + + + + + + G1: Well differentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. + Chris Stoeckert, Helena Ellis + G1 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G1: Well differentiated + + + + + + + + + G2: Moderately differentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. + Chris Stoeckert, Helena Ellis + G2 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G2: Moderately differentiated + + + + + + + + + G3: Poorly differentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. + Chris Stoeckert, Helena Ellis + G3 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G3: Poorly differentiated + + + + + + + + + G4: Undifferentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. + Chris Stoeckert, Helena Ellis + G4 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G4: Undifferentiated + + + + + + + + + G1 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. + Chris Stoeckert, Helena Ellis + Grade 1 + NCI BBRB, OBI + NCI BBRB + G1 (Fuhrman) + + + + + + + + + G2 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. + Chris Stoeckert, Helena Ellis + Grade 2 + NCI BBRB, OBI + NCI BBRB + G2 (Fuhrman) + + + + + + + + + G3 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. + Chris Stoeckert, Helena Ellis + Grade 3 + NCI BBRB, OBI + NCI BBRB + G3 (Fuhrman) + + + + + + + + + G4 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. + Chris Stoeckert, Helena Ellis + Grade 4 + NCI BBRB, OBI + NCI BBRB + G4 (Fuhrman) + + + + + + + + + Low grade ovarian tumor + + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. + Chris Stoeckert, Helena Ellis + Low grade + NCI BBRB, OBI + NCI BBRB + Low grade ovarian tumor + + + + + + + + + High grade ovarian tumor + + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. + Chris Stoeckert, Helena Ellis + High grade + NCI BBRB, OBI + NCI BBRB + High grade ovarian tumor + + + + + + + + + G1 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. + Chris Stoeckert, Helena Ellis + G1 + NCI BBRB, OBI + NCI BBRB + G1 (WHO) + + + + + + + + + G2 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. + Chris Stoeckert, Helena Ellis + G2 + NCI BBRB, OBI + NCI BBRB + G2 (WHO) + + + + + + + + + G3 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. + Chris Stoeckert, Helena Ellis + G3 + NCI BBRB, OBI + NCI BBRB + G3 (WHO) + + + + + + + + + G4 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. + Chris Stoeckert, Helena Ellis + G4 + NCI BBRB, OBI + NCI BBRB + G4 (WHO) + + + + + + + + + pT0 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT0 (colon) + + + + + + + + + pTis (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pTis (colon) + + + + + + + + + pT1 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT1 (colon) + + + + + + + + + pT2 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT2 (colon) + + + + + + + + + pT3 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT3 (colon) + + + + + + + + + pT4a (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT4a (colon) + + + + + + + + + pT4b (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT4b (colon) + + + + + + + + + pT0 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT0 (lung) + + + + + + + + + pTis (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pTis (lung) + + + + + + + + + pT1 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT1 (lung) + + + + + + + + + pT1a (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT1a (lung) + + + + + + + + + pT1b (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT1b (lung) + + + + + + + + + pT2 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT2 (lung) + + + + + + + + + pT2a (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT2a (lung) + + + + + + + + + pT2b (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT2b (lung) + + + + + + + + + pT3 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT3 (lung) + + + + + + + + + pT4 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT4 (lung) + + + + + + + + + pT0 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT0 (kidney) + + + + + + + + + pT1 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT1 (kidney) + + + + + + + + + pT1a (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT1a (kidney) + + + + + + + + + pT1b (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT1b (kidney) + + + + + + + + + pT2 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT2 (kidney) + + + + + + + + + pT2a (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT2a (kidney) + + + + + + + + + pT2b (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT2b (kidney) + + + + + + + + + pT3 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3 (kidney) + + + + + + + + + pT3a (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3a (kidney) + + + + + + + + + pT3b (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3b (kidney) + + + + + + + + + pT3c (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3c (kidney) + + + + + + + + + pT4 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT4 (kidney) + + + + + + + + + pT0 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT0 (ovary) + + + + + + + + + pT1 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1 (ovary) + + + + + + + + + pT1a (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1a (ovary) + + + + + + + + + pT1b (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1b (ovary) + + + + + + + + + pT1c (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1c (ovary) + + + + + + + + + pT2 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2 (ovary) + + + + + + + + + pT2a (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2a (ovary) + + + + + + + + + pT2b (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2b (ovary) + + + + + + + + + pT2c (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2c (ovary) + + + + + + + + + pT3 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3 (ovary) + + + + + + + + + pT3a (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3a (ovary) + + + + + + + + + pT3b (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3b (ovary) + + + + + + + + + pT3c (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3c (ovary) + + + + + + + + + pN0 (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN0 (colon) + + + + + + + + + pN1 (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1 (colon) + + + + + + + + + pN1a (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1a (colon) + + + + + + + + + pN1b (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1b (colon) + + + + + + + + + pN1c (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1c (colon) + + + + + + + + + pN2 (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN2 (colon) + + + + + + + + + pN2a (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN2a (colon) + + + + + + + + + pN2b (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN2b (colon) + + + + + + + + + pN0 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN0 (lung) + + + + + + + + + pN1 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN1 (lung) + + + + + + + + + pN2 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN2 (lung) + + + + + + + + + pN3 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN3 (lung) + + + + + + + + + pN0 (kidney) + + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ + NCI BBRB + pN0 (kidney) + + + + + + + + + pN1 (kidney) + + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ + NCI BBRB + pN1 (kidney) + + + + + + + + + pN0 (ovary) + + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ + NCI BBRB + pN0 (ovary) + + + + + + + + + pN1 (ovary) + + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ + NCI BBRB + pN1 (ovary) + + + + + + + + + cM0 (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 + NCI BBRB + cM0 (colon) + + + + + + + + + cM1 (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 + NCI BBRB + cM1 (colon) + + + + + + + + + cM1a (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + cM1a (colon) + + + + + + + + + cM1b (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + cM1b (colon) + + + + + + + + + pM1 (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + pM1 (colon) + + + + + + + + + pM1a (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + pM1a (colon) + + + + + + + + + pM1b (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + pM1b (colon) + + + + + + + + + cM0 (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM0 (lung) + + + + + + + + + cM1 (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM1 (lung) + + + + + + + + + cM1a (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM1a (lung) + + + + + + + + + cM1b (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM1b (lung) + + + + + + + + + pM1 (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + pM1 (lung) + + + + + + + + + pM1a (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + pM1a (lung) + + + + + + + + + pM1b (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + pM1b (lung) + + + + + + + + + cM0 (kidney) + + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB + cM0 (kidney) + + + + + + + + + cM1 (kidney) + + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB + cM1 (kidney) + + + + + + + + + pM1 (kidney) + + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB + pM1 (kidney) + + + + + + + + + cM0 (ovary) + + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB + cM0 (ovary) + + + + + + + + + cM1 (ovary) + + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB + cM1 (ovary) + + + + + + + + + pM1 (ovary) + + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB + pM1 (ovary) + + + + + + + + + Occult Carcinoma (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. + Chris Stoeckert, Helena Ellis + Occult Carcinoma + http://www.medilexicon.com/dictionary/14371 + NCI BBRB + Occult Carcinoma (AJCC 7th) + + + + + + + + + Stage 0 (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. + Chris Stoeckert, Helena Ellis + Stage 0 + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage 0 (AJCC 7th) + + + + + + + + + Stage I (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. + Chris Stoeckert, Helena Ellis + Stage I + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage I (AJCC 7th) + + + + + + + + + Stage IIA (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. + Chris Stoeckert, Helena Ellis + Stage IIA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIA (AJCC 7th) + + + + + + + + + Stage IIB (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. + Chris Stoeckert, Helena Ellis + Stage IIB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIB (AJCC 7th) + + + + + + + + + Stage IIC (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. + Chris Stoeckert, Helena Ellis + Stage IIC + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIC (AJCC 7th) + + + + + + + + + Stage IIIA (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. + Chris Stoeckert, Helena Ellis + Stage IIIA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIIA (AJCC 7th) + + + + + + + + + Stage IIIB (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. + Chris Stoeckert, Helena Ellis + Stage IIIB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIIB (AJCC 7th) + + + + + + + + + Stage IIIC (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. + Chris Stoeckert, Helena Ellis + Stage IIIC + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIIC (AJCC 7th) + + + + + + + + + Stage IVA (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. + Chris Stoeckert, Helena Ellis + Stage IVA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IVA (AJCC 7th) + + + + + + + + + Stage IVB (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. + Chris Stoeckert, Helena Ellis + Stage IVB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IVB (AJCC 7th) + + + + + + + + + Stage IA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. + Chris Stoeckert, Helena Ellis + Stage IA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IA (FIGO) + + + + + + + + + Stage IA1 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. + Chris Stoeckert, Helena Ellis + Stage IA1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IA1 (FIGO) + + + + + + + + + Stage IA2 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. + Chris Stoeckert, Helena Ellis + Stage IA2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IA2 (FIGO) + + + + + + + + + Stage IB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA + Chris Stoeckert, Helena Ellis + Stage IB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IB (FIGO) + + + + + + + + + Stage IB1 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IB1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IB1 (FIGO) + + + + + + + + + Stage IB2 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IB2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IB2 (FIGO) + + + + + + + + + Stage IIA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. + Chris Stoeckert, Helena Ellis + Stage IIA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIA (FIGO) + + + + + + + + + Stage IIA1 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IIA1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIA1 (FIGO) + + + + + + + + + Stage IIA2 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IIA2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIA2 (FIGO) + + + + + + + + + Stage IIB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. + Chris Stoeckert, Helena Ellis + Stage IIB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIB (FIGO) + + + + + + + + + Stage IIIA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. + Chris Stoeckert, Helena Ellis + Stage IIIA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIIA (FIGO) + + + + + + + + + Stage IIIB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. + Chris Stoeckert, Helena Ellis + Stage IIIB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIIB (FIGO) + + + + + + + + + Stage IVA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. + Chris Stoeckert, Helena Ellis + Stage IVA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IVA (FIGO) + + + + + + + + + Stage IVB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. + Chris Stoeckert, Helena Ellis + Stage IVB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IVB (FIGO) + + + + + + + + + Stage 1 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1 (FIGO) + + + + + + + + + Stage 1A (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1A (FIGO) + + + + + + + + + Stage 1B (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1B (FIGO) + + + + + + + + + Stage 1C (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1C (FIGO) + + + + + + + + + Stage 2 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2 (FIGO) + + + + + + + + + Stage 2A (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2A (FIGO) + + + + + + + + + Stage 2B (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2B (FIGO) + + + + + + + + + Stage 2C (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2C (FIGO) + + + + + + + + + Stage 3 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). + Chris Stoeckert, Helena Ellis + Stage 3 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3 (FIGO) + + + + + + + + + Stage 3A (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . + Chris Stoeckert, Helena Ellis + Stage 3A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3A (FIGO) + + + + + + + + + Stage 3B (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . + Chris Stoeckert, Helena Ellis + Stage 3B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3B (FIGO) + + + + + + + + + Stage 3C (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). + Chris Stoeckert, Helena Ellis + Stage 3C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3C (FIGO) + + + + + + + + + Stage 4 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. + Chris Stoeckert, Helena Ellis + Stage 4 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 4 (FIGO) + + + + + + + + + Stage Unknown (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). + Chris Stoeckert, Helena Ellis + Stage Unknown + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage Unknown (FIGO) + + + + + + + + + 3: symptomatic in bed more than 50% of the day but not bed ridden + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 3: symptomatic in bed more than 50% of the day but not bed ridden + + + + + + + + + 2: symptomatic but in bed less than 50% of the day + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 2: symptomatic but in bed less than 50% of the day + + + + + + + + + 4: bed ridden + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 4: bed ridden + + + + + + + + + 0: asymptomatic + + An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 0: asymptomatic + + + + + + + + + 1: symptomatic but fully ambulatory + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 1: symptomatic but fully ambulatory + + + + + + + + + 100: asymptomatic + + A Karnofsky score vaue specification indicating that a patient is asymptomatic. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 100: asymptomatic + + + + + + + + + 80-90: symptomatic but fully ambulatory + + A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 80-90: symptomatic but fully ambulatory + + + + + + + + + 60-70: symptomatic but in bed less than 50% of the day + + A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 60-70: symptomatic but in bed less than 50% of the day + + + + + + + + + 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden + + A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden + + + + + + + + + meter + A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. + m + + meter + + + + + + + + + kilogram + A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. + kg + + kilogram + + + + + + + + + second + A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + s + sec + + second + + + + + + + + + centimeter + A length unit which is equal to one hundredth of a meter or 10^[-2] m. + cm + + centimeter + + + + + + + + + millimeter + A length unit which is equal to one thousandth of a meter or 10^[-3] m. + mm + + millimeter + + + + + + + + + micrometer + A length unit which is equal to one millionth of a meter or 10^[-6] m. + um + + micrometer + + + + + + + + + nanometer + A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. + nm + + nanometer + + + + + + + + + angstrom + A length unit which is equal to 10 [-10] m. + + angstrom + + + + + + + + + gram + A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. + g + + gram + + + + + + + + + milligram + A mass unit which is equal to one thousandth of a gram or 10^[-3] g. + mg + + milligram + + + + + + + + + microgram + A mass unit which is equal to one millionth of a gram or 10^[-6] g. + ug + + microgram + + + + + + + + + nanogram + A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. + ng + + nanogram + + + + + + + + + picogram + A mass unit which is equal to 10^[-12] g. + pg + + picogram + + + + + + + + + degree Celsius + A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. + C + degree C + + degree Celsius + + + + + + + + + minute + A time unit which is equal to 60 seconds. + min + + minute + + + + + + + + + hour + A time unit which is equal to 3600 seconds or 60 minutes. + h + hr + + hour + + + + + + + + + day + A time unit which is equal to 24 hours. + + day + + + + + + + + + week + A time unit which is equal to 7 days. + + week + + + + + + + + + month + A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. + + month + + + + + + + + + year + A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. + + year + + + + + + + + + micromole + A substance unit equal to a millionth of a mol or 10^[-6] mol. + umol + + micromole + + + + + + + + + nanomole + A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. + nmol + + nanomole + + + + + + + + + picomole + A substance unit equal to 10^[-12] mol. + pmol + + picomole + + + + + + + + + molar + A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). + M + + molar + + + + + + + + + millimolar + A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. + mM + + millimolar + + + + + + + + + micromolar + A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. + uM + + micromolar + + + + + + + + + nanomolar + A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. + nM + + nanomolar + + + + + + + + + picomolar + A unit of molarity which is equal to 10^[-12] M. + pM + + picomolar + + + + + + + + + cubic centimeter + A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. + cc + + cubic centimeter + + + + + + + + + milliliter + A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. + ml + + milliliter + + + + + + + + + liter + A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. + L + + liter + + + + + + + + + cubic decimeter + A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. + + cubic decimeter + + + + + + + + + microliter + A volume unit which is equal to one millionth of a liter or 10^[-6] L. + ul + + microliter + + + + + + + + + nanoliter + A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. + nl + + nanoliter + + + + + + + + + picoliter + A volume unit which is equal to 10^[-12] L. + pl + + picoliter + + + + + + + + + hertz + A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. + + hertz + + + + + + + + + mass percentage + A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. + % w/w + percent weight pr weight + + mass percentage + + + + + + + + + mass volume percentage + A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. + % w/v + percent vol per vol + + mass volume percentage + + + + + + + + + volume percentage + A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. + % v/v + percent vol per vol + + volume percentage + + + + + + + + + gram per liter + A mass unit density which is equal to mass of an object in grams divided by the volume in liters. + g per L + g/L + + gram per liter + + + + + + + + + milligram per milliliter + A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. + mg per ml + mg/ml + + milligram per milliliter + + + + + + + + + degree Fahrenheit + A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. + + degree Fahrenheit + + + + + + + + + pH + A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). + + pH + + + + + + + + + milliliter per liter + A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. + ml per L + ml/l + + milliliter per liter + + + + + + + + + gram per deciliter + A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. + g/dl + + gram per deciliter + + + + + + + + + colony forming unit per volume + A concentration unit which a measure of viable bacterial numbers in a given volume. + + colony forming unit per volume + + + + + + + + + microliters per minute + A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. + + microliters per minute + + + + + + + + + count per nanomolar second + A rate unit which is equal to one over one nanomolar second. + + count per nanomolar second + + + + + + + + + count per molar second + A rate unit which is equal to one over one molar second. + + count per molar second + + + + + + + + + count per nanomolar + A rate unit which is equal to one over one nanomolar. + + count per nanomolar + + + + + + + + + count per molar + A rate unit which is equal to one over one molar. + + count per molar + + + + + + + + + microgram per liter + A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. + ng/ml + ug/L + + microgram per liter + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/imports/ro_import.owl b/imports/ro_import.owl index 328cb8e..3a0fb4a 100644 --- a/imports/ro_import.owl +++ b/imports/ro_import.owl @@ -17,7 +17,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -63,7 +63,6 @@ definition - definition @@ -106,10 +105,7 @@ - - - curator note - + @@ -124,35 +120,13 @@ - - expand expression to - - - - - - - - expand assertion to - - - - - - - - An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. - first order logic expression - + - - - OBO foundry unique label - + @@ -228,21 +202,9 @@ - - - - - - - + - - - - - - - + @@ -264,6 +226,12 @@ + + + + + + @@ -783,19 +751,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos - 2017-07-19T17:30:36Z - has ligand - - - - @@ -1034,10 +989,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - @@ -1267,36 +1218,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - x actively participates in y if and only if x participates in y and x realizes some active role - Chris Mungall - agent in - actively participates in - - - - - - - - - 'heart development' has active participant some Shh protein - - x has participant y if and only if x realizes some active role that inheres in y - This may be obsoleted and replaced by the original 'has agent' relation - Chris Mungall - has agent - - obsolete has active participant - true - - - - @@ -1639,7 +1560,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + @@ -2103,16 +2024,21 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + + + - Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall + Vasundra Touré molecularly controls - activity directly regulates activity of + directly regulates activity of @@ -2121,16 +2047,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + - Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall - inhibits + Vasundra Touré + directly inhibits molecularly decreases activity of - activity directly negatively regulates activity of + directly negatively regulates activity of @@ -2139,16 +2069,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + - Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall - activates + Vasundra Touré + directly activates molecularly increases activity of - activity directly positively regulates activity of + directly positively regulates activity of @@ -2240,13 +2174,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between material entities + causal relation between entities @@ -2397,7 +2331,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall - causally influenced by (material entity to material entity) + causally influenced by (entity-centric) causally influenced by @@ -2429,6 +2363,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + @@ -2439,10 +2375,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b + The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall + Vasundra Touré - causally influences (material entity to material entity) + causally influences (entity-centric) causally influences @@ -2887,6 +2824,19 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. + Vasundra Touré + regulates activity of + + + + @@ -3157,12 +3107,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - @@ -3205,12 +3149,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - @@ -3300,15 +3238,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - ready for release - - - - @@ -3318,15 +3247,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - requires discussion - - - - + diff --git a/src/ontology/imports/faldo_terms.txt b/src/ontology/imports/faldo_terms.txt new file mode 100644 index 0000000..6ebc5bc --- /dev/null +++ b/src/ontology/imports/faldo_terms.txt @@ -0,0 +1,4 @@ +FALDO:0000000 +FALDO:0000001 +FALDO:0000002 + diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl new file mode 100644 index 0000000..4f96918 --- /dev/null +++ b/src/ontology/imports/go_import.owl @@ -0,0 +1,344 @@ + + + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + database_cross_reference + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BFO:0000050 + external + part_of + part_of + part of + + + + + + + + + BFO:0000051 + external + has_part + has_part + has part + + + + + + + + RO:0002091 + external + starts_during + starts_during + starts_during + + + + + + + + RO:0002093 + external + ends_during + ends_during + ends_during + + + + + + + + + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + janelomax + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + biological_process + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + + + + + + + + + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. + janelomax + 2012-12-19T12:21:31Z + GO:0044767 + development + biological_process + single-organism developmental process + GO:0032502 + + + + + developmental process + + + + + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. + GOC:isa_complete + + + + + + + diff --git a/src/ontology/imports/go_terms.txt b/src/ontology/imports/go_terms.txt new file mode 100644 index 0000000..026f97e --- /dev/null +++ b/src/ontology/imports/go_terms.txt @@ -0,0 +1,2 @@ +GO:0008150 + diff --git a/src/ontology/imports/hp_import.owl b/src/ontology/imports/hp_import.owl new file mode 100644 index 0000000..8df896e --- /dev/null +++ b/src/ontology/imports/hp_import.owl @@ -0,0 +1,11363 @@ + + + + + + + + + + + + + + + + + editor preferred term + + + + + + + + + IAO:0000112 + uberon + example_of_usage + true + example_of_usage + example of usage + example of usage + + + + + + + + has curation status + + + + + + + + + definition + definition + + + + + + + + + IAO:0000116 + uberon + editor_note + true + editor_note + editor note + editor note + + + + + + + + + term editor + + + + + + + + + alternative term + + + + + + + + + definition source + + + + + + + + + + + + + + + + + + + + + imported from + + + + + + + + + + + + + + + + + + + + elucidation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + is a defining property chain axiom + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + uberon + dc-description + true + dc-description + description + + + + + + + + + + + + + + + uberon + dc-title + true + dc-title + title + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + database_cross_reference + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + + + + + + + + BFO:0000050 + external + human_stages_ontology + protein + quality + uberon + part_of + part_of + part of + part of + part_of + + + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + BFO:0000051 + chebi_ontology + external + protein + quality + uberon + has_part + false + has_part + We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. + has part + has part + has_part + + + + + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + PATOC:CJM + + + + + + + + + + + + + + + + + preceded by + X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + BFO:0000062 + is preceded by + takes place after + human_stages_ontology + uberon + preceded_by + + preceded_by + preceded by + preceded_by + + + + + is preceded by + SIO:000249 + + + + + takes place after + Allen:precedes + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + BFO:0000063 + uberon + precedes + + precedes + precedes + precedes + + + + + + + + + + + + + + + + + + + occurs in + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + occurs_in + unfolds in + unfolds_in + BFO:0000066 + external + occurs_in + occurs_in + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs in + occurs in + + + + + + + + site of + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + BFO:0000067 + uberon + contains_process + contains_process + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + contains process + + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + RO:0000052 + inheres_in + inheres_in + inheres in + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + RO:0000053 + uberon + bearer_of + bearer_of + bearer of + bearer of + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + RO:0000056 + protein + participates_in + false + participates_in + participates in + participates_in + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + role of + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + protein + uberon + has_quality + false + has_quality + has quality + has quality + has_quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + chebi_ontology + protein + has_role + false + false + has_role + has role + has role + has_role + + + + + + + + + + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + RO:0001000 + protein + derives_from + + derives_from + derives from + derives_from + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + + derives into + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. + dos + 2017-07-19T17:30:36Z + has ligand + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + directly negatively regulated by + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + directly positively regulated by + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + + + + + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + David Osumi-Sutherland + starts_at_end_of + A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. + RO:0002087 + directly preceded by + is directly preceded by + is immediately preceded by + starts_at_end_of + human_stages_ontology + uberon + immediately_preceded_by + immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + immediately_preceded_by + + + + + + A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. + SIO:000251 + + + + + is immediately preceded by + SIO:000251 + + + + + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + + + + + + + + + + + + + + + + A overlaps B if they share some part in common. + x overlaps y if and only if there exists some z such that x has part z and z part of y + BFO_0000051 some (BFO_0000050 some ?Y) + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + RO:0002131 + uberon + overlaps + + overlaps + overlaps + overlaps + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + Chris Mungall + Jennifer Deegan + + + RO:0002162 + uberon + in_taxon + + in_taxon + Connects a biological entity to its taxon of origin. + in taxon + + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + RO:0002180 + protein + uberon + has_component + + false + has_component + has component + has component + has_component + + + + + + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall + David Hill + Tanya Berardini + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + RO:0002211 + external + regulates + regulates + regulates + regulates + + + + + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + negatively regulates (process to process) + + RO:0002212 + external + negatively_regulates + negatively_regulates + negatively regulates + negatively regulates + + + + + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + positively regulates (process to process) + + RO:0002213 + external + positively_regulates + positively_regulates + positively regulates + positively regulates + + + + + + + + + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + Chris Mungall + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + RO:0002215 + protein + uberon + capable_of + + false + capable_of + capable of + capable of + capable_of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + Chris Mungall + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + RO:0002216 + uberon + capable_of_part_of + capable_of_part_of + capable of part of + capable of part of + + + + + + + + + + true + + + + + + + + + + OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role + x actively participates in y if and only if x participates in y and x realizes some active role + Chris Mungall + agent in + Obsoleted as the inverse property was obsoleted. + actively participates in + obsolete actively participates in + true + + + + + + + + + 'heart development' has active participant some Shh protein + + x has participant y if and only if x realizes some active role that inheres in y + This may be obsoleted and replaced by the original 'has agent' relation + Chris Mungall + has agent + + obsolete has active participant + true + + + + + + + + + + + Chris Mungall + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + Relation between occurrents, shares a start boundary with. + inverse of starts with + Chris Mungall + Allen + RO:0002223 + uberon + starts + + starts + starts + starts + + + + + Relation between occurrents, shares a start boundary with. + + Allen:starts + + + + + + + + + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by + RO:0002224 + uberon + starts_with + + starts_with + starts with + starts with + + + + + + + + + + + + Relation between occurrents, shares an end boundary with. + inverse of ends with + Chris Mungall + RO:0002229 + finishes + uberon + ends + + ends + ends + ends + + + + + Relation between occurrents, shares an end boundary with. + + Allen:starts + ZFS:finishes + + + + + + + + + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by + RO:0002230 + uberon + ends_with + + ends_with + ends with + ends with + + + + + + + + + + + + + + + + x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y + Chris Mungall + starts with process that occurs in + + has start location + + + + + + + + + + + + + + + + x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + Chris Mungall + ends with process that occurs in + + has end location + + + + + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + Chris Mungall + consumes + + has input + + + + + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + Chris Mungall + produces + + has output + + + + + + + + + + + + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of + + + + + + + + + + + + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + acts upstream of or within + + + + + + + + + + + + + p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). + This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. + Chris Mungall + results_in_developmental_progression_of + results in developmental progression of + + + + + + + + + + + + an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. + every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + + Chris Mungall + GOC:mtg_berkeley_2013 + results_in_formation_of + results in formation of + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + + + + + + + + + + + + + + q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of inheres in part of + Chris Mungall + + + RO:0002314 + inheres_in_part_of + inheres_in_part_of + inheres in part of + inheres in part of + + + + + + + + + + true + + + + + + + + A relationship that holds via some environmental process + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + evolutionarily related to + + + + + + + + A mereological relationship or a topological relationship + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + mereotopologically related to + + + + + + + + A relationship that holds between entities participating in some developmental process (GO:0032502) + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development + developmentally related to + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + Chris Mungall + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function + RO:0002328 + uberon + functionally_related_to + functionally_related_to + functionally related to + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + Chris Mungall + false + RO:0002329 + uberon + part_of_structure_that_is_capable_of + part_of_structure_that_is_capable_of + part of structure that is capable of + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + Chris Mungall + actively involved in + enables part of + RO:0002331 + protein + involved_in + false + involved_in + involved in + involved_in + + + + + + + + + + + inverse of enables + Chris Mungall + enabled by + + + + + + + + + + + + inverse of regulates + Chris Mungall + regulated by (processual) + + regulated by + + + + + + + + + inverse of negatively regulates + Chris Mungall + + negatively regulated by + + + + + + + + + inverse of positively regulates + Chris Mungall + + positively regulated by + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + uberon + member_of + member_of + member of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + uberon + has_member + has_member + has member + has member + + + + + + + + + + inverse of has input + Chris Mungall + RO:0002352 + uberon + input_of + + + input_of + input of + input of + + + + + + + + + + inverse of has output + Chris Mungall + RO:0002353 + protein + uberon + output_of + + + false + output_of + output of + output of + output_of + + + + + + + + + Chris Mungall + formed as result of + + + + + + + + + + + + inverse of upstream of + Chris Mungall + causally downstream of + + + + + + + + + + + + Chris Mungall + immediately causally downstream of + + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types. + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causally related to + + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + Chris Mungall + causally upstream of + + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + Chris Mungall + + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) + affects + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + Chris Mungall + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + Chris Mungall + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + Chris Mungall + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + Chris Mungall + + involved in negative regulation of + + + + + + + + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union + Chris Mungall + involved in or reguates + involved in or involved in regulation of + + + + + + + + + + + + + + A protein that enables activity in a cytosol. + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + Chris Mungall + executes activity in + enables activity in + + is active in + + + + + + + + + true + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + GOC:cjm + GOC:dos + + + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + Considering relabeling as 'pairwise interacts with' + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + Chris Mungall + binds + molecularly binds with + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + Axiomatization to GO to be added later + Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + phosphorylates + + + + + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. + Chris Mungall + Vasundra Touré + molecularly controls + activity directly regulates activity of + directly regulates activity of + + + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + Chris Mungall + Vasundra Touré + directly inhibits + inhibits + molecularly decreases activity of + activity directly negatively regulates activity of + directly negatively regulates activity of + + + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + Chris Mungall + Vasundra Touré + activates + directly activates + molecularly increases activity of + activity directly positively regulates activity of + directly positively regulates activity of + + + + + + + + Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + helper property (not for use in curation) + + + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + Chris Mungall + + has part that occurs in + + + + + + + + + true + + + + + + + + + Chris Mungall + is kinase activity + + + + + + + + + + + + + + + + + + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. + relation between physical entity and a process or stage + + + + + + + + + + + + + + + + + + + + + x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + Chris Mungall + RO:0002496 + uberon + existence_starts_during_or_after + existence_starts_during_or_after + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence starts during or after + + + + + + + + + + + + + + + + + + + + + x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. + Chris Mungall + RO:0002497 + uberon + existence_ends_during_or_before + existence_ends_during_or_before + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during or before + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + causal agent in process + + + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + + + + + + + + Chris Mungall + depends on + + + + + + + + + + + + + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between entities + causal relation between material entities + + + + + + + + + + Chris Mungall + + causally influenced by (entity-centric) + causally influenced by (material entity to material entity) + causally influenced by + + + + + + + + + Chris Mungall + interaction relation helper property + + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + Chris Mungall + molecular interaction relation helper property + + + + + + + + + + + + + + + + + + + + + Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b + The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). + Chris Mungall + Vasundra Touré + + causally influences (entity-centric) + causally influences (material entity to material entity) + causally influences + + + + + + + + + + A relation that holds between an attribute or a qualifier and another attribute. + Chris Mungall + + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. + RO:0002180 + qualifier + + qualifier + placeholder relation to indicate normality/abnormality. + has modifier + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + Chris Mungall + + directly regulates (processual) + + directly regulates + + + + + + + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + Chris Mungall + has part structure that is capable of + + + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + Chris Mungall + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + capable of negatively regulating + + + + + + + + + + + + + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + + process has causal agent + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + + directly positively regulates (process to process) + + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + directly negatively regulates (process to process) + + directly negatively regulates + + + + + + + + + + + + + + + + + + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + Melissa Haendel + RO:0003000 + uberon + produces + + produces + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + produces + produces + + + + + + + + + + + a produced_by b iff some process that occurs_in b has_output a. + Melissa Haendel + RO:0003001 + uberon + produced_by + + produced_by + produced by + produced_by + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + enables subfunction + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:30Z + acts upstream of or within, positive effect + + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:51Z + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + cjm + 2018-01-26T23:53:14Z + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + cjm + 2018-01-26T23:53:22Z + acts upstream of, negative effect + + + + + + + + + + + cjm + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + + + + + + + + + + cjm + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + + + + + + + + + + + The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. + Vasundra Touré + regulates activity of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + bfo + BFO:0000015 + process + process + + + + + + + + + + disposition + + + + + + + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + + + + + + + + + + + + + + + bfo + BFO:0000019 + quality + quality + + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + bfo + BFO:0000030 + object + + + + + + + + + + + + + + + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + generically dependent continuant + + + + + + + + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + bfo + BFO:0000040 + material entity + material entity + + + + + + + + + + + + + + + immaterial entity + + + + + + + + + + anatomical entity + + + + + + + + + + connected anatomical structure + + + + + + + + + + + material anatomical entity + + + + + + + + + immaterial anatomical entity + + + + + + + + + + cell part (CARO) + cell part + + + + + + + + + organism or virus or viroid + + + + + + + + + biological entity + + + + + + + + + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. + molecular entity + chebi_ontology + entidad molecular + entidades moleculares + entite moleculaire + molecular entities + molekulare Entitaet + CHEBI:23367 + + molecular entity + + + + + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. + fake:2 + + + + + molecular entity + IUPAC + + + + + + entidad molecular + IUPAC + + + + + entidades moleculares + IUPAC + + + + + entite moleculaire + IUPAC + + + + + molecular entities + IUPAC + + + + + molekulare Entitaet + ChEBI + + + + + + + + + A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. + chemical entity + chebi_ontology + CHEBI:24431 + + chemical entity + + + + + chemical entity + UniProt + + + + + + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + + CALOHA:TS-2035 + FMA:68646 + GO:0005623 + KUPO:0000002 + VHOG:0001533 + WBbt:0004017 + XAO:0003012 + cell + CL:0000000 + + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + cell + cell + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CARO:mah + + + + + + + + + + + + + + + + + + + + A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models. + + 2017-01-30T18:53:32Z + https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 + cell + https://github.com/obophenotype/cell-ontology/issues/448 + abnormal cell + + + + + A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models. + GOC:add + GOC:cg + GOC:wdd + + + + + + + + + environmental system + + + + + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + molecular process + GO:0005554 + molecular function + molecular_function + GO:0003674 + + + + + + + + + Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + molecular_function + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + GOC:pdt + + + + + + + + + Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. + Wikipedia:Enzyme + enzyme activity + molecular_function + GO:0003824 + + + + + + + catalytic activity + + + + + Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. + GOC:vw + ISBN:0198506732 + + + + + enzyme activity + GOC:dph + GOC:tb + + + + + + + + + + true + + + + + + + + + Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. + receptor binding + Wikipedia:Ligand_(biochemistry) + receptor ligand + molecular_function + receptor-associated protein activity + GO:0005102 + + + + + + Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'. + signaling receptor binding + + + + + Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. + GOC:bf + GOC:ceb + ISBN:0198506732 + + + + + + + + + The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. + Wikipedia:Binding_(molecular) + ligand + molecular_function + GO:0005488 + + + + Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. + binding + + + + + The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. + GOC:ceb + GOC:mah + ISBN:0198506732 + + + + + + + + + Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). + GO:0001948 + GO:0045308 + MIPS_funcat:16.01 + MIPS_funcat:18.01.07 + Reactome:R-HSA-170835 + Reactome:R-HSA-170846 + protein amino acid binding + glycoprotein binding + molecular_function + GO:0005515 + + + + + + + protein binding + + + + + Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). + GOC:go_curators + + + + + Reactome:R-HSA-170835 + An anchoring protein, ZFYVE9 (SARA), recruits SMAD2/3 + + + + + Reactome:R-HSA-170846 + TGFBR2 recruits TGFBR1 + + + + + + + + + A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). + The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. + GO:0008372 + NIF_Subcellular:sao1337158144 + cell or subcellular entity + cellular component + cellular_component + subcellular entity + GO:0005575 + + + + + + + + + Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. + Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + cellular_component + + + + + A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). + GOC:pdt + NIF_Subcellular:sao1337158144 + + + + + The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. + GOC:go_curators + + + + + subcellular entity + NIF_Subcellular:nlx_subcell_100315 + + + + + + + + + The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. + Wikipedia:Intracellular + internal to cell + protoplasm + cellular_component + nucleocytoplasm + protoplast + GO:0005622 + + + + + + intracellular + + + + + The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. + ISBN:0198506732 + + + + + nucleocytoplasm + GOC:mah + + + + + protoplast + GOC:mah + + + + + + + + + The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. + cell and encapsulating structures + NIF_Subcellular:sao1813327414 + Wikipedia:Cell_(biology) + cellular_component + GO:0005623 + + + + cell + + + + + The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. + GOC:go_curators + + + + + + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + + MIPS_funcat:70.10 + NIF_Subcellular:sao1702920020 + Wikipedia:Cell_nucleus + cell nucleus + horsetail nucleus + cellular_component + GO:0005634 + + + + + + + + + + + + + nucleus + nucleus + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + GOC:go_curators + + + + + horsetail nucleus + GOC:al + GOC:mah + GOC:vw + PMID:15030757 + + + + + + + + + The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). + phosphorus metabolism + biological_process + GO:0006793 + + phosphorus metabolic process + + + + + The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). + GOC:ai + + + + + + + + + The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. + MIPS_funcat:01.04 + phosphate metabolism + biological_process + phosphate metabolic process + GO:0006796 + phosphate-containing compound metabolic process + + + + + The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. + GOC:ai + + + + + + + + + Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + Wikipedia:Cell_signaling + biological_process + GO:0007154 + + + cell communication + + + + + Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. + GO:0023033 + MIPS_funcat:30 + Wikipedia:Signal_transduction + signaling cascade + signalling cascade + biological_process + signaling pathway + signalling pathway + GO:0007165 + + + + + + + Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. + signal transduction + + + + + The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. + GOC:go_curators + GOC:mtg_signaling_feb11 + + + + + signalling pathway + GOC:mah + + + + + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + janelomax + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + biological_process + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + + + + + + + + + The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + janelomax + 2012-10-17T15:46:40Z + GO:0044236 + GO:0044710 + MIPS_funcat:01 + Wikipedia:Metabolism + metabolism + metabolic process resulting in cell growth + metabolism resulting in cell growth + multicellular organism metabolic process + biological_process + single-organism metabolic process + GO:0008152 + + + + + + Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. + metabolic process + + + + + The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + GOC:go_curators + ISBN:0198547684 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044252 + down regulation of metabolic process + down-regulation of metabolic process + downregulation of metabolic process + negative regulation of metabolism + negative regulation of organismal metabolism + inhibition of metabolic process + inhibition of organismal metabolic process + negative regulation of multicellular organismal metabolic process + biological_process + GO:0009892 + negative regulation of metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044253 + positive regulation of metabolism + up regulation of metabolic process + up-regulation of metabolic process + upregulation of metabolic process + activation of metabolic process + positive regulation of multicellular organismal metabolic process + positive regulation of organismal metabolism + stimulation of metabolic process + stimulation of organismal metabolic process + up-regulation of organismal metabolic process + biological_process + GO:0009893 + positive regulation of metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of signal transduction. + GO:0035466 + biological_process + regulation of signaling pathway + regulation of signalling pathway + GO:0009966 + regulation of signal transduction + + + + + Any process that modulates the frequency, rate or extent of signal transduction. + GOC:sm + + + + + regulation of signalling pathway + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of signal transduction. + GO:0035468 + up regulation of signal transduction + up-regulation of signal transduction + upregulation of signal transduction + activation of signal transduction + stimulation of signal transduction + biological_process + positive regulation of signaling pathway + positive regulation of signalling pathway + GO:0009967 + positive regulation of signal transduction + + + + + Any process that activates or increases the frequency, rate or extent of signal transduction. + GOC:sm + + + + + positive regulation of signalling pathway + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. + GO:0035467 + down regulation of signal transduction + down-regulation of signal transduction + downregulation of signal transduction + inhibition of signal transduction + biological_process + negative regulation of signaling pathway + negative regulation of signalling pathway + GO:0009968 + negative regulation of signal transduction + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. + GOC:sm + + + + + negative regulation of signalling pathway + GOC:mah + + + + + + + + + Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + janelomax + 2012-12-11T16:56:55Z + GO:0008151 + GO:0044763 + GO:0050875 + cell physiology + cellular physiological process + cell growth and/or maintenance + biological_process + single-organism cellular process + GO:0009987 + + cellular process + + + + + Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:go_curators + GOC:isa_complete + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + biological_process + GO:0010562 + positive regulation of phosphorus metabolic process + + + + + Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + biological_process + GO:0010563 + negative regulation of phosphorus metabolic process + + + + + Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + biological_process + GO:0010646 + regulation of cell communication + + + + + Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + biological_process + GO:0010647 + positive regulation of cell communication + + + + + Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + biological_process + GO:0010648 + negative regulation of cell communication + + + + + Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + true + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + Reactome:R-HSA-6788855 + Reactome:R-HSA-6788867 + phosphokinase activity + molecular_function + GO:0016301 + + + + + + + Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. + kinase activity + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + ISBN:0198506732 + + + + + Reactome:R-HSA-6788855 + FN3KRP phosphorylates PsiAm, RibAm + + + + + Reactome:R-HSA-6788867 + FN3K phosphorylates ketosamines + + + + + + + + + The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. + Wikipedia:Phosphorylation + biological_process + GO:0016310 + + + phosphorylation + + + + + The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. + ISBN:0198506732 + + + + + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + EC:2 + Reactome:R-HSA-1483089 + Reactome:R-HSA-1483186 + Reactome:R-HSA-5668414 + Reactome:R-HSA-6787403 + Reactome:R-HSA-8868783 + molecular_function + GO:0016740 + + + + + + + + + transferase activity + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + ISBN:0198506732 + + + + + Reactome:R-HSA-1483089 + PE is converted to PS by PTDSS2 + + + + + Reactome:R-HSA-1483186 + PC is converted to PS by PTDSS1 + + + + + Reactome:R-HSA-5668414 + TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK + + + + + Reactome:R-HSA-6787403 + GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA + + + + + Reactome:R-HSA-8868783 + TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 + + + + + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + EC:2.7 + molecular_function + GO:0016772 + + Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. + transferase activity, transferring phosphorus-containing groups + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + GOC:jl + ISBN:0198506732 + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + regulation of phosphate metabolism + biological_process + GO:0019220 + regulation of phosphate metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044246 + regulation of metabolism + regulation of multicellular organismal metabolic process + regulation of organismal metabolic process + biological_process + GO:0019222 + + regulation of metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + regulation of organismal metabolic process + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a signaling process. + 2010-02-16T09:30:50Z + biological_process + regulation of signaling process + regulation of signalling process + GO:0023051 + regulation of signaling + + + + + Any process that modulates the frequency, rate or extent of a signaling process. + GOC:mtg_signal + + + + + regulation of signaling process + GOC:bf + + + + + regulation of signalling process + GOC:mah + + + + + + + + + The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. + janelomax + 2010-02-16T09:30:50Z + GO:0023046 + GO:0044700 + biological signaling + signaling process + signalling + biological_process + signalling process + single organism signaling + GO:0023052 + + + + + + Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. + signaling + + + + + The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. + GOC:mtg_signal + GOC:mtg_signaling_feb11 + GOC:signaling + + + + + signalling process + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. + 2010-02-16T09:30:50Z + positive regulation of signalling process + biological_process + positive regulation of signaling process + GO:0023056 + positive regulation of signaling + + + + + Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. + GOC:mtg_signal + + + + + positive regulation of signalling process + GOC:mah + + + + + positive regulation of signaling process + GOC:bf + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. + 2010-02-16T09:30:50Z + biological_process + negative regulation of signaling process + negative regulation of signalling process + GO:0023057 + negative regulation of signaling + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. + GOC:mtg_signal + + + + + negative regulation of signaling process + GOC:bf + + + + + negative regulation of signalling process + GOC:mah + + + + + + + + + The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. + MIPS_funcat:18.02.07 + molecular_function + GO:0030545 + receptor regulator activity + + + + + The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. + GOC:ceb + + + + + + + + + The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. + receptor activator activity + molecular_function + GO:0030546 + signaling receptor activator activity + + + + + The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. + GOC:ceb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + regulation of cellular metabolism + biological_process + GO:0031323 + regulation of cellular metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + down regulation of cellular metabolic process + down-regulation of cellular metabolic process + downregulation of cellular metabolic process + negative regulation of cellular metabolism + inhibition of cellular metabolic process + biological_process + GO:0031324 + negative regulation of cellular metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + positive regulation of cellular metabolism + up regulation of cellular metabolic process + up-regulation of cellular metabolic process + upregulation of cellular metabolic process + activation of cellular metabolic process + stimulation of cellular metabolic process + biological_process + GO:0031325 + positive regulation of cellular metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. + down regulation of protein binding + down-regulation of protein binding + downregulation of protein binding + inhibition of protein binding + biological_process + GO:0032091 + negative regulation of protein binding + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of protein binding. + up regulation of protein binding + up-regulation of protein binding + upregulation of protein binding + activation of protein binding + stimulation of protein binding + biological_process + GO:0032092 + positive regulation of protein binding + + + + + Any process that activates or increases the frequency, rate or extent of protein binding. + GOC:mah + + + + + + + + + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. + janelomax + 2012-12-19T12:21:31Z + GO:0044767 + development + biological_process + single-organism developmental process + GO:0032502 + + + + + developmental process + + + + + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. + GOC:isa_complete + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + down regulation of kinase activity + down-regulation of kinase activity + downregulation of kinase activity + inhibition of kinase activity + kinase inhibitor + biological_process + GO:0033673 + negative regulation of kinase activity + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + up regulation of kinase activity + up-regulation of kinase activity + upregulation of kinase activity + kinase activator + stimulation of kinase activity + biological_process + GO:0033674 + positive regulation of kinase activity + + + + + Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. + rfoulger + 2010-05-14T01:14:37Z + GO:0007242 + GO:0007243 + GO:0023013 + GO:0023034 + intracellular signaling chain + intracellular protein kinase cascade + intracellular signal transduction pathway + protein kinase cascade + signal transmission via intracellular cascade + biological_process + intracellular signaling cascade + intracellular signaling pathway + signal transduction via intracellular signaling cascade + GO:0035556 + + intracellular signal transduction + + + + + The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. + GOC:bf + GOC:jl + GOC:signaling + ISBN:3527303782 + + + + + intracellular signaling chain + ISBN:3527303782 + + + + + intracellular protein kinase cascade + GOC:signaling + + + + + protein kinase cascade + GOC:signaling + + + + + intracellular signaling cascade + GOC:signaling + + + + + + + + + The increase in size or mass of an entire organism, a part of an organism or a cell. + GO:0048590 + biological_process + growth pattern + non-developmental growth + GO:0040007 + + + + + + See also the biological process term 'cell growth ; GO:0016049'. + growth + + + + + The increase in size or mass of an entire organism, a part of an organism or a cell. + GOC:bf + GOC:ma + + + + + non-developmental growth + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. + biological_process + GO:0040008 + regulation of growth + + + + + Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. + GOC:ems + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. + biological_process + GO:0042325 + regulation of phosphorylation + + + + + Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. + down regulation of phosphorylation + down-regulation of phosphorylation + downregulation of phosphorylation + inhibition of phosphorylation + biological_process + GO:0042326 + negative regulation of phosphorylation + + + + + Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. + up regulation of phosphorylation + up-regulation of phosphorylation + upregulation of phosphorylation + activation of phosphorylation + stimulation of phosphorylation + biological_process + GO:0042327 + positive regulation of phosphorylation + + + + + Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the activity of an enzyme. + GO:0048554 + MIPS_funcat:18.02.01.01 + positive regulation of enzyme activity + up regulation of enzyme activity + up-regulation of enzyme activity + upregulation of enzyme activity + activation of enzyme activity + activation of metalloenzyme activity + positive regulation of metalloenzyme activity + stimulation of enzyme activity + stimulation of metalloenzyme activity + up regulation of metalloenzyme activity + up-regulation of metalloenzyme activity + upregulation of metalloenzyme activity + biological_process + GO:0043085 + + positive regulation of catalytic activity + + + + + Any process that activates or increases the activity of an enzyme. + GOC:ebc + GOC:jl + GOC:tb + GOC:vw + + + + + positive regulation of enzyme activity + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the activity of an enzyme. + GO:0048553 + down regulation of enzyme activity + down-regulation of enzyme activity + down-regulation of metalloenzyme activity + downregulation of enzyme activity + negative regulation of enzyme activity + down regulation of metalloenzyme activity + downregulation of metalloenzyme activity + inhibition of enzyme activity + inhibition of metalloenzyme activity + negative regulation of metalloenzyme activity + biological_process + GO:0043086 + negative regulation of catalytic activity + + + + + Any process that stops or reduces the activity of an enzyme. + GOC:ebc + GOC:jl + GOC:tb + GOC:vw + + + + + negative regulation of enzyme activity + GOC:tb + + + + + + + + + Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. + NIF_Subcellular:sao1539965131 + Wikipedia:Organelle + cellular_component + GO:0043226 + + + + organelle + + + + + Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + NIF_Subcellular:sao414196390 + membrane-enclosed organelle + cellular_component + GO:0043227 + membrane-bounded organelle + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + cellular_component + GO:0043229 + + intracellular organelle + + + + + Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + intracellular membrane-enclosed organelle + cellular_component + GO:0043231 + + intracellular membrane-bounded organelle + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of protein binding. + biological_process + GO:0043393 + regulation of protein binding + + + + + Any process that modulates the frequency, rate or extent of protein binding. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + biological_process + GO:0043549 + regulation of kinase activity + + + + + Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:bf + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + jane + 2009-04-21T04:07:27Z + biological_process + GO:0044092 + negative regulation of molecular function + + + + + Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GO:jl + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + jane + 2009-04-21T04:11:06Z + biological_process + GO:0044093 + positive regulation of molecular function + + + + + Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GO:jl + + + + + + + + + + The chemical reactions and pathways by which individual cells transform chemical substances. + cellular metabolism + biological_process + intermediary metabolism + GO:0044237 + cellular metabolic process + + + + + The chemical reactions and pathways by which individual cells transform chemical substances. + GOC:go_curators + + + + + intermediary metabolism + GOC:mah + + + + + + + + + + OBSOLETE. Any constituent part of a cell, the basic structural and functional unit of all organisms. + + CL:0000000 + NIF_Subcellular:sao628508602 + cellular subcomponent + cellular_component + protoplast + GO:0044464 + + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + cell part + obsolete cell part + true + + + + + OBSOLETE. Any constituent part of a cell, the basic structural and functional unit of all organisms. + GOC:jl + + + + + cellular subcomponent + NIF_Subcellular:sao628508602 + + + + + protoplast + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. + down regulation of growth + down-regulation of growth + downregulation of growth + inhibition of growth + biological_process + GO:0045926 + negative regulation of growth + + + + + Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism. + up regulation of growth + up-regulation of growth + upregulation of growth + activation of growth + stimulation of growth + biological_process + GO:0045927 + positive regulation of growth + + + + + Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + down regulation of phosphate metabolic process + down-regulation of phosphate metabolic process + downregulation of phosphate metabolic process + negative regulation of phosphate metabolism + inhibition of phosphate metabolic process + biological_process + GO:0045936 + negative regulation of phosphate metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + positive regulation of phosphate metabolism + up regulation of phosphate metabolic process + up-regulation of phosphate metabolic process + upregulation of phosphate metabolic process + activation of phosphate metabolic process + stimulation of phosphate metabolic process + biological_process + GO:0045937 + positive regulation of phosphate metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). + midori + 2010-09-13T04:51:59Z + GO:0071884 + receptor agonist activity + signaling molecule + signaling receptor ligand activity + vitamin D receptor activator activity + molecular_function + GO:0048018 + + + Definition discussed in https://github.com/geneontology/go-ontology/issues/14220 + receptor ligand activity + + + + + The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). + GOC:kv + GOC:molecular_function_refactoring + GOC:pdt + + + + + receptor agonist activity + GOC:molecular_function_refactoring + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0043119 + positive regulation of physiological process + up regulation of biological process + up-regulation of biological process + upregulation of biological process + activation of biological process + stimulation of biological process + biological_process + GO:0048518 + + positive regulation of biological process + + + + + Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0043118 + down regulation of biological process + down-regulation of biological process + downregulation of biological process + negative regulation of physiological process + inhibition of biological process + biological_process + GO:0048519 + + negative regulation of biological process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051242 + positive regulation of cellular physiological process + up regulation of cellular process + up-regulation of cellular process + upregulation of cellular process + activation of cellular process + stimulation of cellular process + biological_process + GO:0048522 + positive regulation of cellular process + + + + + Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051243 + down regulation of cellular process + down-regulation of cellular process + downregulation of cellular process + negative regulation of cellular physiological process + inhibition of cellular process + biological_process + GO:0048523 + negative regulation of cellular process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + biological_process + GO:0048583 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + regulation of response to stimulus + + + + + Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + up regulation of response to stimulus + up-regulation of response to stimulus + upregulation of response to stimulus + activation of response to stimulus + stimulation of response to stimulus + biological_process + GO:0048584 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + positive regulation of response to stimulus + + + + + Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + down regulation of response to stimulus + down-regulation of response to stimulus + downregulation of response to stimulus + inhibition of response to stimulus + biological_process + GO:0048585 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + negative regulation of response to stimulus + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0050791 + regulation of physiological process + biological_process + GO:0050789 + + + + + regulation of biological process + + + + + Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:ai + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the activity of an enzyme. + GO:0048552 + MIPS_funcat:18.02.01 + regulation of enzyme activity + regulation of metalloenzyme activity + biological_process + GO:0050790 + + regulation of catalytic activity + + + + + Any process that modulates the activity of an enzyme. + GOC:ai + GOC:ebc + GOC:vw + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + biological_process + GO:0050793 + regulation of developmental process + + + + + Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051244 + regulation of cellular physiological process + biological_process + GO:0050794 + regulation of cellular process + + + + + Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:go_curators + + + + + + + + + Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. + GO:0051869 + MIPS_funcat:34.11 + physiological response to stimulus + biological_process + GO:0050896 + + + + + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + response to stimulus + + + + + Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. + GOC:ai + GOC:bf + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + down regulation of developmental process + down-regulation of developmental process + downregulation of developmental process + inhibition of developmental process + biological_process + GO:0051093 + negative regulation of developmental process + + + + + Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + up regulation of developmental process + up-regulation of developmental process + upregulation of developmental process + activation of developmental process + stimulation of developmental process + biological_process + GO:0051094 + positive regulation of developmental process + + + + + Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + biological_process + GO:0051098 + regulation of binding + + + + + Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + up regulation of binding + up-regulation of binding + upregulation of binding + activation of binding + stimulation of binding + biological_process + GO:0051099 + positive regulation of binding + + + + + Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + down regulation of binding + down-regulation of binding + downregulation of binding + inhibition of binding + biological_process + GO:0051100 + negative regulation of binding + + + + + Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + regulation of phosphorus metabolism + biological_process + GO:0051174 + regulation of phosphorus metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + transferase regulator + biological_process + GO:0051338 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + regulation of transferase activity + + + + + Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + EC:2.-.-.- + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + transferase activator + up regulation of transferase activity + up-regulation of transferase activity + upregulation of transferase activity + activation of transferase activity + stimulation of transferase activity + biological_process + GO:0051347 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + positive regulation of transferase activity + + + + + Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + down regulation of transferase activity + down-regulation of transferase activity + downregulation of transferase activity + transferase inhibitor + inhibition of transferase activity + biological_process + GO:0051348 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + negative regulation of transferase activity + + + + + Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + GOC:ai + + + + + + + + + + Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. + biological_process + GO:0051716 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + cellular response to stimulus + + + + + Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. + GOC:bf + GOC:jl + + + + + + + + + Any process that modulates a measurable attribute of any biological process, quality or function. + regulation + biological_process + GO:0065007 + + + biological regulation + + + + + Any process that modulates a measurable attribute of any biological process, quality or function. + GOC:dph + GOC:isa_complete + GOC:mah + GOC:pr + GOC:vw + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + regulation of a molecular function + biological_process + GO:0065009 + + + + regulation of molecular function + + + + + Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GOC:isa_complete + + + + + + + + + + + + + + + A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. + molecular_function + GO:0098772 + + molecular function regulator + + + + + A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. + GOC:dos + GOC:pt + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + kmv + 2019-08-12T18:01:37Z + cellular_component + GO:0110165 + cellular anatomical entity + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + GOC:kmv + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. + bf + 2012-02-22T11:40:53Z + regulation of receptor ligand + biological_process + GO:1900120 + regulation of receptor binding + + + + + Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. + GOC:TermGenie + GOC:signaling + + + + + regulation of receptor ligand + GOC:TermGenie + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor. + bf + 2012-02-22T11:40:57Z + down regulation of receptor binding + down-regulation of receptor binding + downregulation of receptor binding + inhibition of receptor binding + inhibition of receptor ligand + biological_process + down regulation of receptor-associated protein activity + GO:1900121 + negative regulation of receptor binding + + + + + Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor. + GOC:TermGenie + GOC:signaling + + + + + down regulation of receptor binding + GOC:TermGenie + + + + + down-regulation of receptor binding + GOC:TermGenie + + + + + downregulation of receptor binding + GOC:TermGenie + + + + + inhibition of receptor binding + GOC:TermGenie + + + + + inhibition of receptor ligand + GOC:TermGenie + + + + + down regulation of receptor-associated protein activity + GOC:TermGenie + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor. + bf + 2012-02-22T11:41:00Z + up regulation of receptor binding + upregulation of receptor binding + activation of receptor binding + biological_process + GO:1900122 + positive regulation of receptor binding + + + + + Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor. + GOC:TermGenie + GOC:signaling + + + + + up regulation of receptor binding + GOC:TermGenie + + + + + upregulation of receptor binding + GOC:TermGenie + + + + + activation of receptor binding + GOC:TermGenie + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of intracellular signal transduction. + bf + 2013-12-02T11:32:52Z + GO:0010627 + regulation of intracellular signaling cascade + regulation of intracellular signaling chain + regulation of intracellular protein kinase cascade + regulation of intracellular signal transduction pathway + regulation of signal transmission via intracellular cascade + biological_process + regulation of intracellular signaling pathway + regulation of signal transduction via intracellular signaling cascade + GO:1902531 + regulation of intracellular signal transduction + + + + + Any process that modulates the frequency, rate or extent of intracellular signal transduction. + GOC:TermGenie + GOC:dph + GOC:signaling + GOC:tb + + + + + regulation of intracellular signaling cascade + GOC:TermGenie + + + + + regulation of intracellular signaling chain + GOC:TermGenie + + + + + regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + regulation of intracellular signaling pathway + GOC:TermGenie + + + + + regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. + bf + 2013-12-02T11:33:01Z + GO:0010741 + down regulation of intracellular signal transduction + down regulation of intracellular signaling chain + down-regulation of intracellular signal transduction + down-regulation of intracellular signaling chain + downregulation of intracellular signal transduction + downregulation of intracellular signaling chain + negative regulation of intracellular protein kinase cascade + negative regulation of intracellular signaling cascade + negative regulation of intracellular signaling chain + down regulation of intracellular signal transduction pathway + down regulation of intracellular signaling cascade + down regulation of signal transmission via intracellular cascade + down-regulation of intracellular signal transduction pathway + downregulation of intracellular signal transduction pathway + downregulation of intracellular signaling cascade + downregulation of signal transmission via intracellular cascade + inhibition of intracellular signal transduction + inhibition of intracellular signal transduction pathway + inhibition of intracellular signaling cascade + inhibition of intracellular signaling chain + inhibition of signal transmission via intracellular cascade + negative regulation of intracellular signal transduction pathway + negative regulation of signal transmission via intracellular cascade + biological_process + down regulation of intracellular signaling pathway + down regulation of signal transduction via intracellular signaling cascade + down-regulation of intracellular signaling cascade + down-regulation of intracellular signaling pathway + down-regulation of signal transduction via intracellular signaling cascade + down-regulation of signal transmission via intracellular cascade + downregulation of intracellular signaling pathway + downregulation of signal transduction via intracellular signaling cascade + inhibition of intracellular signaling pathway + inhibition of signal transduction via intracellular signaling cascade + negative regulation of intracellular signaling pathway + negative regulation of signal transduction via intracellular signaling cascade + GO:1902532 + negative regulation of intracellular signal transduction + + + + + Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. + GOC:TermGenie + GOC:dph + GOC:signaling + GOC:tb + + + + + down regulation of intracellular signal transduction + GOC:TermGenie + + + + + down regulation of intracellular signaling chain + GOC:TermGenie + + + + + down-regulation of intracellular signal transduction + GOC:TermGenie + + + + + down-regulation of intracellular signaling chain + GOC:TermGenie + + + + + downregulation of intracellular signal transduction + GOC:TermGenie + + + + + downregulation of intracellular signaling chain + GOC:TermGenie + + + + + negative regulation of intracellular signaling cascade + GOC:TermGenie + + + + + negative regulation of intracellular signaling chain + GOC:TermGenie + + + + + down regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + down regulation of intracellular signaling cascade + GOC:TermGenie + + + + + down regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + down-regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + downregulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + downregulation of intracellular signaling cascade + GOC:TermGenie + + + + + downregulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + inhibition of intracellular signal transduction + GOC:TermGenie + + + + + inhibition of intracellular signal transduction pathway + GOC:TermGenie + + + + + inhibition of intracellular signaling cascade + GOC:TermGenie + + + + + inhibition of intracellular signaling chain + GOC:TermGenie + + + + + inhibition of signal transmission via intracellular cascade + GOC:TermGenie + + + + + negative regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + negative regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + down regulation of intracellular signaling pathway + GOC:TermGenie + + + + + down regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + down-regulation of intracellular signaling cascade + GOC:TermGenie + + + + + down-regulation of intracellular signaling pathway + GOC:TermGenie + + + + + down-regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + down-regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + downregulation of intracellular signaling pathway + GOC:TermGenie + + + + + downregulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + inhibition of intracellular signaling pathway + GOC:TermGenie + + + + + inhibition of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + negative regulation of intracellular signaling pathway + GOC:TermGenie + + + + + negative regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. + bf + 2013-12-02T11:33:10Z + GO:0010740 + positive regulation of intracellular signaling chain + up regulation of intracellular signal transduction + up regulation of intracellular signaling chain + up-regulation of intracellular signal transduction + up-regulation of intracellular signaling chain + upregulation of intracellular signal transduction + upregulation of intracellular signaling chain + activation of intracellular signal transduction + activation of intracellular signal transduction pathway + activation of intracellular signaling cascade + activation of intracellular signaling chain + activation of signal transmission via intracellular cascade + positive regulation of intracellular protein kinase cascade + positive regulation of intracellular signal transduction pathway + positive regulation of signal transmission via intracellular cascade + up regulation of intracellular signal transduction pathway + up regulation of signal transmission via intracellular cascade + up-regulation of intracellular signal transduction pathway + up-regulation of signal transmission via intracellular cascade + upregulation of intracellular signal transduction pathway + upregulation of signal transmission via intracellular cascade + biological_process + activation of intracellular signaling pathway + activation of signal transduction via intracellular signaling cascade + positive regulation of intracellular signaling cascade + positive regulation of intracellular signaling pathway + positive regulation of signal transduction via intracellular signaling cascade + up regulation of intracellular signaling cascade + up regulation of intracellular signaling pathway + up regulation of signal transduction via intracellular signaling cascade + up-regulation of intracellular signaling cascade + up-regulation of intracellular signaling pathway + up-regulation of signal transduction via intracellular signaling cascade + upregulation of intracellular signaling cascade + upregulation of intracellular signaling pathway + upregulation of signal transduction via intracellular signaling cascade + GO:1902533 + positive regulation of intracellular signal transduction + + + + + Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. + GOC:BHF + GOC:TermGenie + GOC:dph + GOC:signaling + GOC:tb + + + + + positive regulation of intracellular signaling chain + GOC:TermGenie + + + + + up regulation of intracellular signal transduction + GOC:TermGenie + + + + + up regulation of intracellular signaling chain + GOC:TermGenie + + + + + up-regulation of intracellular signal transduction + GOC:TermGenie + + + + + up-regulation of intracellular signaling chain + GOC:TermGenie + + + + + upregulation of intracellular signal transduction + GOC:TermGenie + + + + + upregulation of intracellular signaling chain + GOC:TermGenie + + + + + activation of intracellular signal transduction + GOC:TermGenie + + + + + activation of intracellular signal transduction pathway + GOC:TermGenie + + + + + activation of intracellular signaling cascade + GOC:TermGenie + + + + + activation of intracellular signaling chain + GOC:TermGenie + + + + + activation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + positive regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + positive regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + up regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + up regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + up-regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + up-regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + upregulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + upregulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + activation of intracellular signaling pathway + GOC:TermGenie + + + + + activation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + positive regulation of intracellular signaling cascade + GOC:TermGenie + + + + + positive regulation of intracellular signaling pathway + GOC:TermGenie + + + + + positive regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + up regulation of intracellular signaling cascade + GOC:TermGenie + + + + + up regulation of intracellular signaling pathway + GOC:TermGenie + + + + + up regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + up-regulation of intracellular signaling cascade + GOC:TermGenie + + + + + up-regulation of intracellular signaling pathway + GOC:TermGenie + + + + + up-regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + upregulation of intracellular signaling cascade + GOC:TermGenie + + + + + upregulation of intracellular signaling pathway + GOC:TermGenie + + + + + upregulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + + + + UMLS:C0444868 + human_phenotype + HP:0000001 + Root of all terms in the Human Phenotype Ontology. + All + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Deviation from the norm of height with respect to that which is expected according to age and gender norms. + peter + 2008-02-27T02:20:00Z + UMLS:C4025901 + Abnormality of body height + human_phenotype + HP:0000002 + Abnormality of body height + + + + + Deviation from the norm of height with respect to that which is expected according to age and gender norms. + HPO:probinson + + + + + Abnormality of body height + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A phenotypic abnormality. + UMLS:C4021819 + Organ abnormality + human_phenotype + HP:0000118 + This is the root of the phenotypic abnormality subontology of the HPO. + Phenotypic abnormality + + + + + A phenotypic abnormality. + HPO:probinson + + + + + + + + + + + + + + + + + + + + + + + + + + + + + HP:0008904 + UMLS:C0262361 + Abnormal growth + Growth abnormality + Growth issue + human_phenotype + HP:0001507 + Growth abnormality + + + + + Abnormal growth + + + + + + Growth abnormality + + + + + + Growth issue + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + HP:0002146 + HP:0004355 + HP:0004367 + UMLS:C4021768 + Laboratory abnormality + Metabolism abnormality + human_phenotype + HP:0001939 + Abnormality of metabolism/homeostasis + + + + + Laboratory abnormality + + + + + + Metabolism abnormality + + + + + + + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + UBERON:0000105 + developmental stage + stage + human_stages_ontology + HsapDv:0000000 + human life cycle stage + + + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + UBERON:0000105 + + + + + + + + + ncbi_taxonomy + m + mouse + NCBITaxon:10090 + Mus musculus + + + + + m + PRO:DAN + + + + + + mouse + + + + + + + + + + ncbi_taxonomy + euk- + NCBITaxon:2759 + Eukaryota + + + + + euk- + PRO:DAN + + + + + + + + + + ncbi_taxonomy + Fungi/Metazoa group + NCBITaxon:33154 + Opisthokonta + + + + + + + + + ncbi_taxonomy + metazoan- + NCBITaxon:33208 + Metazoa + + + + + metazoan- + PRO:DAN + + + + + + + + + + mammal + ncbi_taxonomy + mammal- + NCBITaxon:40674 + Mammalia + + + + + mammal + + + + + + mammal- + PRO:DAN + + + + + + + + + + zebrafish + ncbi_taxonomy + NCBITaxon:7955 + Danio rerio + + + + + zebrafish + + + + + + + + + + ncbi_taxonomy + h + human + NCBITaxon:9606 + Homo sapiens + + + + + h + PRO:DAN + + + + + + human + PRO:DAN + + + + + + + + + + rodent + ncbi_taxonomy + NCBITaxon:9989 + Rodentia + + + + + rodent + + + + + + + + + + obi + OBI:0100026 + organism + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + quality (PATO) + PATO:0000072 + quality + PATO:0000001 + quality + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + + A scalar optical property that is the intensity, value or amount of perceived light. + color intensity + color lightness + color value + quality + PATO:0000016 + + Color brightness refers to the intensity, lightness or value of the light present. Think of this as a dimmer switch. + color brightness + + + + + A scalar optical property that is the intensity, value or amount of perceived light. + PATOC:MAH + + + + + + + + + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. + quality + PATO:0000047 + + biological sex + + + + + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. + MGED:MGED + + + + + + + + + + A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. + quality + PATO:0000051 + + morphology + + + + + A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. + PATOC:GVG + + + + + + + + + quality + PATO:0000068 + TODO: define this or obsolete it and move children somewhere else. + qualitative + + + + + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + quality + PATO:0000069 + + deviation(from_normal) + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + PATOC:GVG + + + + + + + + + A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. + quality + PATO:0000117 + + + size + + + + + A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. + WordNet:WordNet + + + + + + + + + A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension. + quality + PATO:0000119 + + + height + + + + + A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension. + PATOC:GVG + + + + + + + + + A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. + + quality + aberrant + atypia + atypical + defective + PATO:0000460 + + + + abnormal + + + + + A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. + PATOC:GVG + + + + + + + + + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + PATO:0002079 + Wikipedia:Physical_property + relational physical quality + quality + PATO:0001018 + + physical quality + + + + + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + PATOC:GVG + + + + + + + + + + A quality which inheres in an process. + PATO:0001239 + PATO:0001240 + quality of a process + quality of occurrent + quality of process + relational quality of occurrent + quality + PATO:0001236 + See comments of relational quality of a physical entity. + process quality + + + + + A quality which inheres in an process. + PATOC:GVG + + + + + + + + + A quality which inheres in a continuant. + PATO:0001237 + PATO:0001238 + snap:Quality + monadic quality of a continuant + multiply inhering quality of a physical entity + quality of a continuant + quality of a single physical entity + quality of an object + quality of continuant + monadic quality of an object + monadic quality of continuant + quality + PATO:0001241 + Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. + physical object quality + + + + + A quality which inheres in a continuant. + PATOC:GVG + + + + + + + + + A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. + quality + PATO:0001291 + + electromagnetic (EM) radiation quality + + + + + A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. + Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation + + + + + + + + + An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. + quality + PATO:0001300 + + optical quality + + + + + An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. + PATOC:GVG + + + + + + + + + A monadic quality of continuant that exists at the cellular level of organisation. + quality + PATO:0001396 + cellular quality + + + + + A monadic quality of continuant that exists at the cellular level of organisation. + PATOC:GVG + + + + + + + + + A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. + quality + PATO:0001404 + + nucleate quality + + + + + A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. + PATOC:GVG + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. + quality + PATO:0001405 + + + + anucleate + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. + Biology-online:Biology-online + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. + quality + PATO:0001406 + + + + binucleate + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. + Biology-online:Biology-online + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. + quality + PATO:0001407 + + + + mononucleate + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. + Biology-online:Biology-online + + + + + + + + + A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. + 1-D size + quality + PATO:0001708 + + 1-D extent + + + + + A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. + PATOC:GVG + + + + + + + + + A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. + quality + PATO:0001739 + + radiation quality + + + + + A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. + PATOC:GVG + + + + + + + + + An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. + quality + PATO:0001894 + + phenotypic sex + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. + quality + PATO:0001908 + + + multinucleate + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. + PATOC:GVG + + + + + + + + + An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. + quality + PATO:0001992 + + + cellularity + + + + + An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. + PATOC:GVG + + + + + + + + + A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. + quality + PATO:0001993 + + multicellular + + + + + A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. + PATOC:GVG + + + + + + + + + A quality that inheres in an entire organism or part of an organism. + quality + PATO:0001995 + organismal quality + + + + + A quality that inheres in an entire organism or part of an organism. + PATOC:CJM + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. + gkoutos + 2013-10-21T05:44:34Z + quality + PATO:0002505 + + + nucleated + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. + PATOC:GVG + + + + + + + + + A material entity consisting of multiple components that are causally integrated. + May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 + Chris Mungall + http://www.jbiomedsem.com/content/4/1/43 + system + + + + + + + + An extent of biological sequence. + located_sequence_feature + sequence feature + sequence + located sequence feature + SO:0000110 + sequence_feature + + + + + An extent of biological sequence. + SO:ke + + + + + + + + + A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. + sequence + SO:0000704 + gene + + + + + A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. + SO:immuno_workshop + + + + + + + + + An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. + uberon + UBERON:0000000 + + processual entity + + + + + An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. + span:ProcessualEntity + + + + + + + + + + + + + + + + + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + + + AAO:0010825 + AEO:0000003 + BILA:0000003 + CARO:0000003 + EHDAA2:0003003 + EMAPA:0 + FBbt:00007001 + FMA:305751 + FMA:67135 + GAID:781 + HAO:0000003 + MA:0003000 + MESH:D000825 + TAO:0000037 + TGMA:0001823 + VHOG:0001759 + XAO:0003000 + ZFA:0000037 + biological structure + connected biological structure + uberon + UBERON:0000061 + + anatomical structure + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + CARO:0000003 + + + + + connected biological structure + CARO:0000003 + + + + + + + + + + + + + + + + + + + + + + + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + adult stage + BTO:0001043 + BilaDO:0000004 + EFO:0001272 + FBdv:00005369 + WBls:0000041 + XtroDO:0000084 + fully formed animal stage + juvenile-adult stage + uberon + UBERON:0000066 + + fully formed stage + + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + + + + + + + + + + + + + + + + + + + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + + BilaDO:0000002 + EV:0300001 + FBdv:00005289 + FMA:72652 + HsapDv:0000002 + MmusDv:0000002 + OGES:000000 + OGES:000022 + WBls:0000003 + WBls:0000092 + WBls:0000102 + XAO:1000012 + embryonic stage + uberon + embryogenesis + UBERON:0000068 + embryo stage + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + + + + + + + + + + + + + + + + End of the life of an organism. + ncit:Death is an outcome + XAO:0000437 + XtroDO:0000085 + uberon + death + UBERON:0000071 + death stage + + + + + End of the life of an organism. + XAO:0000437 + + + + + ncit:Death is an outcome + ncit + + + + + + + + + + + + + + + stage succeeding embryo, including mature structure + In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) + BilaDO:0000003 + OGES:000010 + OGES:000014 + OGES:000024 + WBls:0000022 + WBls:0000093 + WBls:0000103 + postembryonic stage + post-hatching stage + uberon + postembryonic + UBERON:0000092 + post-embryonic stage + + + + + + stage succeeding embryo, including mature structure + + + + + + + + + + + + + + + + + + + + + + + + + + + + An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. + FBdv:00000000 + HsapDv:0000001 + MmusDv:0000001 + OGES:000011 + ncithesaurus:Life + entire life cycle + entire lifespan + life + lifespan + uberon + UBERON:0000104 + + life cycle + + + + + + An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. + + + + + + + + + + + + + + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here + the WBls class 'all stages' belongs here as it is the superclass of other WBls stages + we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage + BILS:0000105 + EFO:0000399 + FBdv:00007012 + FMA:24120 + HsapDv:0000000 + MmusDv:0000000 + OlatDv:0000010 + PdumDv:0000090 + WBls:0000002 + XAO:1000000 + ZFS:0000000 + ZFS:0100000 + ncithesaurus:Developmental_Stage + developmental stage + stage + uberon + UBERON:0000105 + + + life cycle stage + + + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + + + + + + + + + + + + + + + + + + + + + + A stage at which the organism is a single cell produced by means of sexual reproduction. + As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] + + BILS:0000106 + BilaDO:0000005 + EFO:0001322 + EHDAA:27 + FBdv:00005288 + NCIT:C12601 + PdumDv:0000100 + VHOG:0000745 + XAO:1000001 + ZFS:0000001 + 1-cell stage + fertilized egg stage + one cell stage + uberon + fertilized egg stage + one-cell stage + zygote + zygotum + UBERON:0000106 + + zygote stage + + + + + + A stage at which the organism is a single cell produced by means of sexual reproduction. + + + + + + As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] + 2012-09-17 + VHOG:0000745 + VHOG + + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 + + + + + fertilized egg stage + BTO:0000854 + + + + + one-cell stage + VHOG:0000745 + + + + + zygote + VHOG:0000745 + + + + + zygotum + + + + + + + + + + + + + + + + + + + + + + + The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. + + BILS:0000107 + BilaDO:0000006 + EFO:0001290 + FBdv:00000054 + MESH:A16.254.270 + MmusDv:0000004 + OGES:000015 + OGES:000020 + PdumDv:0000200 + XAO:1000004 + ZFS:0000046 + uberon + UBERON:0000107 + + cleavage stage + + + + + The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. + + GO:0040016 + + + + + + + + + + + + + + + + + + + + + An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. + consider adding a preceding stage 'morula stage' as part of cleavage + + BILS:0000108 + BilaDO:0000007 + EFO:0001282 + HsapDv:0000006 + MmusDv:0000007 + OGES:000003 + OGES:000016 + OGES:000021 + OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg + WBls:0000005 + XAO:1000003 + ZFS:0000045 + uberon + UBERON:0000108 + + blastula stage + + + + + + An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. + + + + + + + + + + + + + + + + + + + + + + A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. + BILS:0000109 + BilaDO:0000008 + EFO:0001296 + FBdv:00005317 + HsapDv:0000010 + MmusDv:0000013 + OGES:000004 + OGES:000019 + WBls:0000010 + XAO:1000005 + ZFS:0000047 + uberon + blastocystis trilaminaris stage + trilaminar blastocyst stage + trilaminar blastoderm stage + trilaminar disk stage + trilaminar germ stage + trilaminar stage + UBERON:0000109 + + gastrula stage + + + + + + + + + + + BILS + + + + + A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. + GO:0007369 + + + + + blastocystis trilaminaris stage + + + + + + trilaminar blastocyst stage + + + + + + trilaminar blastoderm stage + + + + + + trilaminar disk stage + + + + + + trilaminar germ stage + + + + + + trilaminar stage + + + + + + + + + + + + + + + + + + + + + + Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. + BILS:0000110 + BilaDO:0000009 + HsapDv:0000012 + MmusDv:0000017 + XAO:1000006 + uberon + UBERON:0000110 + neurula stage + + + + + + Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. + GO:0001841 + + + + + + + + + + + + + + + + + + + + + A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. + + BILS:0000111 + BilaDO:0000010 + HsapDv:0000015 + MmusDv:0000018 + OGES:000005 + OGES:000032 + uberon + segmentation stage + UBERON:0000111 + organogenesis stage + + + + + + A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. + + + + + + + + + + Anatomical entity that has mass. + AAO:0010264 + AEO:0000006 + BILA:0000006 + CARO:0000006 + EHDAA2:0003006 + FBbt:00007016 + FMA:67165 + HAO:0000006 + TAO:0001836 + TGMA:0001826 + VHOG:0001721 + uberon + UBERON:0000465 + + material anatomical entity + + + + + Anatomical entity that has mass. + + + + + + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + TODO - split body and mc organism? body continues after death stage + organismal + organism + + + AAO:0010026 + AEO:0000191 + BILA:0000012 + BIRNLEX:18 + BSA:0000038 + BTO:0000042 + CARO:0000012 + EFO:0002906 + EHDAA2:0003103 + EHDAA2:0003191 + EHDAA:1 + EMAPA:25765 + EV:0100016 + FBbt:00000001 + FMA:256135 + HAO:0000012 + NCIT:C13041 + TADS:0000001 + TAO:0001094 + TGMA:0001832 + VHOG:0000671 + WBbt:0007833 + XAO:0003004 + ZFA:0001094 + galen:Organism + ncithesaurus:Whole_Organism + multi-cellular organism + animal + uberon + Koerper + body + whole body + whole organism + UBERON:0000468 + + + + + multicellular organism + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + + + CARO:0000012 + + + + + organism + FBbt:00000001 + VHOG:0000671 + WBbt:0007833 + + + + + multi-cellular organism + CARO:0000012 + + + + + animal + BTO:0000042 + + + + + Koerper + BTO:0001489 + + + + + body + AEO:0000103 + BIRNLEX:18 + FMA:256135 + NCIT:C13041 + + + + + whole body + BTO:0001489 + + + + + whole organism + FBbt:00000001 + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + AAO:0010841 + AEO:0000000 + BILA:0000000 + BIRNLEX:6 + CARO:0000000 + EHDAA2:0002229 + FBbt:10000000 + FBbt_root:00000000 + FMA:62955 + HAO:0000000 + MA:0000001 + NCIT:C12219 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + WBbt:0000100 + XAO:0000000 + ZFA:0100000 + uberon + UBERON:0001062 + + anatomical entity + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + FMA:62955 + + + + + UMLS:C1515976 + ncithesaurus:Anatomic_Structure_System_or_Substance + + + + + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + FBbt:00100313 + multicellular structure + uberon + UBERON:0010000 + + multicellular anatomical structure + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + + + + + multicellular structure + FBbt:00100313 + + + + + + + + + + + + + + pending final vetting + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From has_ligand to ligand activity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From ligand activity to has_ligand + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/hp_terms.txt b/src/ontology/imports/hp_terms.txt new file mode 100644 index 0000000..288ba1b --- /dev/null +++ b/src/ontology/imports/hp_terms.txt @@ -0,0 +1,4 @@ +HP:0000000 +HP:0000001 +HP:0000002 + diff --git a/src/ontology/imports/hsapdv_import.owl b/src/ontology/imports/hsapdv_import.owl new file mode 100644 index 0000000..7de5edb --- /dev/null +++ b/src/ontology/imports/hsapdv_import.owl @@ -0,0 +1,143 @@ + + + + + + + + + + + + + + + + + definition + + + + + + + + database_cross_reference + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BFO:0000050 + human_stages_ontology + part_of + part_of + part of + + + + + + + + + + + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + UBERON:0000105 + developmental stage + stage + human_stages_ontology + HsapDv:0000000 + human life cycle stage + + + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + UBERON:0000105 + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/hsapdv_terms.txt b/src/ontology/imports/hsapdv_terms.txt new file mode 100644 index 0000000..4590f5c --- /dev/null +++ b/src/ontology/imports/hsapdv_terms.txt @@ -0,0 +1,2 @@ +http://purl.obolibrary.org/obo/HsapDv_0000000 + diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index bb1af6d..c6acda1 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -7,11 +7,9 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" - xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - + @@ -27,12 +25,6 @@ - - - - - - @@ -81,18 +73,6 @@ - - - - in branch - An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. - GROUP:OBI - OBI_0000277 - in branch - - - - @@ -215,56 +195,9 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - curator note - - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - - curator note - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. - term tracker item - - - - - - - - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'term requester' can credit the person, organization or project who request the ontology term. - ontology term requester - - - - - - - - is denotator type - relates an class defined in an ontology, to the type of it's denotator - In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') - Alan Ruttenberg - is denotator type - + @@ -283,137 +216,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to - - - - - - - - expand assertion to - ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. - Chris Mungall - expand assertion to - - - - - - - - first order logic expression - PERSON:Alan Ruttenberg - first order logic expression - - - - - - - - antisymmetric property - part_of antisymmetric property xsd:true - use boolean value xsd:true to indicate that the property is an antisymmetric property - Alan Ruttenberg - antisymmetric property - - - - - - - - OBO foundry unique label - - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> - OBO foundry unique label - - - - - - - - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) - Person:Alan Ruttenberg - has ID digit count - - - - - - - - Datatype: idrange:1 -Annotations: 'has ID range allocated to': "Chris Mungall" -EquivalentTo: xsd:integer[> 2151 , <= 2300] - - Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms - Person:Alan Ruttenberg - has ID range allocated to - - - - - - - - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relating an ontology used to record id policy to the ontology namespace whose policy it manages - Person:Alan Ruttenberg - has ID policy for - - - - - - - - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. - Person:Alan Ruttenberg - has ID prefix - - - - @@ -429,93 +231,19 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - has associated axiom(nl) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom associated with a term expressed using natural language - - has associated axiom(nl) - + - - has associated axiom(fol) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom expressed in first order logic using CLIF syntax - - has associated axiom(fol) - - - - - - - - is allocated id range - Add as annotation triples in the granting ontology - Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" - PERSON:Alan Ruttenberg - is allocated id range - - - - - - - - A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. - David Osumi-Sutherland - #40 - VFB - 2018-09-21T16:43:39Z - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. - may be identical to - - - - - - - - Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. - Chris Mungall, Jie Zheng - https://github.com/geneontology/go-ontology/issues/15532 - https://github.com/information-artifact-ontology/ontology-metadata/issues/32 - GO ontology - scheduled for obsoletion on or after - + - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - - has axiom label - - - - - - - - term replaced by - - Add as annotation triples in the granting ontology - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - term replaced by - + @@ -525,108 +253,24 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. - ontology file - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - cjm - 2018-05-20T20:55:03Z - ontology module - - - - - - - - - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - cjm - 2018-05-20T20:55:30Z - base ontology module - - - - - - - - - - An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. - source ontology module - cjm - 2018-05-20T20:55:47Z - editors ontology module - - - - - - - - - An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. - TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module - cjm - 2018-05-20T20:56:13Z - main release ontology module - - - - - - - - - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - cjm - 2018-05-20T20:56:23Z - bridge ontology module - - - - - - - - - - A subset ontology module that is intended to be imported from another ontology. - TODO: add axioms that indicate this is the output of a module extraction process. - import file - cjm - 2018-05-20T20:56:47Z - import ontology module - - - - - - - - - - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - cjm - 2018-05-20T20:58:11Z - subset ontology module - - - - - - - - - - - A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. - cjm - 2018-05-20T20:58:38Z - curation subset ontology module - - - - - - - - - An ontology module that is intended for usage in analysis or discovery applications. - cjm - 2018-05-20T20:58:49Z - analysis subset ontology module - - - - - - - - - A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. - ribbon subset - cjm - 2018-05-20T20:59:19Z - single layer subset ontology module - - - - - - - - - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - cjm - 2018-05-20T20:59:57Z - exclusion subset ontology module - - - - - - - - - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - cjm - 2018-05-20T21:00:14Z - external import ontology module - - - - - - - - - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - cjm - 2018-05-20T21:14:16Z - species subset ontology module - - - - - - - - - - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - cjm - 2018-05-20T21:20:33Z - reasoned ontology module - - - - - - - - - - An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. - TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process - cjm - 2018-05-20T21:21:12Z - generated ontology module - - - - - - - - - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - cjm - 2018-05-20T21:21:21Z - template generated ontology module - - - - - - - - - - - - cjm - 2018-05-20T21:28:15Z - taxonomic bridge ontology module - - - - - - - - - cjm - 2018-05-22T04:15:54Z - ontology module subsetted by expressivity - - - - - - - - - A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. - -Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). - -An ontology is OBO Basic if and only if it has the following characteristics: -DAG -Unidirectional -No Dangling Clauses -Fully Asserted -Fully Labeled -No equivalence axioms -Singly labeled edges -No qualifier lists -No disjointness axioms -No owl-axioms header -No imports - cjm - 2018-05-22T04:16:10Z - obo basic subset ontology module - - - - - - - - - - cjm - 2018-05-22T04:16:28Z - ontology module subsetted by OWL profile - - - - - - - - - cjm - 2018-05-22T04:16:48Z - EL++ ontology module - - - - @@ -2301,22 +1658,6 @@ No imports - - - - - - - - - - - - - - - - @@ -2340,22 +1681,6 @@ No imports - - - - - - - - - - - - - - - - + + + + + + + + editor preferred term + + + + + + + + + IAO:0000112 + uberon + example_of_usage + true + example_of_usage + example of usage + example of usage + + + + + + + + has curation status + + + + + + + + + definition + definition + + + + + + + + + IAO:0000116 + uberon + editor_note + true + editor_note + editor note + editor note + + + + + + + + + term editor + + + + + + + + + alternative term + + + + + + + + + definition source + + + + + + + + + + + + + + + + + + + + + imported from + + + + + + + + + + + + + + + + + + + + elucidation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + is a defining property chain axiom + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + uberon + dc-description + true + dc-description + description + + + + + + + + + + + + + + + uberon + dc-title + true + dc-title + title + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + database_cross_reference + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + + + + + + + + BFO:0000050 + external + protein + quality + uberon + part_of + part_of + part of + part of + part_of + + + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + BFO:0000051 + chebi_ontology + external + protein + quality + uberon + has_part + false + has_part + We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. + has part + has part + has_part + + + + + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + PATOC:CJM + + + + + + + + + + + + + + + + + + + + + preceded by + X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + BFO:0000062 + is preceded by + takes place after + uberon + preceded_by + + preceded_by + preceded by + preceded_by + + + + + is preceded by + SIO:000249 + + + + + takes place after + Allen:precedes + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + BFO:0000063 + uberon + precedes + + precedes + precedes + precedes + + + + + + + + + + + + + + + + + + + occurs in + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + occurs_in + unfolds in + unfolds_in + BFO:0000066 + external + occurs_in + occurs_in + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs in + occurs in + + + + + + + + site of + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + BFO:0000067 + uberon + contains_process + contains_process + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + contains process + + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + RO:0000053 + uberon + bearer_of + bearer_of + bearer of + bearer of + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + RO:0000056 + protein + participates_in + false + participates_in + participates in + participates_in + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + role of + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + protein + uberon + has_quality + false + has_quality + has quality + has quality + has_quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + chebi_ontology + protein + has_role + false + false + has_role + has role + has role + has_role + + + + + + + + + + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + RO:0001000 + protein + derives_from + + derives_from + derives from + derives_from + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + + derives into + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. + dos + 2017-07-19T17:30:36Z + has ligand + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + directly negatively regulated by + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + directly positively regulated by + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + + + + + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + David Osumi-Sutherland + starts_at_end_of + A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. + RO:0002087 + directly preceded by + is directly preceded by + is immediately preceded by + starts_at_end_of + uberon + immediately_preceded_by + immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + immediately_preceded_by + + + + + + A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. + SIO:000251 + + + + + is immediately preceded by + SIO:000251 + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + external + starts_during + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + starts_during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + external + ends_during + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during + ends_during + + + + + + + + + + + + + + + + + + + + + + + + + + A overlaps B if they share some part in common. + x overlaps y if and only if there exists some z such that x has part z and z part of y + BFO_0000051 some (BFO_0000050 some ?Y) + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + RO:0002131 + uberon + overlaps + + overlaps + overlaps + overlaps + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + Chris Mungall + Jennifer Deegan + + + RO:0002162 + uberon + in_taxon + + in_taxon + Connects a biological entity to its taxon of origin. + in taxon + + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + RO:0002180 + protein + uberon + has_component + + false + has_component + has component + has component + has_component + + + + + + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall + David Hill + Tanya Berardini + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + RO:0002211 + external + regulates + regulates + regulates + regulates + + + + + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + negatively regulates (process to process) + + RO:0002212 + external + negatively_regulates + negatively_regulates + negatively regulates + negatively regulates + + + + + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + positively regulates (process to process) + + RO:0002213 + external + positively_regulates + positively_regulates + positively regulates + positively regulates + + + + + + + + + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + Chris Mungall + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + RO:0002215 + protein + uberon + capable_of + + false + capable_of + capable of + capable of + capable_of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + Chris Mungall + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + RO:0002216 + uberon + capable_of_part_of + capable_of_part_of + capable of part of + capable of part of + + + + + + + + + + true + + + + + + + + + + x actively participates in y if and only if x participates in y and x realizes some active role + Chris Mungall + agent in + actively participates in + + + + + + + + + 'heart development' has active participant some Shh protein + + x has participant y if and only if x realizes some active role that inheres in y + This may be obsoleted and replaced by the original 'has agent' relation + Chris Mungall + has agent + + obsolete has active participant + true + + + + + + + + + + + Chris Mungall + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + Relation between occurrents, shares a start boundary with. + inverse of starts with + Chris Mungall + Allen + RO:0002223 + uberon + starts + + starts + starts + starts + + + + + Relation between occurrents, shares a start boundary with. + + Allen:starts + + + + + + + + + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by + RO:0002224 + uberon + starts_with + + starts_with + starts with + starts with + + + + + + + + + + + + Relation between occurrents, shares an end boundary with. + inverse of ends with + Chris Mungall + RO:0002229 + finishes + uberon + ends + + ends + ends + ends + + + + + Relation between occurrents, shares an end boundary with. + + Allen:starts + ZFS:finishes + + + + + + + + + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by + RO:0002230 + uberon + ends_with + + ends_with + ends with + ends with + + + + + + + + + + + + + + + + x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y + Chris Mungall + starts with process that occurs in + + has start location + + + + + + + + + + + + + + + + x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + Chris Mungall + ends with process that occurs in + + has end location + + + + + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + Chris Mungall + consumes + + has input + + + + + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + Chris Mungall + produces + + has output + + + + + + + + + + + + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of + + + + + + + + + + + + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + acts upstream of or within + + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + + + + + + + + + + + + + + q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of inheres in part of + Chris Mungall + + + inheres in part of + + + + + + + + + + true + + + + + + + + A relationship that holds via some environmental process + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + evolutionarily related to + + + + + + + + A mereological relationship or a topological relationship + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + mereotopologically related to + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + Chris Mungall + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function + RO:0002328 + uberon + functionally_related_to + functionally_related_to + functionally related to + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + Chris Mungall + false + RO:0002329 + uberon + part_of_structure_that_is_capable_of + part_of_structure_that_is_capable_of + part of structure that is capable of + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + Chris Mungall + actively involved in + enables part of + RO:0002331 + protein + involved_in + false + involved_in + involved in + involved_in + + + + + + + + + + + inverse of enables + Chris Mungall + enabled by + + + + + + + + + + + + inverse of regulates + Chris Mungall + regulated by (processual) + + regulated by + + + + + + + + + inverse of negatively regulates + Chris Mungall + + negatively regulated by + + + + + + + + + inverse of positively regulates + Chris Mungall + + positively regulated by + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + uberon + member_of + member_of + member of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + uberon + has_member + has_member + has member + has member + + + + + + + + + + inverse of has input + Chris Mungall + RO:0002352 + uberon + input_of + + + input_of + input of + input of + + + + + + + + + + inverse of has output + Chris Mungall + RO:0002353 + protein + uberon + output_of + + + false + output_of + output of + output of + output_of + + + + + + + + + + + + inverse of upstream of + Chris Mungall + causally downstream of + + + + + + + + + + + + Chris Mungall + immediately causally downstream of + + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types. + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causally related to + + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + Chris Mungall + causally upstream of + + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + Chris Mungall + + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) + affects + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + Chris Mungall + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + Chris Mungall + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + Chris Mungall + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + Chris Mungall + + involved in negative regulation of + + + + + + + + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union + Chris Mungall + involved in or reguates + involved in or involved in regulation of + + + + + + + + + + + + + + A protein that enables activity in a cytosol. + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + Chris Mungall + executes activity in + enables activity in + + is active in + + + + + + + + + true + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + GOC:cjm + GOC:dos + + + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + Considering relabeling as 'pairwise interacts with' + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + Chris Mungall + binds + molecularly binds with + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + Axiomatization to GO to be added later + Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + phosphorylates + + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + Chris Mungall + molecularly controls + activity directly regulates activity of + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + Chris Mungall + inhibits + molecularly decreases activity of + activity directly negatively regulates activity of + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + Chris Mungall + activates + molecularly increases activity of + activity directly positively regulates activity of + + + + + + + + Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + helper property (not for use in curation) + + + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + Chris Mungall + + has part that occurs in + + + + + + + + + true + + + + + + + + + Chris Mungall + is kinase activity + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + causal agent in process + + + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + + + + + + + + Chris Mungall + depends on + + + + + + + + + + + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between material entities + + + + + + + + + + Chris Mungall + + causally influenced by (material entity to material entity) + causally influenced by + + + + + + + + + Chris Mungall + interaction relation helper property + + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + Chris Mungall + molecular interaction relation helper property + + + + + + + + + + + + + + + + + + + Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b + Chris Mungall + + causally influences (material entity to material entity) + causally influences + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + Chris Mungall + + directly regulates (processual) + + directly regulates + + + + + + + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + Chris Mungall + has part structure that is capable of + + + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + Chris Mungall + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + capable of negatively regulating + + + + + + + + + + + + + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + + process has causal agent + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + + directly positively regulates (process to process) + + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + directly negatively regulates (process to process) + + directly negatively regulates + + + + + + + + + + + + + + + + + + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + Melissa Haendel + RO:0003000 + uberon + produces + + produces + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + produces + produces + + + + + + + + + + + a produced_by b iff some process that occurs_in b has_output a. + Melissa Haendel + RO:0003001 + uberon + produced_by + + produced_by + produced by + produced_by + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + enables subfunction + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:30Z + acts upstream of or within, positive effect + + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:51Z + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + cjm + 2018-01-26T23:53:14Z + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + cjm + 2018-01-26T23:53:22Z + acts upstream of, negative effect + + + + + + + + + + + cjm + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + + + + + + + + + + cjm + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + + + + + + + + chebi_ontology + has_functional_parent + false + false + has functional parent + + + + + + + + chebi_ontology + is_substituent_group_from + false + false + is substituent group from + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + bfo + BFO:0000015 + process + process + + + + + + + + + + disposition + + + + + + + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + + + + + + + + + + + + + + + bfo + BFO:0000019 + quality + quality + + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + bfo + BFO:0000030 + object + + + + + + + + + + + + + + + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + generically dependent continuant + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + bfo + BFO:0000040 + material entity + material entity + + + + + + + + + + anatomical entity + + + + + + + + + + connected anatomical structure + + + + + + + + + + + material anatomical entity + + + + + + + + + + cell part (CARO) + cell part + + + + + + + + + organism or virus or viroid + + + + + + + + + biological entity + + + + + + + + + Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. + -1 + 0.000548579903 + 0.0 + KEGG:C05359 + PMID:21614077 + Wikipedia:Electron + electron + chebi_ontology + Elektron + beta + beta(-) + beta-particle + e + e(-) + e- + negatron + CHEBI:10545 + + electron + + + + + PMID:21614077 + Europe PMC + + + + + electron + ChEBI + + + + + electron + IUPAC + + + + + + electron + KEGG_COMPOUND + + + + + Elektron + ChEBI + + + + + beta + IUPAC + + + + + beta(-) + ChEBI + + + + + beta-particle + IUPAC + + + + + e + IUPAC + + + + + e(-) + UniProt + + + + + e- + KEGG_COMPOUND + + + + + negatron + IUPAC + + + + + + + + + + + + + + + + A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. + 0 + (C5H8O6PR)n.C10H17O10PR2 + CHEBI:13672 + CHEBI:14859 + CHEBI:8312 + KEGG:C00419 + Polynucleotide + chebi_ontology + polynucleotides + CHEBI:15986 + + polynucleotide + + + + + Polynucleotide + KEGG_COMPOUND + + + + + polynucleotides + ChEBI + + + + + + + + + That part of DNA or RNA that may be involved in pairing. + CHEBI:13873 + CHEBI:25598 + CHEBI:2995 + KEGG:C00701 + Wikipedia:Nucleobase + chebi_ontology + Base + nucleobases + CHEBI:18282 + + nucleobase + + + + + Base + KEGG_COMPOUND + + + + + nucleobases + ChEBI + + + + + + + + + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. + molecular entity + chebi_ontology + entidad molecular + entidades moleculares + entite moleculaire + molecular entities + molekulare Entitaet + CHEBI:23367 + + molecular entity + + + + + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. + fake:2 + + + + + molecular entity + IUPAC + + + + + + entidad molecular + IUPAC + + + + + entidades moleculares + IUPAC + + + + + entite moleculaire + IUPAC + + + + + molecular entities + IUPAC + + + + + molekulare Entitaet + ChEBI + + + + + + + + + A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. + chemical entity + chebi_ontology + CHEBI:24431 + + chemical entity + + + + + chemical entity + UniProt + + + + + + + + + A role played by the molecular entity or part thereof within a biological context. + chebi_ontology + biological function + CHEBI:24432 + + biological role + + + + + biological function + ChEBI + + + + + + + + + + + + + + + A defined linked collection of atoms or a single atom within a molecular entity. + group + chebi_ontology + Gruppe + Rest + groupe + grupo + grupos + CHEBI:24433 + + group + + + + + group + IUPAC + + + + + + Gruppe + ChEBI + + + + + Rest + ChEBI + + + + + groupe + IUPAC + + + + + grupo + IUPAC + + + + + grupos + IUPAC + + + + + + + + + + + A cyclic compound having as ring members atoms of carbon and at least of one other element. + chebi_ontology + organic heterocycle + organic heterocyclic compounds + CHEBI:24532 + + organic heterocyclic compound + + + + + organic heterocycle + ChEBI + + + + + organic heterocyclic compounds + ChEBI + + + + + + + + + Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. + molecule + chebi_ontology + Molekuel + molecula + molecules + neutral molecular compounds + CHEBI:25367 + + molecule + + + + + molecule + IUPAC + + + + + Molekuel + ChEBI + + + + + molecula + IUPAC + + + + + molecules + IUPAC + + + + + neutral molecular compounds + IUPAC + + + + + + + + + + + + + + + + 0 + N + 14.007 + 14.00307 + WebElements:N + nitrogen + chebi_ontology + 7N + N + Stickstoff + azote + nitrogen + nitrogeno + CHEBI:25555 + + nitrogen atom + + + + + nitrogen + IUPAC + + + + + + 7N + IUPAC + + + + + N + IUPAC + + + + + Stickstoff + ChEBI + + + + + azote + IUPAC + + + + + nitrogen + ChEBI + + + + + nitrogeno + ChEBI + + + + + + + + + nonmetal + chebi_ontology + Nichtmetall + Nichtmetalle + no metal + no metales + non-metal + non-metaux + nonmetal + nonmetals + CHEBI:25585 + + nonmetal atom + + + + + nonmetal + IUPAC + + + + + + Nichtmetall + ChEBI + + + + + Nichtmetalle + ChEBI + + + + + no metal + ChEBI + + + + + no metales + ChEBI + + + + + non-metal + ChEBI + + + + + non-metaux + ChEBI + + + + + nonmetal + ChEBI + + + + + nonmetals + ChEBI + + + + + + + + + + + + + + + + 0 + C + InChI=1S/C + OKTJSMMVPCPJKN-UHFFFAOYSA-N + 12.01070 + 12.00000 + [C] + CHEBI:23009 + CHEBI:3399 + CAS:7440-44-0 + KEGG:C06265 + WebElements:C + carbon + chebi_ontology + 6C + C + Carbon + Kohlenstoff + carbon + carbone + carbonium + carbono + CHEBI:27594 + + carbon atom + + + + + CAS:7440-44-0 + ChemIDplus + + + + + CAS:7440-44-0 + KEGG COMPOUND + + + + + carbon + IUPAC + + + + + + 6C + IUPAC + + + + + C + IUPAC + + + + + C + KEGG_COMPOUND + + + + + Carbon + KEGG_COMPOUND + + + + + Kohlenstoff + ChEBI + + + + + carbon + ChEBI + + + + + carbone + ChEBI + + + + + carbonium + ChEBI + + + + + carbono + ChEBI + + + + + + + + + A particle not known to have substructure. + elementary particle + chebi_ontology + elementary particles + CHEBI:33233 + + fundamental particle + + + + + elementary particle + IUPAC + + + + + + elementary particles + ChEBI + + + + + + + + + + + + + + + + Any substituent group or skeleton containing carbon. + chebi_ontology + organic groups + CHEBI:33247 + + organic group + + + + + organic groups + ChEBI + + + + + + + + + + + + + + + + + + + + + A chemical entity constituting the smallest component of an element having the chemical properties of the element. + CHEBI:22671 + CHEBI:23907 + atom + chebi_ontology + atome + atomo + atoms + atomus + element + elements + CHEBI:33250 + + atom + + + + + atom + IUPAC + + + + + + atome + IUPAC + + + + + atomo + IUPAC + + + + + atoms + ChEBI + + + + + atomus + ChEBI + + + + + element + ChEBI + + + + + elements + ChEBI + + + + + + + + + + + + + + + A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. + nucleus + chebi_ontology + Atomkern + Kern + noyau + noyau atomique + nuclei + nucleo + nucleo atomico + nucleus atomi + CHEBI:33252 + + atomic nucleus + + + + + nucleus + IUPAC + + + + + + Atomkern + ChEBI + + + + + Kern + ChEBI + + + + + noyau + IUPAC + + + + + noyau atomique + ChEBI + + + + + nuclei + ChEBI + + + + + nucleo + IUPAC + + + + + nucleo atomico + ChEBI + + + + + nucleus atomi + ChEBI + + + + + + + + + + Heavy nuclear particle: proton or neutron. + nucleon + chebi_ontology + Nukleon + Nukleonen + nucleons + CHEBI:33253 + + nucleon + + + + + nucleon + IUPAC + + + + + nucleon + IUPAC + + + + + + Nukleon + ChEBI + + + + + Nukleonen + ChEBI + + + + + nucleons + ChEBI + + + + + + + + + A nutrient is a food component that an organism uses to survive and grow. + chebi_ontology + nutrients + CHEBI:33284 + + nutrient + + + + + nutrients + ChEBI + + + + + + + + + A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. + chebi_ontology + heteroorganic entities + organoelement compounds + CHEBI:33285 + + heteroorganic entity + + + + + heteroorganic entities + ChEBI + + + + + organoelement compounds + ChEBI + + + + + + + + + Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. + pnictogens + chebi_ontology + group 15 elements + group V elements + nitrogenoideos + nitrogenoides + pnictogene + pnictogenes + CHEBI:33300 + + pnictogen + + + + + pnictogens + IUPAC + + + + + + group 15 elements + ChEBI + + + + + group V elements + ChEBI + + + + + nitrogenoideos + ChEBI + + + + + nitrogenoides + ChEBI + + + + + pnictogene + ChEBI + + + + + pnictogenes + ChEBI + + + + + + + + + + + + + + + A p-block molecular entity containing any pnictogen. + pnictogen molecular entity + chebi_ontology + pnictogen molecular entities + CHEBI:33302 + + pnictogen molecular entity + + + + + pnictogen molecular entity + ChEBI + + + + + pnictogen molecular entities + ChEBI + + + + + + + + + group 14 elements + chebi_ontology + carbon group element + carbon group elements + carbonoides + cristallogene + cristallogenes + group IV elements + CHEBI:33306 + + carbon group element atom + + + + + group 14 elements + IUPAC + + + + + + carbon group element + ChEBI + + + + + carbon group elements + ChEBI + + + + + carbonoides + ChEBI + + + + + cristallogene + ChEBI + + + + + cristallogenes + ChEBI + + + + + group IV elements + ChEBI + + + + + + + + + An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. + main group elements + chebi_ontology + Hauptgruppenelement + Hauptgruppenelemente + main group element + CHEBI:33318 + + main group element atom + + + + + main group elements + IUPAC + + + + + + Hauptgruppenelement + ChEBI + + + + + Hauptgruppenelemente + ChEBI + + + + + main group element + ChEBI + + + + + + + + + Any main group element atom belonging to the p-block of the periodic table. + chebi_ontology + p-block element + p-block elements + CHEBI:33560 + + p-block element atom + + + + + p-block element + ChEBI + + + + + p-block elements + ChEBI + + + + + + + + + + + + + + + A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. + chebi_ontology + main group compounds + main group molecular entities + CHEBI:33579 + + main group molecular entity + + + + + main group compounds + ChEBI + + + + + main group molecular entities + ChEBI + + + + + + + + + + + + + + + carbon group molecular entity + chebi_ontology + carbon group molecular entities + CHEBI:33582 + + carbon group molecular entity + + + + + carbon group molecular entity + ChEBI + + + + + carbon group molecular entities + ChEBI + + + + + + + + + Any molecule that consists of a series of atoms joined together to form a ring. + Wikipedia:Cyclic_compound + chebi_ontology + cyclic compounds + CHEBI:33595 + + cyclic compound + + + + + cyclic compounds + ChEBI + + + + + + + + + A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character. + aromatic compounds + aromatic molecular entity + chebi_ontology + aromatics + aromatische Verbindungen + CHEBI:33655 + + aromatic compound + + + + + aromatic compounds + IUPAC + + + + + + aromatic molecular entity + IUPAC + + + + + + aromatics + ChEBI + + + + + aromatische Verbindungen + ChEBI + + + + + + + + + + chebi_ontology + organic aromatic compounds + CHEBI:33659 + + organic aromatic compound + + + + + organic aromatic compounds + ChEBI + + + + + + + + + + + + + + + A main group molecular entity that contains one or more atoms of a p-block element. + chebi_ontology + p-block compounds + p-block molecular entities + p-block molecular entitiy + CHEBI:33675 + + p-block molecular entity + + + + + p-block compounds + ChEBI + + + + + p-block molecular entities + ChEBI + + + + + p-block molecular entitiy + ChEBI + + + + + + + + + + A macromolecule formed by a living organism. + biopolymer + chebi_ontology + Biopolymere + biomacromolecules + biopolymers + CHEBI:33694 + + biomacromolecule + + + + + biopolymer + IUPAC + + + + + + Biopolymere + ChEBI + + + + + biomacromolecules + ChEBI + + + + + biopolymers + ChEBI + + + + + + + + + chebi_ontology + genetically encoded biomacromolecules + genetically encoded biopolymers + information biomacromolecules + information biopolymers + information macromolecule + information macromolecules + CHEBI:33695 + + information biomacromolecule + + + + + genetically encoded biomacromolecules + ChEBI + + + + + genetically encoded biopolymers + ChEBI + + + + + information biomacromolecules + ChEBI + + + + + information biopolymers + ChEBI + + + + + information macromolecule + ChEBI + + + + + information macromolecules + ChEBI + + + + + + + + + + + + + + + + + + + + + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + nucleic acids + chebi_ontology + NA + Nukleinsaeure + Nukleinsaeuren + acide nucleique + acides nucleiques + acido nucleico + acidos nucleicos + CHEBI:33696 + + nucleic acid + + + + + nucleic acids + IUPAC + + + + + + NA + ChEBI + + + + + Nukleinsaeure + ChEBI + + + + + Nukleinsaeuren + ChEBI + + + + + acide nucleique + ChEBI + + + + + acides nucleiques + ChEBI + + + + + acido nucleico + ChEBI + + + + + acidos nucleicos + ChEBI + + + + + + + + + chebi_ontology + canonical nucleoside residues + common nucleoside residues + nucleoside residue + standard nucleoside residues + CHEBI:33791 + + canonical nucleoside residue + + + + + canonical nucleoside residues + ChEBI + + + + + common nucleoside residues + CBN + + + + + nucleoside residue + CBN + + + + + standard nucleoside residues + ChEBI + + + + + + + + + + Any organic molecule that consists of atoms connected in the form of a ring. + chebi_ontology + organic cyclic compounds + CHEBI:33832 + + organic cyclic compound + + + + + organic cyclic compounds + ChEBI + + + + + + + + + + A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). + heteroarenes + chebi_ontology + hetarenes + CHEBI:33833 + + heteroarene + + + + + heteroarenes + IUPAC + + + + + + hetarenes + IUPAC + + + + + + + + + A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. + Wikipedia:Macromolecule + macromolecule + chebi_ontology + macromolecules + polymer + polymer molecule + polymers + CHEBI:33839 + + macromolecule + + + + + macromolecule + IUPAC + + + + + + macromolecules + ChEBI + + + + + polymer + ChEBI + + + + + polymer molecule + IUPAC + + + + + polymers + ChEBI + + + + + + + + + chebi_ontology + CHEBI:33937 + + macronutrient + + + + + + + + + + Any heteroorganic entity containing at least one carbon-nitrogen bond. + organonitrogen compounds + chebi_ontology + organonitrogens + CHEBI:35352 + + organonitrogen compound + + + + + organonitrogen compounds + IUPAC + + + + + + organonitrogens + ChEBI + + + + + + + + + + Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin). + chebi_ontology + leptons + CHEBI:36338 + + lepton + + + + + leptons + ChEBI + + + + + + + + + + Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). + chebi_ontology + baryons + CHEBI:36339 + + baryon + + + + + baryons + ChEBI + + + + + + + + + Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. + fermion + chebi_ontology + fermions + CHEBI:36340 + + fermion + + + + + fermion + IUPAC + + + + + + fermions + ChEBI + + + + + + + + A particle smaller than an atom. + chebi_ontology + subatomic particles + CHEBI:36342 + + subatomic particle + + + + + subatomic particles + ChEBI + + + + + + + + + A subatomic particle known to have substructure (i.e. consisting of smaller particles). + chebi_ontology + composite particles + CHEBI:36343 + + composite particle + + + + + composite particles + ChEBI + + + + + + + + + Hadron is a subatomic particle which experiences the strong force. + chebi_ontology + hadrons + CHEBI:36344 + + hadron + + + + + hadrons + ChEBI + + + + + + + + + A nucleus or any of its constituents in any of their energy states. + nuclear particle + chebi_ontology + CHEBI:36347 + + nuclear particle + + + + + nuclear particle + IUPAC + + + + + + + + + + + + + + + + Any molecular entity consisting of more than one atom. + chebi_ontology + polyatomic entities + CHEBI:36357 + + polyatomic entity + + + + + polyatomic entities + ChEBI + + + + + + + + + + Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. + chebi_ontology + heterocyclic organonitrogen compounds + organonitrogen heterocyclic compounds + CHEBI:38101 + + organonitrogen heterocyclic compound + + + + + heterocyclic organonitrogen compounds + ChEBI + + + + + organonitrogen heterocyclic compounds + ChEBI + + + + + + + + + chebi_ontology + canonical nucleotide residues + CHEBI:50297 + + canonical nucleotide residue + + + + + canonical nucleotide residues + ChEBI + + + + + + + + + chebi_ontology + nucleotide residues + CHEBI:50319 + + nucleotide residue + + + + + nucleotide residues + ChEBI + + + + + + + + + chebi_ontology + nucleoside residues + CHEBI:50320 + + nucleoside residue + + + + + nucleoside residues + ChEBI + + + + + + + + + + + + + + + Any molecular entity that contains carbon. + CHEBI:25700 + CHEBI:33244 + chebi_ontology + organic compounds + organic entity + organic molecular entities + CHEBI:50860 + + organic molecular entity + + + + + organic compounds + ChEBI + + + + + organic entity + ChEBI + + + + + organic molecular entities + ChEBI + + + + + + + + A role is particular behaviour which a material entity may exhibit. + chebi_ontology + CHEBI:50906 + + role + + + + + + + + + + + + + + + CHEBI:25556 + CHEBI:7594 + KEGG:C06061 + chebi_ontology + Nitrogenous compounds + nitrogen compounds + nitrogen molecular entities + CHEBI:51143 + + nitrogen molecular entity + + + + + Nitrogenous compounds + KEGG_COMPOUND + + + + + nitrogen compounds + ChEBI + + + + + nitrogen molecular entities + ChEBI + + + + + + + + + chebi_ontology + CHEBI:52211 + + physiological role + + + + + + + + + A cyclic compound having as ring members atoms of at least two different elements. + Heterocyclic compound + chebi_ontology + compuesto heterociclico + compuestos heterociclicos + heterocycle + heterocyclic compounds + CHEBI:5686 + + heterocyclic compound + + + + + Heterocyclic compound + KEGG_COMPOUND + + + + + compuesto heterociclico + IUPAC + + + + + compuestos heterociclicos + IUPAC + + + + + heterocycle + ChEBI + + + + + heterocyclic compounds + ChEBI + + + + + + + + + + + + + + + + Any compound that has a nucleobase as a part. + chebi_ontology + nucleobase-containing compound + nucleobase-containing compounds + nucleobase-containing molecular entities + CHEBI:61120 + + nucleobase-containing molecular entity + + + + + nucleobase-containing compound + SUBMITTER + + + + + nucleobase-containing compounds + ChEBI + + + + + nucleobase-containing molecular entities + ChEBI + + + + + + + + + + Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. + chebi_ontology + organic compound + organic compounds + organic molecules + CHEBI:72695 + + organic molecule + + + + + organic compound + ChEBI + + + + + organic compounds + ChEBI + + + + + organic molecules + ChEBI + + + + + + + + + Any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants. + chebi_ontology + dietary component + dietary components + food components + CHEBI:78295 + + food component + + + + + dietary component + ChEBI + + + + + dietary components + ChEBI + + + + + food components + ChEBI + + + + + + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + + CALOHA:TS-2035 + FMA:68646 + GO:0005623 + KUPO:0000002 + VHOG:0001533 + WBbt:0004017 + XAO:0003012 + cell + CL:0000000 + + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + cell + cell + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CARO:mah + + + + + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + molecular process + GO:0005554 + molecular function + molecular_function + GO:0003674 + + + + + + + + + Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + molecular_function + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + GOC:pdt + + + + + + + + + Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. + Wikipedia:Enzyme + enzyme activity + molecular_function + GO:0003824 + + + + + + + catalytic activity + + + + + Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. + GOC:vw + ISBN:0198506732 + + + + + enzyme activity + GOC:dph + GOC:tb + + + + + + + + + + true + + + + + + + + + Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. + receptor binding + Wikipedia:Ligand_(biochemistry) + receptor ligand + molecular_function + receptor-associated protein activity + GO:0005102 + + + + + + Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'. + signaling receptor binding + + + + + Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. + GOC:bf + GOC:ceb + ISBN:0198506732 + + + + + + + + + The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. + Wikipedia:Binding_(molecular) + ligand + molecular_function + GO:0005488 + + + + Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. + binding + + + + + The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. + GOC:ceb + GOC:mah + ISBN:0198506732 + + + + + + + + + Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). + GO:0001948 + GO:0045308 + MIPS_funcat:16.01 + MIPS_funcat:18.01.07 + Reactome:R-HSA-170835 + Reactome:R-HSA-170846 + protein amino acid binding + glycoprotein binding + molecular_function + GO:0005515 + + + + + + + protein binding + + + + + Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). + GOC:go_curators + + + + + Reactome:R-HSA-170835 + An anchoring protein, ZFYVE9 (SARA), recruits SMAD2/3 + + + + + Reactome:R-HSA-170846 + TGFBR2 recruits TGFBR1 + + + + + + + + + A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). + The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. + GO:0008372 + NIF_Subcellular:sao1337158144 + cell or subcellular entity + cellular component + cellular_component + subcellular entity + GO:0005575 + + + + + + + + + Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. + Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + cellular_component + + + + + A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). + GOC:pdt + NIF_Subcellular:sao1337158144 + + + + + The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. + GOC:go_curators + + + + + subcellular entity + NIF_Subcellular:nlx_subcell_100315 + + + + + + + + + The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. + Wikipedia:Intracellular + internal to cell + protoplasm + cellular_component + nucleocytoplasm + protoplast + GO:0005622 + + + + + + intracellular + + + + + The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. + ISBN:0198506732 + + + + + nucleocytoplasm + GOC:mah + + + + + protoplast + GOC:mah + + + + + + + + + The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. + cell and encapsulating structures + NIF_Subcellular:sao1813327414 + Wikipedia:Cell_(biology) + cellular_component + GO:0005623 + + + + cell + + + + + The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. + GOC:go_curators + + + + + + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + + MIPS_funcat:70.10 + NIF_Subcellular:sao1702920020 + Wikipedia:Cell_nucleus + cell nucleus + horsetail nucleus + cellular_component + GO:0005634 + + + + + + + + + + + + + nucleus + nucleus + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + GOC:go_curators + + + + + horsetail nucleus + GOC:al + GOC:mah + GOC:vw + PMID:15030757 + + + + + + + + + The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). + phosphorus metabolism + biological_process + GO:0006793 + + phosphorus metabolic process + + + + + The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). + GOC:ai + + + + + + + + + The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. + MIPS_funcat:01.04 + phosphate metabolism + biological_process + phosphate metabolic process + GO:0006796 + phosphate-containing compound metabolic process + + + + + The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. + GOC:ai + + + + + + + + + Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + Wikipedia:Cell_signaling + biological_process + GO:0007154 + + + cell communication + + + + + Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. + GO:0023033 + MIPS_funcat:30 + Wikipedia:Signal_transduction + signaling cascade + signalling cascade + biological_process + signaling pathway + signalling pathway + GO:0007165 + + + + + + + Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. + signal transduction + + + + + The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. + GOC:go_curators + GOC:mtg_signaling_feb11 + + + + + signalling pathway + GOC:mah + + + + + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + janelomax + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + biological_process + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + + + + + + + + + The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + janelomax + 2012-10-17T15:46:40Z + GO:0044236 + GO:0044710 + MIPS_funcat:01 + Wikipedia:Metabolism + metabolism + metabolic process resulting in cell growth + metabolism resulting in cell growth + multicellular organism metabolic process + biological_process + single-organism metabolic process + GO:0008152 + + + + + + Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. + metabolic process + + + + + The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. + GOC:go_curators + ISBN:0198547684 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044252 + down regulation of metabolic process + down-regulation of metabolic process + downregulation of metabolic process + negative regulation of metabolism + negative regulation of organismal metabolism + inhibition of metabolic process + inhibition of organismal metabolic process + negative regulation of multicellular organismal metabolic process + biological_process + GO:0009892 + negative regulation of metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044253 + positive regulation of metabolism + up regulation of metabolic process + up-regulation of metabolic process + upregulation of metabolic process + activation of metabolic process + positive regulation of multicellular organismal metabolic process + positive regulation of organismal metabolism + stimulation of metabolic process + stimulation of organismal metabolic process + up-regulation of organismal metabolic process + biological_process + GO:0009893 + positive regulation of metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of signal transduction. + GO:0035466 + biological_process + regulation of signaling pathway + regulation of signalling pathway + GO:0009966 + regulation of signal transduction + + + + + Any process that modulates the frequency, rate or extent of signal transduction. + GOC:sm + + + + + regulation of signalling pathway + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of signal transduction. + GO:0035468 + up regulation of signal transduction + up-regulation of signal transduction + upregulation of signal transduction + activation of signal transduction + stimulation of signal transduction + biological_process + positive regulation of signaling pathway + positive regulation of signalling pathway + GO:0009967 + positive regulation of signal transduction + + + + + Any process that activates or increases the frequency, rate or extent of signal transduction. + GOC:sm + + + + + positive regulation of signalling pathway + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. + GO:0035467 + down regulation of signal transduction + down-regulation of signal transduction + downregulation of signal transduction + inhibition of signal transduction + biological_process + negative regulation of signaling pathway + negative regulation of signalling pathway + GO:0009968 + negative regulation of signal transduction + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. + GOC:sm + + + + + negative regulation of signalling pathway + GOC:mah + + + + + + + + + Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + janelomax + 2012-12-11T16:56:55Z + GO:0008151 + GO:0044763 + GO:0050875 + cell physiology + cellular physiological process + cell growth and/or maintenance + biological_process + single-organism cellular process + GO:0009987 + + cellular process + + + + + Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:go_curators + GOC:isa_complete + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + biological_process + GO:0010562 + positive regulation of phosphorus metabolic process + + + + + Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + biological_process + GO:0010563 + negative regulation of phosphorus metabolic process + + + + + Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + biological_process + GO:0010646 + regulation of cell communication + + + + + Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + biological_process + GO:0010647 + positive regulation of cell communication + + + + + Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + biological_process + GO:0010648 + negative regulation of cell communication + + + + + Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. + GOC:dph + GOC:tb + + + + + + + + + + + + + + + + + + true + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + Reactome:R-HSA-6788855 + Reactome:R-HSA-6788867 + phosphokinase activity + molecular_function + GO:0016301 + + + + + + + Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. + kinase activity + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + ISBN:0198506732 + + + + + Reactome:R-HSA-6788855 + FN3KRP phosphorylates PsiAm, RibAm + + + + + Reactome:R-HSA-6788867 + FN3K phosphorylates ketosamines + + + + + + + + + The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. + Wikipedia:Phosphorylation + biological_process + GO:0016310 + + + phosphorylation + + + + + The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. + ISBN:0198506732 + + + + + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + EC:2 + Reactome:R-HSA-1483089 + Reactome:R-HSA-1483186 + Reactome:R-HSA-5668414 + Reactome:R-HSA-6787403 + Reactome:R-HSA-8868783 + molecular_function + GO:0016740 + + + + + + + + + transferase activity + + + + + Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + ISBN:0198506732 + + + + + Reactome:R-HSA-1483089 + PE is converted to PS by PTDSS2 + + + + + Reactome:R-HSA-1483186 + PC is converted to PS by PTDSS1 + + + + + Reactome:R-HSA-5668414 + TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK + + + + + Reactome:R-HSA-6787403 + GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA + + + + + Reactome:R-HSA-8868783 + TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 + + + + + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + EC:2.7 + molecular_function + GO:0016772 + + Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. + transferase activity, transferring phosphorus-containing groups + + + + + Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). + GOC:jl + ISBN:0198506732 + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + regulation of phosphate metabolism + biological_process + GO:0019220 + regulation of phosphate metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GO:0044246 + regulation of metabolism + regulation of multicellular organismal metabolic process + regulation of organismal metabolic process + biological_process + GO:0019222 + + regulation of metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. + GOC:go_curators + + + + + regulation of organismal metabolic process + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a signaling process. + 2010-02-16T09:30:50Z + biological_process + regulation of signaling process + regulation of signalling process + GO:0023051 + regulation of signaling + + + + + Any process that modulates the frequency, rate or extent of a signaling process. + GOC:mtg_signal + + + + + regulation of signaling process + GOC:bf + + + + + regulation of signalling process + GOC:mah + + + + + + + + + The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. + janelomax + 2010-02-16T09:30:50Z + GO:0023046 + GO:0044700 + biological signaling + signaling process + signalling + biological_process + signalling process + single organism signaling + GO:0023052 + + + + + + Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. + signaling + + + + + The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. + GOC:mtg_signal + GOC:mtg_signaling_feb11 + GOC:signaling + + + + + signalling process + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. + 2010-02-16T09:30:50Z + positive regulation of signalling process + biological_process + positive regulation of signaling process + GO:0023056 + positive regulation of signaling + + + + + Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. + GOC:mtg_signal + + + + + positive regulation of signalling process + GOC:mah + + + + + positive regulation of signaling process + GOC:bf + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. + 2010-02-16T09:30:50Z + biological_process + negative regulation of signaling process + negative regulation of signalling process + GO:0023057 + negative regulation of signaling + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. + GOC:mtg_signal + + + + + negative regulation of signaling process + GOC:bf + + + + + negative regulation of signalling process + GOC:mah + + + + + + + + + The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. + MIPS_funcat:18.02.07 + molecular_function + GO:0030545 + receptor regulator activity + + + + + The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. + GOC:ceb + + + + + + + + + The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. + receptor activator activity + molecular_function + GO:0030546 + signaling receptor activator activity + + + + + The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. + GOC:ceb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + regulation of cellular metabolism + biological_process + GO:0031323 + regulation of cellular metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + down regulation of cellular metabolic process + down-regulation of cellular metabolic process + downregulation of cellular metabolic process + negative regulation of cellular metabolism + inhibition of cellular metabolic process + biological_process + GO:0031324 + negative regulation of cellular metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + positive regulation of cellular metabolism + up regulation of cellular metabolic process + up-regulation of cellular metabolic process + upregulation of cellular metabolic process + activation of cellular metabolic process + stimulation of cellular metabolic process + biological_process + GO:0031325 + positive regulation of cellular metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. + down regulation of protein binding + down-regulation of protein binding + downregulation of protein binding + inhibition of protein binding + biological_process + GO:0032091 + negative regulation of protein binding + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of protein binding. + up regulation of protein binding + up-regulation of protein binding + upregulation of protein binding + activation of protein binding + stimulation of protein binding + biological_process + GO:0032092 + positive regulation of protein binding + + + + + Any process that activates or increases the frequency, rate or extent of protein binding. + GOC:mah + + + + + + + + + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. + janelomax + 2012-12-19T12:21:31Z + GO:0044767 + development + biological_process + single-organism developmental process + GO:0032502 + + + + + developmental process + + + + + A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. + GOC:isa_complete + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + down regulation of kinase activity + down-regulation of kinase activity + downregulation of kinase activity + inhibition of kinase activity + kinase inhibitor + biological_process + GO:0033673 + negative regulation of kinase activity + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + up regulation of kinase activity + up-regulation of kinase activity + upregulation of kinase activity + kinase activator + stimulation of kinase activity + biological_process + GO:0033674 + positive regulation of kinase activity + + + + + Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. + rfoulger + 2010-05-14T01:14:37Z + GO:0007242 + GO:0007243 + GO:0023013 + GO:0023034 + intracellular signaling chain + intracellular protein kinase cascade + intracellular signal transduction pathway + protein kinase cascade + signal transmission via intracellular cascade + biological_process + intracellular signaling cascade + intracellular signaling pathway + signal transduction via intracellular signaling cascade + GO:0035556 + + intracellular signal transduction + + + + + The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. + GOC:bf + GOC:jl + GOC:signaling + ISBN:3527303782 + + + + + intracellular signaling chain + ISBN:3527303782 + + + + + intracellular protein kinase cascade + GOC:signaling + + + + + protein kinase cascade + GOC:signaling + + + + + intracellular signaling cascade + GOC:signaling + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. + biological_process + GO:0042325 + regulation of phosphorylation + + + + + Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. + down regulation of phosphorylation + down-regulation of phosphorylation + downregulation of phosphorylation + inhibition of phosphorylation + biological_process + GO:0042326 + negative regulation of phosphorylation + + + + + Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. + up regulation of phosphorylation + up-regulation of phosphorylation + upregulation of phosphorylation + activation of phosphorylation + stimulation of phosphorylation + biological_process + GO:0042327 + positive regulation of phosphorylation + + + + + Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. + GOC:jl + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the activity of an enzyme. + GO:0048554 + MIPS_funcat:18.02.01.01 + positive regulation of enzyme activity + up regulation of enzyme activity + up-regulation of enzyme activity + upregulation of enzyme activity + activation of enzyme activity + activation of metalloenzyme activity + positive regulation of metalloenzyme activity + stimulation of enzyme activity + stimulation of metalloenzyme activity + up regulation of metalloenzyme activity + up-regulation of metalloenzyme activity + upregulation of metalloenzyme activity + biological_process + GO:0043085 + + positive regulation of catalytic activity + + + + + Any process that activates or increases the activity of an enzyme. + GOC:ebc + GOC:jl + GOC:tb + GOC:vw + + + + + positive regulation of enzyme activity + GOC:tb + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the activity of an enzyme. + GO:0048553 + down regulation of enzyme activity + down-regulation of enzyme activity + down-regulation of metalloenzyme activity + downregulation of enzyme activity + negative regulation of enzyme activity + down regulation of metalloenzyme activity + downregulation of metalloenzyme activity + inhibition of enzyme activity + inhibition of metalloenzyme activity + negative regulation of metalloenzyme activity + biological_process + GO:0043086 + negative regulation of catalytic activity + + + + + Any process that stops or reduces the activity of an enzyme. + GOC:ebc + GOC:jl + GOC:tb + GOC:vw + + + + + negative regulation of enzyme activity + GOC:tb + + + + + + + + + Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. + NIF_Subcellular:sao1539965131 + Wikipedia:Organelle + cellular_component + GO:0043226 + + + + organelle + + + + + Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + NIF_Subcellular:sao414196390 + membrane-enclosed organelle + cellular_component + GO:0043227 + membrane-bounded organelle + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + cellular_component + GO:0043229 + + intracellular organelle + + + + + Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + intracellular membrane-enclosed organelle + cellular_component + GO:0043231 + + intracellular membrane-bounded organelle + + + + + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of protein binding. + biological_process + GO:0043393 + regulation of protein binding + + + + + Any process that modulates the frequency, rate or extent of protein binding. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + biological_process + GO:0043549 + regulation of kinase activity + + + + + Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + GOC:bf + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + jane + 2009-04-21T04:07:27Z + biological_process + GO:0044092 + negative regulation of molecular function + + + + + Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GO:jl + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + jane + 2009-04-21T04:11:06Z + biological_process + GO:0044093 + positive regulation of molecular function + + + + + Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GO:jl + + + + + + + + + + The chemical reactions and pathways by which individual cells transform chemical substances. + cellular metabolism + biological_process + intermediary metabolism + GO:0044237 + cellular metabolic process + + + + + The chemical reactions and pathways by which individual cells transform chemical substances. + GOC:go_curators + + + + + intermediary metabolism + GOC:mah + + + + + + + + + OBSOLETE. Any constituent part of a cell, the basic structural and functional unit of all organisms. + + CL:0000000 + NIF_Subcellular:sao628508602 + cellular subcomponent + cellular_component + protoplast + GO:0044464 + + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + cell part + obsolete cell part + true + + + + + OBSOLETE. Any constituent part of a cell, the basic structural and functional unit of all organisms. + GOC:jl + + + + + cellular subcomponent + NIF_Subcellular:sao628508602 + + + + + protoplast + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + down regulation of phosphate metabolic process + down-regulation of phosphate metabolic process + downregulation of phosphate metabolic process + negative regulation of phosphate metabolism + inhibition of phosphate metabolic process + biological_process + GO:0045936 + negative regulation of phosphate metabolic process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + positive regulation of phosphate metabolism + up regulation of phosphate metabolic process + up-regulation of phosphate metabolic process + upregulation of phosphate metabolic process + activation of phosphate metabolic process + stimulation of phosphate metabolic process + biological_process + GO:0045937 + positive regulation of phosphate metabolic process + + + + + Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. + GOC:go_curators + + + + + + + + + + + + + + + + The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). + midori + 2010-09-13T04:51:59Z + GO:0071884 + receptor agonist activity + signaling molecule + signaling receptor ligand activity + vitamin D receptor activator activity + molecular_function + GO:0048018 + + + Definition discussed in https://github.com/geneontology/go-ontology/issues/14220 + receptor ligand activity + + + + + The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). + GOC:kv + GOC:molecular_function_refactoring + GOC:pdt + + + + + receptor agonist activity + GOC:molecular_function_refactoring + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0043119 + positive regulation of physiological process + up regulation of biological process + up-regulation of biological process + upregulation of biological process + activation of biological process + stimulation of biological process + biological_process + GO:0048518 + + positive regulation of biological process + + + + + Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0043118 + down regulation of biological process + down-regulation of biological process + downregulation of biological process + negative regulation of physiological process + inhibition of biological process + biological_process + GO:0048519 + + negative regulation of biological process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051242 + positive regulation of cellular physiological process + up regulation of cellular process + up-regulation of cellular process + upregulation of cellular process + activation of cellular process + stimulation of cellular process + biological_process + GO:0048522 + positive regulation of cellular process + + + + + Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051243 + down regulation of cellular process + down-regulation of cellular process + downregulation of cellular process + negative regulation of cellular physiological process + inhibition of cellular process + biological_process + GO:0048523 + negative regulation of cellular process + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + biological_process + GO:0048583 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + regulation of response to stimulus + + + + + Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + up regulation of response to stimulus + up-regulation of response to stimulus + upregulation of response to stimulus + activation of response to stimulus + stimulation of response to stimulus + biological_process + GO:0048584 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + positive regulation of response to stimulus + + + + + Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + down regulation of response to stimulus + down-regulation of response to stimulus + downregulation of response to stimulus + inhibition of response to stimulus + biological_process + GO:0048585 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + negative regulation of response to stimulus + + + + + Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. + GOC:jid + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GO:0050791 + regulation of physiological process + biological_process + GO:0050789 + + + + + regulation of biological process + + + + + Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. + GOC:ai + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the activity of an enzyme. + GO:0048552 + MIPS_funcat:18.02.01 + regulation of enzyme activity + regulation of metalloenzyme activity + biological_process + GO:0050790 + + regulation of catalytic activity + + + + + Any process that modulates the activity of an enzyme. + GOC:ai + GOC:ebc + GOC:vw + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + biological_process + GO:0050793 + regulation of developmental process + + + + + Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GO:0051244 + regulation of cellular physiological process + biological_process + GO:0050794 + regulation of cellular process + + + + + Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + GOC:go_curators + + + + + + + + + Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. + GO:0051869 + MIPS_funcat:34.11 + physiological response to stimulus + biological_process + GO:0050896 + + + + + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + response to stimulus + + + + + Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. + GOC:ai + GOC:bf + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + down regulation of developmental process + down-regulation of developmental process + downregulation of developmental process + inhibition of developmental process + biological_process + GO:0051093 + negative regulation of developmental process + + + + + Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + up regulation of developmental process + up-regulation of developmental process + upregulation of developmental process + activation of developmental process + stimulation of developmental process + biological_process + GO:0051094 + positive regulation of developmental process + + + + + Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + biological_process + GO:0051098 + regulation of binding + + + + + Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + up regulation of binding + up-regulation of binding + upregulation of binding + activation of binding + stimulation of binding + biological_process + GO:0051099 + positive regulation of binding + + + + + Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + down regulation of binding + down-regulation of binding + downregulation of binding + inhibition of binding + biological_process + GO:0051100 + negative regulation of binding + + + + + Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + regulation of phosphorus metabolism + biological_process + GO:0051174 + regulation of phosphorus metabolic process + + + + + Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + transferase regulator + biological_process + GO:0051338 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + regulation of transferase activity + + + + + Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. + EC:2.-.-.- + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + transferase activator + up regulation of transferase activity + up-regulation of transferase activity + upregulation of transferase activity + activation of transferase activity + stimulation of transferase activity + biological_process + GO:0051347 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + positive regulation of transferase activity + + + + + Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + GOC:ai + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + down regulation of transferase activity + down-regulation of transferase activity + downregulation of transferase activity + transferase inhibitor + inhibition of transferase activity + biological_process + GO:0051348 + + This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. + negative regulation of transferase activity + + + + + Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. + GOC:ai + + + + + + + + + + Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. + biological_process + GO:0051716 + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + cellular response to stimulus + + + + + Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. + GOC:bf + GOC:jl + + + + + + + + + Any process that modulates a measurable attribute of any biological process, quality or function. + regulation + biological_process + GO:0065007 + + + biological regulation + + + + + Any process that modulates a measurable attribute of any biological process, quality or function. + GOC:dph + GOC:isa_complete + GOC:mah + GOC:pr + GOC:vw + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + regulation of a molecular function + biological_process + GO:0065009 + + + + regulation of molecular function + + + + + Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. + GOC:isa_complete + + + + + + + + + + + + + + + A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. + molecular_function + GO:0098772 + + molecular function regulator + + + + + A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. + GOC:dos + GOC:pt + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + kmv + 2019-08-12T18:01:37Z + cellular_component + GO:0110165 + cellular anatomical entity + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + GOC:kmv + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. + bf + 2012-02-22T11:40:53Z + regulation of receptor ligand + biological_process + GO:1900120 + regulation of receptor binding + + + + + Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. + GOC:TermGenie + GOC:signaling + + + + + regulation of receptor ligand + GOC:TermGenie + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor. + bf + 2012-02-22T11:40:57Z + down regulation of receptor binding + down-regulation of receptor binding + downregulation of receptor binding + inhibition of receptor binding + inhibition of receptor ligand + biological_process + down regulation of receptor-associated protein activity + GO:1900121 + negative regulation of receptor binding + + + + + Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor. + GOC:TermGenie + GOC:signaling + + + + + down regulation of receptor binding + GOC:TermGenie + + + + + down-regulation of receptor binding + GOC:TermGenie + + + + + downregulation of receptor binding + GOC:TermGenie + + + + + inhibition of receptor binding + GOC:TermGenie + + + + + inhibition of receptor ligand + GOC:TermGenie + + + + + down regulation of receptor-associated protein activity + GOC:TermGenie + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor. + bf + 2012-02-22T11:41:00Z + up regulation of receptor binding + upregulation of receptor binding + activation of receptor binding + biological_process + GO:1900122 + positive regulation of receptor binding + + + + + Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor. + GOC:TermGenie + GOC:signaling + + + + + up regulation of receptor binding + GOC:TermGenie + + + + + upregulation of receptor binding + GOC:TermGenie + + + + + activation of receptor binding + GOC:TermGenie + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that modulates the frequency, rate or extent of intracellular signal transduction. + bf + 2013-12-02T11:32:52Z + GO:0010627 + regulation of intracellular signaling cascade + regulation of intracellular signaling chain + regulation of intracellular protein kinase cascade + regulation of intracellular signal transduction pathway + regulation of signal transmission via intracellular cascade + biological_process + regulation of intracellular signaling pathway + regulation of signal transduction via intracellular signaling cascade + GO:1902531 + regulation of intracellular signal transduction + + + + + Any process that modulates the frequency, rate or extent of intracellular signal transduction. + GOC:TermGenie + GOC:dph + GOC:signaling + GOC:tb + + + + + regulation of intracellular signaling cascade + GOC:TermGenie + + + + + regulation of intracellular signaling chain + GOC:TermGenie + + + + + regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + regulation of intracellular signaling pathway + GOC:TermGenie + + + + + regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. + bf + 2013-12-02T11:33:01Z + GO:0010741 + down regulation of intracellular signal transduction + down regulation of intracellular signaling chain + down-regulation of intracellular signal transduction + down-regulation of intracellular signaling chain + downregulation of intracellular signal transduction + downregulation of intracellular signaling chain + negative regulation of intracellular protein kinase cascade + negative regulation of intracellular signaling cascade + negative regulation of intracellular signaling chain + down regulation of intracellular signal transduction pathway + down regulation of intracellular signaling cascade + down regulation of signal transmission via intracellular cascade + down-regulation of intracellular signal transduction pathway + downregulation of intracellular signal transduction pathway + downregulation of intracellular signaling cascade + downregulation of signal transmission via intracellular cascade + inhibition of intracellular signal transduction + inhibition of intracellular signal transduction pathway + inhibition of intracellular signaling cascade + inhibition of intracellular signaling chain + inhibition of signal transmission via intracellular cascade + negative regulation of intracellular signal transduction pathway + negative regulation of signal transmission via intracellular cascade + biological_process + down regulation of intracellular signaling pathway + down regulation of signal transduction via intracellular signaling cascade + down-regulation of intracellular signaling cascade + down-regulation of intracellular signaling pathway + down-regulation of signal transduction via intracellular signaling cascade + down-regulation of signal transmission via intracellular cascade + downregulation of intracellular signaling pathway + downregulation of signal transduction via intracellular signaling cascade + inhibition of intracellular signaling pathway + inhibition of signal transduction via intracellular signaling cascade + negative regulation of intracellular signaling pathway + negative regulation of signal transduction via intracellular signaling cascade + GO:1902532 + negative regulation of intracellular signal transduction + + + + + Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. + GOC:TermGenie + GOC:dph + GOC:signaling + GOC:tb + + + + + down regulation of intracellular signal transduction + GOC:TermGenie + + + + + down regulation of intracellular signaling chain + GOC:TermGenie + + + + + down-regulation of intracellular signal transduction + GOC:TermGenie + + + + + down-regulation of intracellular signaling chain + GOC:TermGenie + + + + + downregulation of intracellular signal transduction + GOC:TermGenie + + + + + downregulation of intracellular signaling chain + GOC:TermGenie + + + + + negative regulation of intracellular signaling cascade + GOC:TermGenie + + + + + negative regulation of intracellular signaling chain + GOC:TermGenie + + + + + down regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + down regulation of intracellular signaling cascade + GOC:TermGenie + + + + + down regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + down-regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + downregulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + downregulation of intracellular signaling cascade + GOC:TermGenie + + + + + downregulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + inhibition of intracellular signal transduction + GOC:TermGenie + + + + + inhibition of intracellular signal transduction pathway + GOC:TermGenie + + + + + inhibition of intracellular signaling cascade + GOC:TermGenie + + + + + inhibition of intracellular signaling chain + GOC:TermGenie + + + + + inhibition of signal transmission via intracellular cascade + GOC:TermGenie + + + + + negative regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + negative regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + down regulation of intracellular signaling pathway + GOC:TermGenie + + + + + down regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + down-regulation of intracellular signaling cascade + GOC:TermGenie + + + + + down-regulation of intracellular signaling pathway + GOC:TermGenie + + + + + down-regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + down-regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + downregulation of intracellular signaling pathway + GOC:TermGenie + + + + + downregulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + inhibition of intracellular signaling pathway + GOC:TermGenie + + + + + inhibition of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + negative regulation of intracellular signaling pathway + GOC:TermGenie + + + + + negative regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + + + + + + + + + + + + + + + + + + + + + + + Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. + bf + 2013-12-02T11:33:10Z + GO:0010740 + positive regulation of intracellular signaling chain + up regulation of intracellular signal transduction + up regulation of intracellular signaling chain + up-regulation of intracellular signal transduction + up-regulation of intracellular signaling chain + upregulation of intracellular signal transduction + upregulation of intracellular signaling chain + activation of intracellular signal transduction + activation of intracellular signal transduction pathway + activation of intracellular signaling cascade + activation of intracellular signaling chain + activation of signal transmission via intracellular cascade + positive regulation of intracellular protein kinase cascade + positive regulation of intracellular signal transduction pathway + positive regulation of signal transmission via intracellular cascade + up regulation of intracellular signal transduction pathway + up regulation of signal transmission via intracellular cascade + up-regulation of intracellular signal transduction pathway + up-regulation of signal transmission via intracellular cascade + upregulation of intracellular signal transduction pathway + upregulation of signal transmission via intracellular cascade + biological_process + activation of intracellular signaling pathway + activation of signal transduction via intracellular signaling cascade + positive regulation of intracellular signaling cascade + positive regulation of intracellular signaling pathway + positive regulation of signal transduction via intracellular signaling cascade + up regulation of intracellular signaling cascade + up regulation of intracellular signaling pathway + up regulation of signal transduction via intracellular signaling cascade + up-regulation of intracellular signaling cascade + up-regulation of intracellular signaling pathway + up-regulation of signal transduction via intracellular signaling cascade + upregulation of intracellular signaling cascade + upregulation of intracellular signaling pathway + upregulation of signal transduction via intracellular signaling cascade + GO:1902533 + positive regulation of intracellular signal transduction + + + + + Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. + GOC:BHF + GOC:TermGenie + GOC:dph + GOC:signaling + GOC:tb + + + + + positive regulation of intracellular signaling chain + GOC:TermGenie + + + + + up regulation of intracellular signal transduction + GOC:TermGenie + + + + + up regulation of intracellular signaling chain + GOC:TermGenie + + + + + up-regulation of intracellular signal transduction + GOC:TermGenie + + + + + up-regulation of intracellular signaling chain + GOC:TermGenie + + + + + upregulation of intracellular signal transduction + GOC:TermGenie + + + + + upregulation of intracellular signaling chain + GOC:TermGenie + + + + + activation of intracellular signal transduction + GOC:TermGenie + + + + + activation of intracellular signal transduction pathway + GOC:TermGenie + + + + + activation of intracellular signaling cascade + GOC:TermGenie + + + + + activation of intracellular signaling chain + GOC:TermGenie + + + + + activation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + positive regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + positive regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + up regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + up regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + up-regulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + up-regulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + upregulation of intracellular signal transduction pathway + GOC:TermGenie + + + + + upregulation of signal transmission via intracellular cascade + GOC:TermGenie + + + + + activation of intracellular signaling pathway + GOC:TermGenie + + + + + activation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + positive regulation of intracellular signaling cascade + GOC:TermGenie + + + + + positive regulation of intracellular signaling pathway + GOC:TermGenie + + + + + positive regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + up regulation of intracellular signaling cascade + GOC:TermGenie + + + + + up regulation of intracellular signaling pathway + GOC:TermGenie + + + + + up regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + up-regulation of intracellular signaling cascade + GOC:TermGenie + + + + + up-regulation of intracellular signaling pathway + GOC:TermGenie + + + + + up-regulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + upregulation of intracellular signaling cascade + GOC:TermGenie + + + + + upregulation of intracellular signaling pathway + GOC:TermGenie + + + + + upregulation of signal transduction via intracellular signaling cascade + GOC:TermGenie + + + + + + + + the observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan + MPheno.ontology + MP:0000001 + mammalian phenotype + + + + + the observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan + MGI:csmith + + + + + + + + OBSOLETE. + Anatomy + MPheno.ontology + MP:0000002 + obsolete Morphology + true + + + + + OBSOLETE. + MGI:csmith + + + + + + + + + + + + + + + + + + + + + + + + + the observable morphological and physiological characteristics of the basic structural and functional unit of all mammalian organisms that are manifested through development and lifespan + cell phenotype + MPheno.ontology + MP:0005384 + cellular phenotype + + + + + + + + + ncbi_taxonomy + m + mouse + NCBITaxon:10090 + Mus musculus + + + + + m + PRO:DAN + + + + + + mouse + + + + + + + + + + Viruses + ncbi_taxonomy + viral- + NCBITaxon:10239 + virus + + + + + viral- + PRO:DAN + + + + + + + + + + ncbi_taxonomy + euk- + NCBITaxon:2759 + Eukaryota + + + + + euk- + PRO:DAN + + + + + + + + + + ncbi_taxonomy + Fungi/Metazoa group + NCBITaxon:33154 + Opisthokonta + + + + + + + + + ncbi_taxonomy + metazoan- + NCBITaxon:33208 + Metazoa + + + + + metazoan- + PRO:DAN + + + + + + + + + + mammal + ncbi_taxonomy + mammal- + NCBITaxon:40674 + Mammalia + + + + + mammal + + + + + + mammal- + PRO:DAN + + + + + + + + + + zebrafish + ncbi_taxonomy + NCBITaxon:7955 + Danio rerio + + + + + zebrafish + + + + + + + + + + ncbi_taxonomy + h + human + NCBITaxon:9606 + Homo sapiens + + + + + h + PRO:DAN + + + + + + human + PRO:DAN + + + + + + + + + + rodent + ncbi_taxonomy + NCBITaxon:9989 + Rodentia + + + + + rodent + + + + + + + + + + obi + OBI:0100026 + organism + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + quality (PATO) + PATO:0000072 + quality + PATO:0000001 + quality + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + + A scalar optical property that is the intensity, value or amount of perceived light. + color intensity + color lightness + color value + quality + PATO:0000016 + + Color brightness refers to the intensity, lightness or value of the light present. Think of this as a dimmer switch. + color brightness + + + + + A scalar optical property that is the intensity, value or amount of perceived light. + PATOC:MAH + + + + + + + + + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. + quality + PATO:0000047 + + biological sex + + + + + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. + MGED:MGED + + + + + + + + + A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. + quality + PATO:0000384 + + + male + + + + + A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. + MGED:MGED + + + + + + + + + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + PATO:0002079 + Wikipedia:Physical_property + relational physical quality + quality + PATO:0001018 + + physical quality + + + + + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + PATOC:GVG + + + + + + + + + A quality which inheres in a continuant. + PATO:0001237 + PATO:0001238 + snap:Quality + monadic quality of a continuant + multiply inhering quality of a physical entity + quality of a continuant + quality of a single physical entity + quality of an object + quality of continuant + monadic quality of an object + monadic quality of continuant + quality + PATO:0001241 + Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. + physical object quality + + + + + A quality which inheres in a continuant. + PATOC:GVG + + + + + + + + + A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. + quality + PATO:0001291 + + electromagnetic (EM) radiation quality + + + + + A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. + Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation + + + + + + + + + An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. + quality + PATO:0001300 + + optical quality + + + + + An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. + PATOC:GVG + + + + + + + + + A monadic quality of continuant that exists at the cellular level of organisation. + quality + PATO:0001396 + cellular quality + + + + + A monadic quality of continuant that exists at the cellular level of organisation. + PATOC:GVG + + + + + + + + + A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. + quality + PATO:0001404 + + nucleate quality + + + + + A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. + PATOC:GVG + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. + quality + PATO:0001405 + + + + anucleate + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. + Biology-online:Biology-online + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. + quality + PATO:0001406 + + + + binucleate + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. + Biology-online:Biology-online + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. + quality + PATO:0001407 + + + + mononucleate + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. + Biology-online:Biology-online + + + + + + + + + A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. + quality + PATO:0001739 + + radiation quality + + + + + A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. + PATOC:GVG + + + + + + + + + An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. + quality + PATO:0001894 + + phenotypic sex + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. + quality + PATO:0001908 + + + multinucleate + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. + PATOC:GVG + + + + + + + + + An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. + quality + PATO:0001992 + + + cellularity + + + + + An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. + PATOC:GVG + + + + + + + + + A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. + quality + PATO:0001993 + + multicellular + + + + + A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. + PATOC:GVG + + + + + + + + + A quality that inheres in an entire organism or part of an organism. + quality + PATO:0001995 + organismal quality + + + + + A quality that inheres in an entire organism or part of an organism. + PATOC:CJM + + + + + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. + gkoutos + 2013-10-21T05:44:34Z + quality + PATO:0002505 + + + nucleated + + + + + A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. + PATOC:GVG + + + + + + + + An extent of biological sequence. + located_sequence_feature + sequence feature + sequence + located sequence feature + SO:0000110 + sequence_feature + + + + + An extent of biological sequence. + SO:ke + + + + + + + + + A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. + sequence + SO:0000704 + gene + + + + + A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. + SO:immuno_workshop + + + + + + + + + An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. + uberon + UBERON:0000000 + + processual entity + + + + + An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. + span:ProcessualEntity + + + + + + + + + + + + + + + + + + + + + + + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + adult stage + BTO:0001043 + BilaDO:0000004 + EFO:0001272 + FBdv:00005369 + WBls:0000041 + XtroDO:0000084 + fully formed animal stage + juvenile-adult stage + uberon + UBERON:0000066 + + fully formed stage + + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + + + + + + + + + + + + + + + + + + + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + + BilaDO:0000002 + EV:0300001 + FBdv:00005289 + FMA:72652 + HsapDv:0000002 + MmusDv:0000002 + OGES:000000 + OGES:000022 + WBls:0000003 + WBls:0000092 + WBls:0000102 + XAO:1000012 + embryonic stage + uberon + embryogenesis + UBERON:0000068 + embryo stage + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + + + + + + + + + + + + + + + + End of the life of an organism. + ncit:Death is an outcome + XAO:0000437 + XtroDO:0000085 + uberon + death + UBERON:0000071 + death stage + + + + + End of the life of an organism. + XAO:0000437 + + + + + ncit:Death is an outcome + ncit + + + + + + + + + + + + + + + stage succeeding embryo, including mature structure + In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) + BilaDO:0000003 + OGES:000010 + OGES:000014 + OGES:000024 + WBls:0000022 + WBls:0000093 + WBls:0000103 + postembryonic stage + post-hatching stage + uberon + postembryonic + UBERON:0000092 + post-embryonic stage + + + + + + stage succeeding embryo, including mature structure + + + + + + + + + + + + + + + + + + + + + + + + + + + + An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. + FBdv:00000000 + HsapDv:0000001 + MmusDv:0000001 + OGES:000011 + ncithesaurus:Life + entire life cycle + entire lifespan + life + lifespan + uberon + UBERON:0000104 + + life cycle + + + + + + An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. + + + + + + + + + + + + + + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here + the WBls class 'all stages' belongs here as it is the superclass of other WBls stages + we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage + BILS:0000105 + EFO:0000399 + FBdv:00007012 + FMA:24120 + HsapDv:0000000 + MmusDv:0000000 + OlatDv:0000010 + PdumDv:0000090 + WBls:0000002 + XAO:1000000 + ZFS:0000000 + ZFS:0100000 + ncithesaurus:Developmental_Stage + developmental stage + stage + uberon + UBERON:0000105 + + + life cycle stage + + + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + + + + + + + + + + + + + + + + + + + + + + A stage at which the organism is a single cell produced by means of sexual reproduction. + As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] + + BILS:0000106 + BilaDO:0000005 + EFO:0001322 + EHDAA:27 + FBdv:00005288 + NCIT:C12601 + PdumDv:0000100 + VHOG:0000745 + XAO:1000001 + ZFS:0000001 + 1-cell stage + fertilized egg stage + one cell stage + uberon + fertilized egg stage + one-cell stage + zygote + zygotum + UBERON:0000106 + + zygote stage + + + + + + A stage at which the organism is a single cell produced by means of sexual reproduction. + + + + + + As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] + 2012-09-17 + VHOG:0000745 + VHOG + + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 + + + + + fertilized egg stage + BTO:0000854 + + + + + one-cell stage + VHOG:0000745 + + + + + zygote + VHOG:0000745 + + + + + zygotum + + + + + + + + + + + + + + + + + + + + + + + The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. + + BILS:0000107 + BilaDO:0000006 + EFO:0001290 + FBdv:00000054 + MESH:A16.254.270 + MmusDv:0000004 + OGES:000015 + OGES:000020 + PdumDv:0000200 + XAO:1000004 + ZFS:0000046 + uberon + UBERON:0000107 + + cleavage stage + + + + + The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. + + GO:0040016 + + + + + + + + + + + + + + + + + + + + + An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. + consider adding a preceding stage 'morula stage' as part of cleavage + + BILS:0000108 + BilaDO:0000007 + EFO:0001282 + HsapDv:0000006 + MmusDv:0000007 + OGES:000003 + OGES:000016 + OGES:000021 + OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg + WBls:0000005 + XAO:1000003 + ZFS:0000045 + uberon + UBERON:0000108 + + blastula stage + + + + + + An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. + + + + + + + + + + + + + + + + + + + + + + A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. + BILS:0000109 + BilaDO:0000008 + EFO:0001296 + FBdv:00005317 + HsapDv:0000010 + MmusDv:0000013 + OGES:000004 + OGES:000019 + WBls:0000010 + XAO:1000005 + ZFS:0000047 + uberon + blastocystis trilaminaris stage + trilaminar blastocyst stage + trilaminar blastoderm stage + trilaminar disk stage + trilaminar germ stage + trilaminar stage + UBERON:0000109 + + gastrula stage + + + + + + + + + + + BILS + + + + + A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. + GO:0007369 + + + + + blastocystis trilaminaris stage + + + + + + trilaminar blastocyst stage + + + + + + trilaminar blastoderm stage + + + + + + trilaminar disk stage + + + + + + trilaminar germ stage + + + + + + trilaminar stage + + + + + + + + + + + + + + + + + + + + + + Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. + BILS:0000110 + BilaDO:0000009 + HsapDv:0000012 + MmusDv:0000017 + XAO:1000006 + uberon + UBERON:0000110 + neurula stage + + + + + + Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. + GO:0001841 + + + + + + + + + + + + + + + + + + + + + A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. + + BILS:0000111 + BilaDO:0000010 + HsapDv:0000015 + MmusDv:0000018 + OGES:000005 + OGES:000032 + uberon + segmentation stage + UBERON:0000111 + organogenesis stage + + + + + + A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + AAO:0010841 + AEO:0000000 + BILA:0000000 + CARO:0000000 + EHDAA2:0002229 + FBbt:10000000 + FBbt_root:00000000 + FMA:62955 + HAO:0000000 + MA:0000001 + NCIT:C12219 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + WBbt:0000100 + XAO:0000000 + ZFA:0100000 + uberon + UBERON:0001062 + + anatomical entity + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + FMA:62955 + + + + + UMLS:C1515976 + ncithesaurus:Anatomic_Structure_System_or_Substance + + + + + + + + + phenotype + + + + + + + + + + + + + + pending final vetting + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From ligand activity to has_ligand + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From has_ligand to ligand activity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/mp_terms.txt b/src/ontology/imports/mp_terms.txt new file mode 100644 index 0000000..4e741f5 --- /dev/null +++ b/src/ontology/imports/mp_terms.txt @@ -0,0 +1,4 @@ +MP:0000000 +MP:0000001 +MP:0000002 + diff --git a/src/ontology/imports/ncbitaxon_import.owl b/src/ontology/imports/ncbitaxon_import.owl new file mode 100644 index 0000000..3c8b9da --- /dev/null +++ b/src/ontology/imports/ncbitaxon_import.owl @@ -0,0 +1,1778 @@ + + + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + database_cross_reference + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + all + root + + + + + all + + + + + + + + + + + GC_ID:1 + PMID:15371245 + ncbi_taxonomy + Muridae + + + + + + + + + + GC_ID:1 + Mus + mice + mouse + ncbi_taxonomy + Mus <genus> + + + + + Mus + + + + + + mice + + + + + + mouse + + + + + + + + + + + NCBITaxon:85055 + GC_ID:1 + house mouse + mouse + ncbi_taxonomy + mice C57BL/6xCBA/CaJ hybrid + Mus musculus + + + + + house mouse + + + + + + mouse + + + + + + mice C57BL/6xCBA/CaJ hybrid + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Vira + Viridae + viruses + Viruses + + + + + viruses + + + + + + Vira + + + + + + Viridae + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Teleostomi + + + + + + + + + NCBITaxon:40673 + GC_ID:1 + bony vertebrates + ncbi_taxonomy + Euteleostomi + + + + + bony vertebrates + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Neoteleostei + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Eurypterygii + Eurypterygia + + + + + Eurypterygii + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Ctenosquamata + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Acanthomorpha + Acanthomorphata + + + + + Acanthomorpha + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Euacanthomorpha + Euacanthomorphacea + + + + + Euacanthomorpha + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + biota + cellular organisms + + + + + biota + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Dipnotetrapodomorpha + + + + + + + + + GC_ID:1 + PMID:11743200 + PMID:11791233 + ncbi_taxonomy + Boreotheria + Boreoeutheria + + + + + Boreotheria + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Osteoglossocephalai + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Euteleosteomorpha + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Percomorphaceae + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Stiassnyiformes + Ovalentaria + + + + + Stiassnyiformes + + + + + + + + + + + NCBITaxon:32456 + GC_ID:1 + ncbi_taxonomy + Atherinomorpha + Atherinomorphae + + + + + Atherinomorpha + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Actinopteri + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Clupeocephala + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Otophysa + Otophysi + + + + + Otophysa + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Cypriniphysi + Cypriniphysae + + + + + Cypriniphysi + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Ostarioclupeomorpha + Otocephala + Otomorpha + + + + + Ostarioclupeomorpha + + + + + + Otocephala + + + + + + + + + + + GC_ID:1 + mice and others + ncbi_taxonomy + Sciurognathi + Myomorpha + + + + + mice and others + + + + + + Sciurognathi + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Homo/Pan/Gorilla group + Homininae + + + + + Homo/Pan/Gorilla group + + + + + + + + + + + GC_ID:1 + PMID:23020233 + PMID:30257078 + eucaryotes + eukaryotes + ncbi_taxonomy + Eucarya + Eucaryotae + Eukarya + Eukaryotae + eukaryotes + Eukaryota + + + + + eucaryotes + + + + + + eukaryotes + + + + + + Eucarya + + + + + + Eucaryotae + + + + + + Eukarya + + + + + + Eukaryotae + + + + + + eukaryotes + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Adrianichthyoidei + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Cyprinoidea + Cyprinoidei + + + + + Cyprinoidea + + + + + + + + + + + GC_ID:1 + PMID:11214319 + PMID:12082125 + PMID:12878460 + PMID:15522813 + ncbi_taxonomy + Euarchontoglires + + + + + + + + + GC_ID:1 + PMID:11214319 + PMID:12082125 + PMID:15522813 + Rodents and rabbits + ncbi_taxonomy + Glires + + + + + Rodents and rabbits + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Anthropoidea + Simiiformes + + + + + Anthropoidea + + + + + + + + + + + GC_ID:1 + ape + apes + ncbi_taxonomy + Hominoidea + + + + + ape + + + + + + apes + + + + + + + + + + + GC_ID:1 + teleost fishes + ncbi_taxonomy + Teleostei + + + + + teleost fishes + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Ostariophysi + + + + + + + + + GC_ID:1 + tetrapods + ncbi_taxonomy + Tetrapoda + + + + + tetrapods + + + + + + + + + + GC_ID:1 + amniotes + ncbi_taxonomy + Amniota + + + + + amniotes + + + + + + + + + + GC_ID:1 + Theria + ncbi_taxonomy + Theria <mammals> + + + + + Theria + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Fungi/Metazoa group + opisthokonts + Opisthokonta + + + + + Fungi/Metazoa group + + + + + + opisthokonts + + + + + + + + + + + GC_ID:1 + metazoans + multicellular animals + ncbi_taxonomy + Animalia + animals + Metazoa + + + + + metazoans + + + + + + multicellular animals + + + + + + Animalia + + + + + + animals + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Bilateria + + + + + + + + + GC_ID:1 + deuterostomes + ncbi_taxonomy + Deuterostomia + + + + + deuterostomes + + + + + + + + + + GC_ID:1 + PMID:15019624 + PMID:15371245 + ncbi_taxonomy + Muroidea + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Haplorrhini + + + + + + + + + + NCBITaxon:109679 + GC_ID:1 + ncbi_taxonomy + Murinae + + + + + + + + + + GC_ID:1 + mammals + ncbi_taxonomy + mammals + Mammalia + + + + + mammals + + + + + + mammals + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Neopterygi + Neopterygii + + + + + Neopterygi + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Adrianichthyidae + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Eumetazoa + + + + + + + + + + GC_ID:1 + medakas, needlefish and others + ncbi_taxonomy + Beloniformes + + + + + medakas, needlefish and others + + + + + + + + + + + GC_ID:1 + chordates + ncbi_taxonomy + chordates + Chordata + + + + + chordates + + + + + + chordates + + + + + + + + + + GC_ID:1 + Vertebrata + vertebrates + ncbi_taxonomy + vertebrates + Vertebrata <vertebrates> + + + + + Vertebrata + + + + + + vertebrates + + + + + + vertebrates + + + + + + + + + + GC_ID:1 + Gnathostomata + jawed vertebrates + ncbi_taxonomy + Gnathostomata <vertebrates> + + + + + Gnathostomata + + + + + + jawed vertebrates + + + + + + + + + + + GC_ID:1 + fish + fishes + ray-finned fishes + ncbi_taxonomy + Actinopterygi + Osteichthyes + bony fishes + Actinopterygii + + + + + fish + + + + + + fishes + + + + + + ray-finned fishes + + + + + + Actinopterygi + + + + + + Osteichthyes + + + + + + bony fishes + + + + + + + + + + + GC_ID:1 + carps and others + ncbi_taxonomy + Cypriniformes + + + + + carps and others + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Cyprinidae + + + + + + + + + + NCBITaxon:46777 + NCBITaxon:487617 + GC_ID:1 + ncbi_taxonomy + Brachydanio + Celestichthys + Danio + + + + + Brachydanio + + + + + + Celestichthys + + + + + + + + + + + NCBITaxon:27702 + NCBITaxon:37966 + GC_ID:1 + leopard danio + zebra danio + zebra fish + zebrafish + ncbi_taxonomy + Brachidanio rerio + Brachydanio rerio + Brachydanio rerio frankei + Cyprinus rerio + Danio frankei + Danio rerio frankei + Danio rerio + + + + + leopard danio + + + + + + zebra danio + + + + + + zebra fish + + + + + + zebrafish + + + + + + Brachidanio rerio + + + + + + Brachydanio rerio + + + + + + Brachydanio rerio frankei + + + + + + Cyprinus rerio + + + + + + Danio frankei + + + + + + Danio rerio frankei + + + + + + + + + + + GC_ID:1 + medakas + ricefishes + ncbi_taxonomy + Oryziatinae + Oryziinae + + + + + medakas + + + + + + ricefishes + + + + + + Oryziatinae + + + + + + + + + + + NCBITaxon:123687 + GC_ID:1 + ncbi_taxonomy + Orizias + Xenopoecilus + Oryzias + + + + + Orizias + + + + + + Xenopoecilus + + + + + + + + + + + GC_ID:1 + Japanese medaka + Japanese rice fish + medaka + ncbi_taxonomy + Orizias latipes + Poecilia latipes + Oryzias latipes + + + + + Japanese medaka + + + + + + Japanese rice fish + + + + + + medaka + + + + + + Orizias latipes + + + + + + Poecilia latipes + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Sarcopterygii + + + + + + + + + + GC_ID:1 + Mus + ncbi_taxonomy + Mus <subgenus> + + + + + Mus + + + + + + + + + + + GC_ID:1 + Craniata + ncbi_taxonomy + Craniata <chordates> + + + + + Craniata + + + + + + + + + + GC_ID:1 + eutherian mammals + placental mammals + placentals + ncbi_taxonomy + Placentalia + placentals + Eutheria + + + + + eutherian mammals + + + + + + placental mammals + + + + + + placentals + + + + + + Placentalia + + + + + + placentals + + + + + + + + + + + GC_ID:1 + primate + ncbi_taxonomy + Primata + primates + Primates + + + + + primate + + + + + + Primata + + + + + + primates + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Catarrhini + + + + + + + + + + GC_ID:1 + great apes + ncbi_taxonomy + Pongidae + Hominidae + + + + + Pongidae + + + + + + great apes + + + + + + + + + + + GC_ID:1 + humans + ncbi_taxonomy + Homo + + + + + humans + + + + + + + + + + + GC_ID:1 + human + man + ncbi_taxonomy + Home sapiens + Homo sampiens + Homo sapeins + Homo sapian + Homo sapians + Homo sapien + Homo sapience + Homo sapiense + Homo sapients + Homo sapines + Homo spaiens + Homo spiens + Humo sapiens + Homo sapiens + + + + + human + + + + + + man + + + + + + Home sapiens + + + + + + Homo sampiens + + + + + + Homo sapeins + + + + + + Homo sapian + + + + + + Homo sapians + + + + + + Homo sapien + + + + + + Homo sapience + + + + + + Homo sapiense + + + + + + Homo sapients + + + + + + Homo sapines + + + + + + Homo spaiens + + + + + + Homo spiens + + + + + + Humo sapiens + + + + + + + + + + + GC_ID:1 + rodent + ncbi_taxonomy + rodents + Rodentia + + + + + rodent + + + + + + rodents + + + + + + + + diff --git a/src/ontology/imports/ncbitaxon_terms.txt b/src/ontology/imports/ncbitaxon_terms.txt new file mode 100644 index 0000000..96551be --- /dev/null +++ b/src/ontology/imports/ncbitaxon_terms.txt @@ -0,0 +1,2 @@ +NCBITaxon:1 + diff --git a/src/ontology/imports/oban_import.owl b/src/ontology/imports/oban_import.owl new file mode 100644 index 0000000..1261028 --- /dev/null +++ b/src/ontology/imports/oban_import.owl @@ -0,0 +1,14 @@ + + + + + + diff --git a/src/ontology/imports/oban_terms.txt b/src/ontology/imports/oban_terms.txt new file mode 100644 index 0000000..47c0ce4 --- /dev/null +++ b/src/ontology/imports/oban_terms.txt @@ -0,0 +1,4 @@ +OBAN:0000000 +OBAN:0000001 +OBAN:0000002 + diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl new file mode 100644 index 0000000..26bc5d0 --- /dev/null +++ b/src/ontology/imports/obi_import.owl @@ -0,0 +1,9486 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + + + + + + + example + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + + + + + + + + definition + definition + textual definition + + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + textual definition + + + + + + + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + + editor note + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + alternative term + + + + + + + + definition source + + formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + + + + + + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + imported from + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + + elucidation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Description may include but is not limited to: an abstract, + table of contents, reference to a graphical representation + of content or a free-text account of the content. + An account of the content of the resource. + + Description + Description + + + + + + + + + + + + + + + Typically, a Title will be a name by which the resource is + formally known. + + A name given to the resource. + + Title + Title + + + + + + + + Mark Miller + 2018-05-11T13:47:29Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + has part + + + + + + + + + + + + + + + + realized in + this disease is realized in this disease course + this fragility is realized in this shattering + this investigator role is realized in this investigation + is realized by + realized_in + [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + + + + + + + + + + + + + + + realizes + this disease course realizes this disease + this investigation realizes this investigator role + this shattering realizes this fragility + to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + + + + + + + + + This document is about information artifacts and their representations + + is_about is a (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + + + A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. + denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically + 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. +g denotes r =def +r is a portion of reality +there is some c that is a concretization of g +every c that is a concretization of g specifically denotes r + person:Alan Ruttenberg + Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan + + denotes + + + + + + + + + + + + + + + + has_specified_input + has_specified_input + see is_input_of example_of_usage + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot + + has_specified_input + + + + + + + + + + + + + + + is_specified_input_of + some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters + is_specified_input_of + + + + + + + + + + + + + + + + has_specified_output + has_specified_output + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot + + has_specified_output + + + + + + + + + + + + + + + is_specified_output_of + is_specified_output_of + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters + + is_specified_output_of + + + + + + + + + + + achieves_planned_objective + A cell sorting process achieves the objective specification 'material separation objective' + + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. + BP, AR, PPPB branch + PPPB branch derived + modified according to email thread from 1/23/09 in accordince with DT and PPPB branch + achieves_planned_objective + + + + + + + + + has grain + + the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. + Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form + PERSON: Alan Ruttenberg + PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 + has grain + + + + + + + + + + objective_achieved_by + + This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. + OBI + OBI + objective_achieved_by + + + + + + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + + + + + + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as + + + + + + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + quality of + + + + + + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + role of + + + + + + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + + + + + + disposition of + + + + + + + + + + + + + + + + + derives from + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + + derives from + + + + + + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + derives into + + + + + + + + + + move to BFO? + Allen + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporal relation + + + + + + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + + + + + + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + continuant + Continuant + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + + + + + occurrent + Occurrent + An entity that has temporal parts and that happens, unfolds or develops through time. + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + + + + + + + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process + + + + + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + + + + + + + + + + disposition + Disposition + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocytosis and exocytosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + disposition + + + + + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + + + + + + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + + + + + + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + + + + + + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + + + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + + + + + + + + + quality + Quality + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + quality + + + + + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + + + + + + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + + + + + + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + + + + + + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] + + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + + + + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + + + + + + + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant + + + + + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + + + + + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + + + + + molecular entity + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. + We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well + + molecular entity + + + + + + + + + nucleic acid + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + + nucleic acid + + + + + + + + + macromolecule + A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. + polymer + + macromolecule + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell line cell + A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture + A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture + + + cell line cell + + + + + + + + + + + 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. + + + + + + + + + + + + + + + + + + + + + cell line + A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). + A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). + + + cell line + + + + + + + + + cell + cell + PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + + cell + cell + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + primary cultured cell + A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. + + primary cultured cell + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured cell + A cell in vitro that is or has been maintained or propagated as part of a cell culture. + + cultured cell + + + + + + + + + B cell + A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. + + B cell + + + + + + + + + lymphocyte + A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. + + lymphocyte + + + + + + + + + + + + + + + + experimentally modified cell in vitro + A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. + + experimentally modified cell in vitro + + + + + + + + + mononuclear cell + A leukocyte with a single non-segmented nucleus in the mature form. + + mononuclear cell + + + + + + + + + + biological_process + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + + biological_process + + + + + + + + + measurement unit label + Examples of measurement unit labels are liters, inches, weight per volume. + + A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. + 2009-03-16: provenance: a term measurement unit was +proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and +Cristian Cocos, and subsequently moved to IAO where the objective for +which the original term was defined was satisfied with the definition +of this, different, term. + 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + measurement unit label + + + + + + + + + objective specification + In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. + + a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. + 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." + 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. + Answers the question, why did you do this experiment? + PERSON: Alan Ruttenberg + PERSON: Barry Smith + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + goal specification + OBI Plan and Planned Process/Roles Branch + OBI_0000217 + objective specification + + + + + + + + + Pour the contents of flask 1 into flask 2 + + a directive information entity that describes an action the bearer will take + Alan Ruttenberg + OBI Plan and Planned Process branch + action specification + + + + + + + + + datum label + + A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label + http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n + GROUP: IAO + 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. + + datum label + + + + + + + + + software + + Software is a plan specification composed of a series of instructions that can be +interpreted by or directly executed by a processing unit. + see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert + PERSON: Melanie Courtot + GROUP: OBI + software + + + + + + + + + + + + + + + + + + + + information carrier + In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. + + A quality of an information bearer that imparts the information content + 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. + 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. + PERSON: Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + information carrier + + + + + + + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item + + + + + + + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + A generically dependent continuant that is about some thing. + 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + + + + + + + + + + + + + + + + An information content entity whose concretizations indicate to their bearer how to realize them in a process. + 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. + 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO + Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + directive information entity + + + + + + + + + dot plot + Dot plot of SSC-H and FSC-H. + + A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000123 + group:OBI + dot plot + + + + + + + + + graph + + A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. + PERSON: Lawrence Hunter + person:Alan Ruttenberg + person:Allyson Lister + OBI_0000240 + group:OBI + graph + + + + + + + + + algorithm + PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. + + A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. + Philippe Rocca-Serra + PlanAndPlannedProcess Branch + OBI_0000270 + adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) + algorithm + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data format specification + + A data format specification is the information content borne by the document published defining the specification. +Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file + 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes +information. Example: The ISO document specifying what encompasses an +XML document; The instructions in a XSD file" + PERSON: Alan Ruttenberg + PlanAndPlannedProcess Branch + OBI branch derived + OBI_0000187 + data format specification + + + + + + + + + data set + Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). + + A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. + 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type + 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000042 + group:OBI + data set + + + + + + + + + image + + An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. + person:Alan Ruttenberg + person:Allyson + person:Chris Stoeckert + OBI_0000030 + group:OBI + image + + + + + + + + + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part + + + + + + + + + + + + + + + + + + + + + plan specification + PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. + + A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. + 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2014-03-31: A plan specification can have other parts, such as conditional specifications. + Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved + Alan Ruttenberg + OBI Plan and Planned Process branch + OBI_0000344 + 2/3/2009 Comment from OBI review. + +Action specification not well enough specified. +Conditional specification not well enough specified. +Question whether all plan specifications have objective specifications. + +Request that IAO either clarify these or change definitions not to use them + plan specification + + + + + + + + + + + + + + + + + + + + + + + + + material information bearer + A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. + a brain + a hard drive + + A material entity in which a concretization of an information content entity inheres. + GROUP: IAO + material information bearer + + + + + + + + + histogram + + A histogram is a report graph which is a statistical description of a +distribution in terms of occurrence frequencies of different event classes. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + GROUP:OBI + histogram + + + + + + + + + heatmap + + A heatmap is a report graph which is a graphical representation of data +where the values taken by a variable(s) are shown as colors in a +two-dimensional map. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + GROUP:OBI + heatmap + + + + + + + + + dendrogram + Dendrograms are often used in computational biology to +illustrate the clustering of genes. + + A dendrogram is a report graph which is a tree diagram +frequently used to illustrate the arrangement of the clusters produced by a +clustering algorithm. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + WEB: http://en.wikipedia.org/wiki/Dendrogram + dendrogram + + + + + + + + + scatter plot + Comparison of gene expression values in two samples can be displayed in a scatter plot + + A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + scattergraph + WEB: http://en.wikipedia.org/wiki/Scatterplot + scatter plot + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification + + + + + + + + + figure + Any picture, diagram or table + + An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. + PERSON: Lawrence Hunter + figure + + + + + + + + + diagram + A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. + + A figure that expresses one or more propositions + PERSON: Lawrence Hunter + diagram + + + + + + + + + document + A journal article, patent application, laboratory notebook, or a book + + A collection of information content entities intended to be understood together as a whole + PERSON: Lawrence Hunter + document + + + + + + + + + + + + + + + + + + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + + + + + + + Mus musculus + house mouse + mouse + + Mus musculus + + + + + + + + + Viruses + + Viruses + + + + + + + + + Euteleostomi + bony vertebrates + + Euteleostomi + + + + + + + + + Bacteria + eubacteria + + Bacteria + + + + + + + + + Archaea + + Archaea + + + + + + + + + Eukaryota + eucaryotes + eukaryotes + + Eukaryota + + + + + + + + + Euarchontoglires + + Euarchontoglires + + + + + + + + + Tetrapoda + tetrapods + + Tetrapoda + + + + + + + + + Amniota + amniotes + + Amniota + + + + + + + + + Opisthokonta + + Opisthokonta + + + + + + + + + Bilateria + + Bilateria + + + + + + + + + Murinae + + Murinae + + + + + + + + + Mammalia + mammals + + Mammalia + + + + + + + + + Vertebrata <Metazoa> + Vertebrata + vertebrates + + Vertebrata <Metazoa> + + + + + + + + + Danio rerio + leopard danio + zebra danio + zebra fish + zebrafish + + Danio rerio + + + + + + + + + Homo sapiens + human + human being + man + + Homo sapiens + + + + + + + + + Rodentia + rodent + + Rodentia + + + + + + + + + + + + + + + + + + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy + + A processual entity that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + planned process + + + + + + + + + regulator role + Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 + + a regulatory role involved with making and/or enforcing relevant legislation and governmental orders + Person:Jennifer Fostel + regulator + OBI + regulator role + + + + + + + + + regulatory role + Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 + + a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. + GROUP: Role branch + OBI, CDISC + govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent + regulatory role + + + + + + + + + material supplier role + Jackson Labs is an organization which provide mice as experimental material + + a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. + Supplier role is a special kind of service, e.g. biobank + PERSON:Jennifer Fostel + material provider role + supplier + material supplier role + + + + + + + + + + + + + + + classified data set + + A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. + PERSON: James Malone + PERSON: Monnie McGee + data set with assigned class labels + classified data set + + + + + + + + + + + + + + + + + + + + processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + Is a material entity that is created or changed during material processing. + PERSON: Alan Ruttenberg + processed material + + + + + + + + + culture medium + A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 + + a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. + changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 +Modification made by JZ. + Person: Jennifer Fostel, Jie Zheng + OBI + culture medium + + + + + + + + + reagent role + Buffer, dye, a catalyst, a solvating agent. + + A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. + PERSON:Matthew Brush + reagent + PERSON:Matthew Brush + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + +May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. + + (copied from ReO) +Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. + +Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. + +In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). + reagent role + + + + + + + + + + + + + + + + + + + + + + + + + + + material processing + A cell lysis, production of a cloning vector, creating a buffer. + + A planned process which results in physical changes in a specified input material + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca Serra + material transformation + OBI branch derived + material processing + + + + + + + + + + + + + + + + + + + + + + + + + specimen role + liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. + + a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + blood taken from animal: animal continues in study, whereas blood has role specimen. +something taken from study subject, leaves the study and becomes the specimen. + parasite example +- when parasite in people we study people, people are subjects and parasites are specimen +- when parasite extracted, they become subject in the following study +specimen can later be subject. + GROUP: Role Branch + OBI + specimen role + + + + + + + + + population + PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. + + a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area + 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: +http://code.google.com/p/popcomm-ontology/ + PERSON: Philippe Rocca-Serra + adapted from Oxford English Dictionnary + rem1: collection somehow always involve a selection process + population + + + + + + + + + organization + PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. + + An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. + BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: + +1) there are organization_member_roles (president, treasurer, branch +editor), with individual persons as bearers + +2) there are organization_roles (employer, owner, vendor, patent holder) + +3) an organization has a charter / rules / bylaws, which specify what roles +there are, how they should be realized, and how to modify the +charter/rules/bylaws themselves. + +It is debatable what the organization itself is (some kind of dependent +continuant or an aggregate of people). This also determines who/what the +bearer of organization_roles' are. My personal favorite is still to define +organization as a kind of 'legal entity', but thinking it through leads to +all kinds of questions that are clearly outside the scope of OBI. + +Interestingly enough, it does not seem to matter much where we place +organization itself, as long as we can subclass it (University, Corporation, +Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, +W3C, University of Oklahoma), and have it play roles. + +This leads to my proposal: We define organization through the statements 1 - +3 above, but without an 'is a' statement for now. We can leave it in its +current place in the is_a hierarchy (material entity) or move it up to +'continuant'. We leave further clarifications to BFO, and close this issue +for now. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra + PERSON: Susanna Sansone + GROUP: OBI + organization + + + + + + + + + + + + + + + + + + + + regulatory agency + The US Environmental Protection Agency + + A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. + GROUP: OBI Biomaterial Branch + WEB: en.wikipedia.org/wiki/Regulator + regulatory agency + + + + + + + + + material transformation objective + The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. + + an objective specifiction that creates an specific output object from input materials. + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + artifact creation objective + GROUP: OBI PlanAndPlannedProcess Branch + material transformation objective + + + + + + + + + + + + + + + + + + + + + + + + + + + manufacturing + + Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process + Manufacturing implies reproducibility and responsibility AR + This includes a single scientist making a processed material for personal use. + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + GROUP: OBI PlanAndPlannedProcess Branch + manufacturing + + + + + + + + + manufacturing objective + + is the objective to manufacture a material of a certain function (device) + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + GROUP: OBI PlanAndPlannedProcess Branch + manufacturing objective + + + + + + + + + + + + + + + + + + + + + + + + + + + + manufacturer role + With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. + + Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. + GROUP: Role Branch + OBI + manufacturer role + + + + + + + + + + + + + + + + + material separation objective + The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. + + is an objective to transform a material entity into spatially separated components. + PPPB branch + PPPB branch + material separation objective + + + + + + + + + + + + + + + clustered data set + A clustered data set is the output of a K means clustering data transformation + + A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. + PERSON: James Malone + PERSON: Monnie McGee + data set with assigned discovered class labels + AR thinks could be a data item instead + clustered data set + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + specimen collection process + drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation + + A planned process with the objective of collecting a specimen. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. + Philly2013: The specimen_role for the specimen is created during the specimen collection process. + label changed to 'specimen collection process' on 10/27/2014, details see tracker: +http://sourceforge.net/p/obi/obi-terms/716/ + Bjoern Peters + specimen collection + 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession + 6/9/09: used at workshop + specimen collection process + + + + + + + + + + + + + + + + + + + + + + + class prediction data transformation + + A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. + James Malone + supervised classification data transformation + PERSON: James Malone + class prediction data transformation + + + + + + + + + + portioning objective + The objective to obtain multiple aliquots of an enzyme preparation. + + A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. + portioning objective + + + + + + + + + separation into different composition objective + The objective to obtain cells contained in a sample of blood. + + A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). + We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives + separation into different composition objective + + + + + + + + + specimen collection objective + The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. + + A objective specification to obtain a material entity for potential use as an input during an investigation. + Bjoern Peters + Bjoern Peters + specimen collection objective + + + + + + + + + + + + + + + support vector machine + + A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. + James Malone + Ryan Brinkman + SVM + PERSON: Ryan Brinkman + support vector machine + + + + + + + + + decision tree induction objective + + A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. + James Malone + decision tree induction objective + + + + + + + + + + + + + + + decision tree building data transformation + + A decision tree building data transformation is a data transformation that has objective decision tree induction. + James Malone + PERSON: James Malone + decision tree building data transformation + + + + + + + + + GenePattern software + + a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. + James Malone + Person:Helen Parkinson + WEB: http://www.broadinstitute.org/cancer/software/genepattern/ + GenePattern software + + + + + + + + + peak matching + + Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold + James Malone + Ryan Brinkman + PERSON: Ryan Brinkman + peak matching + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k-nearest neighbors + + A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. + James Malone + k-NN + PERSON: James Malone + k-nearest neighbors + + + + + + + + + + + + + + + CART + + A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. + James Malone + classification and regression trees + BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. + CART + + + + + + + + + + + + + + + statistical model validation + Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia + + A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. + Helen Parkinson + http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 + statistical model validation + + + + + + + + + material maintenance objective + + An objective specification maintains some or all of the qualities of a material over time. + PERSON: Bjoern Peters + PERSON: Bjoern Peters + material maintenance objective + + + + + + + + + + + + + + + + + + + + + + + + + manufacturer + + A person or organization that has a manufacturer role + manufacturer + + + + + + + + + + + + + + + material maintenance + + a process with that achieves the objective to maintain some or all of the characteristics of an input material over time + material maintenance + + + + + + + + + + + + + + + + + + + + + + + + + + + + service provider role + Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. + + is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person + PERSON:Helen Parkinson + service provider role + + + + + + + + + + + + + + + + + + processed specimen + A tissue sample that has been sliced and stained for a histology study. +A blood specimen that has been centrifuged to obtain the white blood cells. + + A specimen that has been intentionally physically modified. + Bjoern Peters + Bjoern Peters + A tissue sample that has been sliced and stained for a histology study. + processed specimen + + + + + + + + + categorical label + The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. + + A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. + Bjoern Peters + Bjoern Peters + categorical label + + + + + + + + + questionnaire + + A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. + JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. +JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. + Need to clarify if this is a document or a directive information entity (or what their connection is)) + PERSON: Jessica Turner + Merriam-Webster + questionnaire + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + secondary cultured cell + + A cultured cell that has been passaged or derives from a cell that has been passaged in culture. + The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. + Person: Matthew Brush + PERSON: Matthew Brush + A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. + secondary cultured cell + + + + + + + + + + + + + + + establishing cell line + + a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). + 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. + Person: Matthew Brush + PERSON:Matthew Brush + establishing cell line + + + + + + + + + + + + + + + + + + + + + + + + + + reagent + + A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. + 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device. + PERSON:Matthew Brush + PERSON:Matthew Brush + (copied from ReO) +Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. + +Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. + +In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). + reagent + + + + + + + + + + + + + + + + + + + + + + + + + + + secondary cultured cell population + + A cultured cell population that is derived through one or more passages in culture. + The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. + PERSON:Matthew Brush + secondary cell culture sample + PERSON:Matthew Brush + The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally. + secondary cultured cell population + + + + + + + + + cell freezing medium + + A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. + PERSON: Matthew Brush + cell freezing medium + + + + + + + + + categorical value specification + + A value specification that is specifies one category out of a fixed number of nominal categories + PERSON:Bjoern Peters + categorical value specification + + + + + + + + + value specification + The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. + + An information content entity that specifies a value within a classification scheme or on a quantitative scale. + This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. + PERSON:Bjoern Peters + value specification + + + + + + + + + + + + + + + + + + + + collection of specimens + Blood cells collected from multiple donors over the course of a study. + + A material entity that has two or more specimens as its parts. + Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ + Person: Chris Stoeckert, Jie Zheng + OBIB, OBI + Biobank + collection of specimens + + + + + + + + + histologic grade according to AJCC 7th edition + G4: Undifferentiated + G1:Well differentiated + + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade according to AJCC 7th edition + + + + + + + + + histologic grade according to the Fuhrman Nuclear Grading System + + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. + Chris Stoeckert, Helena Ellis + Histologic Grade (Fuhrman Nuclear Grading System) + NCI BBRB, OBI + NCI BBRB + histologic grade according to the Fuhrman Nuclear Grading System + + + + + + + + + histologic grade for ovarian tumor + + A categorical value specification that is a histologic grade assigned to a ovarian tumor. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade for ovarian tumor + + + + + + + + + histologic grade for ovarian tumor according to a two-tier grading system + + A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade for ovarian tumor according to a two-tier grading system + + + + + + + + + histologic grade for ovarian tumor according to the World Health Organization + + A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade for ovarian tumor according to the World Health Organization + + + + + + + + + pathologic primary tumor stage for colon and rectum according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for colon and rectum according to AJCC 7th edition + + + + + + + + + pathologic primary tumor stage for lung according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread lung primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for lung according to AJCC 7th edition + + + + + + + + + pathologic primary tumor stage for kidney according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for kidney according to AJCC 7th edition + + + + + + + + + pathologic primary tumor stage for ovary according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for ovary according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for colon and rectum according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for colon and rectum according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for lung according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for lung according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for kidney according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for kidney according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for ovary according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for ovary according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for colon according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: colon distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for colon according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for lung according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: lung distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for lung according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for kidney according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: kidney distant Metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for kidney according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for ovary according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: ovarian distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for ovary according to AJCC 7th edition + + + + + + + + + clinical tumor stage group according to AJCC 7th edition + + A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. + Chris Stoeckert, Helena Ellis + Clinical tumor stage group (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + clinical tumor stage group according to AJCC 7th edition + + + + + + + + + International Federation of Gynecology and Obstetrics cervical cancer stage value specification + + A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. + Chris Stoeckert, Helena Ellis + Clinical FIGO stage + NCI BBRB, OBI + NCI BBRB + International Federation of Gynecology and Obstetrics cervical cancer stage value specification + + + + + + + + + International Federation of Gynecology and Obstetrics ovarian cancer stage value specification + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. + Chris Stoeckert, Helena Ellis + Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) + NCI BBRB, OBI + NCI BBRB + International Federation of Gynecology and Obstetrics ovarian cancer stage value specification + + + + + + + + + performance status value specification + + A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). + Chris Stoeckert, Helena Ellis + Performance Status Scale + https://en.wikipedia.org/wiki/Performance_status + NCI BBRB + performance status value specification + + + + + + + + + Eastern Cooperative Oncology Group score value specification + + A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. + Chris Stoeckert, Helena Ellis + ECOG score + NCI BBRB, OBI + NCI BBRB + Eastern Cooperative Oncology Group score value specification + + + + + + + + + Karnofsky score vaue specification + + A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. + Chris Stoeckert, Helena Ellis + Karnofsky Score + NCI BBRB, OBI + NCI BBRB + Karnofsky score vaue specification + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Epstein Barr virus transformed B cell + PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. + + A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity + PERSON: Susanna Sansone + GROUP: OBI Biomaterial Branch + Epstein Barr virus transformed B cell + + + + + + + + + + + + + + + + + + + organism + animal + fungus + plant + virus + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI. + GROUP: OBI Biomaterial Branch + WEB: http://en.wikipedia.org/wiki/Organism + organism + + + + + + + + + + + + + + + + + + + + specimen + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + + A material entity that has the specimen role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + PERSON: James Malone + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch + specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured cell population + A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). + +A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). + + A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. + 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. + PERSON:Matthew Brush + cell culture sample + PERSON:Matthew Brush + The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. + cultured cell population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + data transformation + The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. + + A planned process that produces output data from input data. + Elisabetta Manduchi + Helen Parkinson + James Malone + Melanie Courtot + Philippe Rocca-Serra + Richard Scheuermann + Ryan Brinkman + Tina Hernandez-Boussard + data analysis + data processing + Branch editors + data transformation + + + + + + + + + + + + + + + leave one out cross validation method + The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 + + is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data + 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 + Person:Helen Parkinson + leave one out cross validation method + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + k-means clustering + + A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). + Elisabetta Manduchi + James Malone + Philippe Rocca-Serra + WEB: http://en.wikipedia.org/wiki/K-means + k-means clustering + + + + + + + + + + + + + + + + + + + + + + + hierarchical clustering + + A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). + James Malone + WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering + hierarchical clustering + + + + + + + + + + + + + + + + + + + + + + + dimensionality reduction + + A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. + Elisabetta Manduchi + James Malone + Melanie Courtot + Philippe Rocca-Serra + data projection + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + dimensionality reduction + + + + + + + + + principal components analysis dimensionality reduction + + A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. + Elisabetta Manduchi + James Malone + Melanie Courtot + Philippe Rocca-Serra + pca data reduction + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + principal components analysis dimensionality reduction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + data visualization + Generation of a heatmap from a microarray dataset + + An planned process that creates images, diagrams or animations from the input data. + Elisabetta Manduchi + James Malone + Melanie Courtot + Tina Boussard + data encoding as image + visualization + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + PERSON: Tina Boussard + Possible future hierarchy might include this: +information_encoding +>data_encoding +>>image_encoding + data visualization + + + + + + + + + data transformation objective + normalize objective + + An objective specification to transformation input data into output data + Modified definition in 2013 Philly OBI workshop + James Malone + PERSON: James Malone + data transformation objective + + + + + + + + + + + + + + + partitioning data transformation + + A partitioning data transformation is a data transformation that has objective partitioning. + James Malone + PERSON: James Malone + partitioning data transformation + + + + + + + + + partitioning objective + A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. + + A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. + Elisabetta Manduchi + James Malone + PERSON: Elisabetta Manduchi + partitioning objective + + + + + + + + + + + + + + + + + + + + + + + class discovery data transformation + + A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. + James Malone + clustering data transformation + unsupervised classification data transformation + PERSON: James Malone + class discovery data transformation + + + + + + + + + class discovery objective + + A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. + James Malone + clustering objective + discriminant analysis objective + unsupervised classification objective + PERSON: Elisabetta Manduchi + PERSON: James Malone + class discovery objective + + + + + + + + + class prediction objective + + A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and +class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. + James Malone + classification objective + supervised classification objective + PERSON: Elisabetta Manduchi + PERSON: James Malone + class prediction objective + + + + + + + + + cross validation objective + + A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. + James Malone + rotation estimation objective + WEB: http://en.wikipedia.org/wiki/Cross_validation + cross validation objective + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + clustered data visualization + + A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. + James Malone + clustered data visualization + + + + + + + + + + + + + + + + + + + + + + + + + + + material component separation + Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification + + a material processing in which components of an input material become segregated in space + Bjoern Peters + IEDB + material component separation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + maintaining cell culture + When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture + + a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing + PlanAndPlannedProcess Branch + OBI branch derived + maintaining cell culture + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'establishing cell culture' + + a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). + PERSON:Matthew Brush + PERSON:Matthew Brush + A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. + establishing cell culture + + + + + + + + + + + + + + + + + + + + + + + + + + + cell culture splitting + The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. + + The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing + PlanAndPlannedProcess Branch + cell culture passaging + OBI branch derived + An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone. + cell culture splitting + + + + + + + + + biological sex + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. + + biological sex + + + + + + + + + behavioral quality + An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. + + behavioral quality + + + + + + + + + female + A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. + + female + + + + + + + + + male + A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. + + male + + + + + + + + + physical object quality + A quality which inheres in a continuant. + + physical object quality + + + + + + + + + phenotypic sex + An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. + + phenotypic sex + + + + + + + + + organismal quality + A quality that inheres in an entire organism or part of an organism. + + organismal quality + + + + + + + + + handedness + A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. + + handedness + + + + + + + + + left handedness + Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. + + left handedness + + + + + + + + + right handedness + Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. + + right handedness + + + + + + + + + ambidextrous handedness + Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. + + ambidextrous handedness + + + + + + + + + region + A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. + primary structure of sequence macromolecule + sequence + + region + + + + + + + + + contig + A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. + + contig + + + + + + + + + sequence_assembly + A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. + + sequence_assembly + + + + + + + + + assembly + A region of the genome of known length that is composed by ordering and aligning two or more different regions. + + assembly + + + + + + + + + experimental_feature + A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. + + experimental_feature + + + + + + + + + life cycle stage + A spatiotemporal region encompassing some part of the life cycle of an organism. + + life cycle stage + + + + + + + + + length unit + A unit which is a standard measure of the distance between two points. + + length unit + + + + + + + + + mass unit + A unit which is a standard measure of the amount of matter/energy of a physical object. + + mass unit + + + + + + + + + time unit + A unit which is a standard measure of the dimension in which events occur in sequence. + + time unit + + + + + + + + + temperature unit + A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. + + temperature unit + + + + + + + + + substance unit + A unit which is a standardised quantity of an element or compound with uniform composition. + + substance unit + + + + + + + + + concentration unit + A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. + + concentration unit + + + + + + + + + volume unit + A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. + + volume unit + + + + + + + + + frequency unit + A unit which is a standard measure of the number of repetitive actions in a particular time. + + frequency unit + + + + + + + + + volumetric flow rate unit + A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . + + volumetric flow rate unit + + + + + + + + + rate unit + A unit which represents a standard measurement occurrence of a process per unit time. + + rate unit + + + + + + + + Obsolete Class + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + PERSON:Alan Ruttenberg + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + core + + + + + + + + + placeholder removed + + + + + + + + + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + + This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. + We expect to be able to mine these new reasons and add instances as required. + other + true + + + + + + + + + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + Transformation-ML + Transformation-ML file describing parameter transformations used in a GvHD experiment. + + Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) + person:Jennifer Fostel + web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf + Transformation-ML + + + + + + + + + ACS + d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment. + + ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) + person:Jennifer Fostel + web-page:http://www.isac-net.org/content/view/607/150/ + ACS + + + + + + + + + XML + RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document + + XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) + person:Jennifer Fostel + web-page:http://www.w3.org/XML/ + XML + + + + + + + + + RDF + A FOAF file, a SKOS file, an OWL file. + + RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) + person:Jennifer Fostel + web-page:http://www.w3.org/RDF/ + RDF + + + + + + + + + zip + MagicDraw MDZIP archive, Java JAR file. + + zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) + person:Jennifer Fostel + web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ + zip + + + + + + + + + tar + Example.tar file. + + tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) + person:Jennifer Fostel + web-page:http://www.gnu.org/software/tar/manual/ + tar + + + + + + + + + FCS + d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment. + + FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) + person:Jennifer Fostel + web-page:http://www.fcspress.com/ + FCS + + + + + + + + + Compensation-ML + compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment + + Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) + person:Jennifer Fostel + web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf + Compensation-ML + + + + + + + + + Gating-ML + foogate.xml, Gating-ML file describing gates used in a GvHD experiment. + + Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) + person:Jennifer Fostel + web-page:http://www.flowcyt.org/gating/ + Gating-ML + + + + + + + + + OWL + OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file. + + OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) + person:Jennifer Fostel + web-page:http://www.w3.org/2004/OWL/ + OWL + + + + + + + + + + + + + + + + + + + + + Affymetrix + Affymetrix supplied microarray + + An organization which supplies technology, tools and protocols for use in high throughput applications + Affymetrix + + + + + + + + + + + + + + + Thermo + + Philippe Rocca-Serra + Thermo + + + + + + + + + + + + + + + Waters + + Philippe Rocca-Serra + Waters + + + + + + + + + + + + + + + BIO-RAD + + Philippe Rocca-Serra + BIO-RAD + + + + + + + + + GenePattern hierarchical clustering + + James Malone + GenePattern hierarchical clustering + + + + + + + + + + + + + + + Ambion + + Philippe Rocca-Serra + Ambion + + + + + + + + + + + + + + + Helicos + + Philippe Rocca-Serra + Helicos + + + + + + + + + + + + + + + Roche + + Philippe Rocca-Serra + Roche + + + + + + + + + + + + + + + Illumina + + Philippe Rocca-Serra + Illumina + + + + + + + + + GenePattern PCA + + GenePattern PCA + + + + + + + + + + GenePattern module SVM + + GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. + James Malone + Ryan Brinkman + GenePattern module SVM + + + + + + + + + GenePattern k-nearest neighbors + + James Malone + GenePattern k-nearest neighbors + + + + + + + + + GenePattern LOOCV + + GenePattern LOOCV + + + + + + + + + GenePattern k-means clustering + + James Malone + GenePattern k-means clustering + + + + + + + + + + + + + + + Agilent + + Philippe Rocca-Serra + Agilent + + + + + + + + + + GenePattern module KMeansClustering + + GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. + James Malone + PERSON: James Malone + GenePattern module KMeansClustering + + + + + + + + + GenePattern CART + + James Malone + GenePattern CART + + + + + + + + + + + GenePattern module CARTXValidation + + GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. + GenePattern module CARTXValidation + + + + + + + + + + + + + + + Li-Cor + + Philippe Rocca-Serra + Li-Cor + + + + + + + + + + + + + + + Bruker Corporation + + Philippe Rocca-Serra + Bruker Corporation + + + + + + + + + GenePattern module KNNXValidation + + GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. + James Malone + PERSON: James Malone + GenePattern module KNNXValidation + + + + + + + + + + GenePattern module PeakMatch + + GenePattern module PeakMatch + + + + + + + + + + GenePattern module KNN + + GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. + James Malone + GenePattern module KNN + + + + + + + + + + GenePattern module HierarchicalClustering + + GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. + James Malone + PERSON: James Malone + GenePattern module HierarchicalClustering + + + + + + + + + GenePattern SVM + + James Malone + GenePattern SVM + + + + + + + + + + + + + + + Applied Biosystems + + Philippe Rocca-Serra + Applied Biosystems + + + + + + + + + + GenePattern module PCA + + GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. + James Malone + PERSON: James Malone + GenePattern module PCA + + + + + + + + + GenePattern peak matching + + James Malone + Ryan Brinkman + GenePattern peak matching + + + + + + + + + + + + + + + Bruker Daltonics + + Philippe Rocca-Serra + Bruker Daltonics + + + + + + + + + GenePattern HeatMapViewer data visualization + + The GenePattern process of generating Heat Maps from clustered data. + James Malone + GenePattern HeatMapViewer data visualization + + + + + + + + + GenePattern HierarchicalClusteringViewer data visualization + + The GenePattern process of generating hierarchical clustering visualization from clustered data. + James Malone + GenePattern HierarchicalClusteringViewer data visualization + + + + + + + + + + GenePattern module HeatMapViewer + + A GenePattern software module which is used to generate a heatmap view of data. + James Malone + GenePattern module HeatMapViewer + + + + + + + + + + GenePattern module HierarchicalClusteringViewer + + A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. + James Malone + GenePattern module HierarchicalClusteringViewer + + + + + + + + + + + + + + + Sysmex Corporation, Kobe, Japan + + WEB:http://www.sysmex.com/@2009/08/06 + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + Sysmex Corporation, Kobe, Japan + + + + + + + + + + + + + + + U.S. Food and Drug Administration + + FDA + U.S. Food and Drug Administration + + + + + + + + + + + + + + + right handed + + right handed + + + + + + + + + + + + + + + ambidexterous + + ambidexterous + + + + + + + + + + + + + + + left handed + + left handed + + + + + + + + + Edingburgh handedness inventory + + The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. + PERSON:Alan Ruttenberg + PERSON:Jessica Turner + PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 + WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html + Edingburgh handedness inventory + + + + + + + + + + + + + + + eBioscience + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.ebioscience.com/@2011/04/11 + eBioscience + + + + + + + + + + + + + + + Cytopeia + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.cytopeia.com/@2011/04/11 + Cytopeia + + + + + + + + + + + + + + + Exalpha Biological + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.exalpha.com/@2011/04/11 + Exalpha Biological + + + + + + + + + + + + + + + Apogee Flow Systems + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.apogeeflow.com/@2011/04/11 + Apogee Flow Systems + + + + + + + + + + + + + + + Exbio Antibodies + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.exbio.cz/@2011/04/11 + Exbio Antibodies + + + + + + + + + + + + + + + Becton Dickinson (BD Biosciences) + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.bdbiosciences.com/@2011/04/11 + Becton Dickinson (BD Biosciences) + + + + + + + + + + + + + + + Dako Cytomation + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.dakousa.com/@2011/04/11 + Dako Cytomation + + + + + + + + + + + + + + + Millipore + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.guavatechnologies.com/@2011/04/11 + Millipore + + + + + + + + + + + + + + + Antigenix + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.antigenix.com/@2011/04/11 + Antigenix + + + + + + + + + + + + + + + Partec + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.partec.de/@2011/04/11 + Partec + + + + + + + + + + + + + + + Beckman Coulter + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.beckmancoulter.com/@2011/04/11 + Beckman Coulter + + + + + + + + + + + + + + + Advanced Instruments Inc. (AI Companies) + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.aicompanies.com/@2011/04/11 + Advanced Instruments Inc. (AI Companies) + + + + + + + + + + + + + + + Miltenyi Biotec + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.miltenyibiotec.com/@2011/04/11 + Miltenyi Biotec + + + + + + + + + + + + + + + AES Chemunex + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.aeschemunex.com/@2011/04/11 + AES Chemunex + + + + + + + + + + + + + + + Bentley Instruments + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://bentleyinstruments.com/@2011/04/11 + Bentley Instruments + + + + + + + + + + + + + + + Invitrogen + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.invitrogen.com/@2011/04/11 + Invitrogen + + + + + + + + + + + + + + + Luminex + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.luminexcorp.com/@2011/04/11 + Luminex + + + + + + + + + + + + + + + CytoBuoy + + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.cytobuoy.com/@2011/04/11 + CytoBuoy + + + + + + + + + + + + + + + Nimblegen + + An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. + Person: Jie Zheng + Nimblegen + + + + + + + + + + + + + + + Pacific Biosciences + + An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. + Person: Jie Zheng + Pacific Biosciences + + + + + + + + + + + + + + + NanoString Technologies + + An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. + NanoString Technologies + + + + + + + + + Thermo Fisher Scientific + + An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific + NCI BBRB + Thermo Fisher Scientific + + + + + + + + + G1: Well differentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. + Chris Stoeckert, Helena Ellis + G1 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G1: Well differentiated + + + + + + + + + G2: Moderately differentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. + Chris Stoeckert, Helena Ellis + G2 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G2: Moderately differentiated + + + + + + + + + G3: Poorly differentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. + Chris Stoeckert, Helena Ellis + G3 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G3: Poorly differentiated + + + + + + + + + G4: Undifferentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. + Chris Stoeckert, Helena Ellis + G4 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G4: Undifferentiated + + + + + + + + + G1 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. + Chris Stoeckert, Helena Ellis + Grade 1 + NCI BBRB, OBI + NCI BBRB + G1 (Fuhrman) + + + + + + + + + G2 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. + Chris Stoeckert, Helena Ellis + Grade 2 + NCI BBRB, OBI + NCI BBRB + G2 (Fuhrman) + + + + + + + + + G3 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. + Chris Stoeckert, Helena Ellis + Grade 3 + NCI BBRB, OBI + NCI BBRB + G3 (Fuhrman) + + + + + + + + + G4 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. + Chris Stoeckert, Helena Ellis + Grade 4 + NCI BBRB, OBI + NCI BBRB + G4 (Fuhrman) + + + + + + + + + Low grade ovarian tumor + + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. + Chris Stoeckert, Helena Ellis + Low grade + NCI BBRB, OBI + NCI BBRB + Low grade ovarian tumor + + + + + + + + + High grade ovarian tumor + + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. + Chris Stoeckert, Helena Ellis + High grade + NCI BBRB, OBI + NCI BBRB + High grade ovarian tumor + + + + + + + + + G1 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. + Chris Stoeckert, Helena Ellis + G1 + NCI BBRB, OBI + NCI BBRB + G1 (WHO) + + + + + + + + + G2 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. + Chris Stoeckert, Helena Ellis + G2 + NCI BBRB, OBI + NCI BBRB + G2 (WHO) + + + + + + + + + G3 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. + Chris Stoeckert, Helena Ellis + G3 + NCI BBRB, OBI + NCI BBRB + G3 (WHO) + + + + + + + + + G4 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. + Chris Stoeckert, Helena Ellis + G4 + NCI BBRB, OBI + NCI BBRB + G4 (WHO) + + + + + + + + + pT0 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT0 (colon) + + + + + + + + + pTis (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pTis (colon) + + + + + + + + + pT1 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT1 (colon) + + + + + + + + + pT2 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT2 (colon) + + + + + + + + + pT3 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT3 (colon) + + + + + + + + + pT4a (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT4a (colon) + + + + + + + + + pT4b (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT4b (colon) + + + + + + + + + pT0 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT0 (lung) + + + + + + + + + pTis (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pTis (lung) + + + + + + + + + pT1 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT1 (lung) + + + + + + + + + pT1a (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT1a (lung) + + + + + + + + + pT1b (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT1b (lung) + + + + + + + + + pT2 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT2 (lung) + + + + + + + + + pT2a (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT2a (lung) + + + + + + + + + pT2b (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT2b (lung) + + + + + + + + + pT3 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT3 (lung) + + + + + + + + + pT4 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT4 (lung) + + + + + + + + + pT0 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT0 (kidney) + + + + + + + + + pT1 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT1 (kidney) + + + + + + + + + pT1a (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT1a (kidney) + + + + + + + + + pT1b (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT1b (kidney) + + + + + + + + + pT2 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT2 (kidney) + + + + + + + + + pT2a (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT2a (kidney) + + + + + + + + + pT2b (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT2b (kidney) + + + + + + + + + pT3 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3 (kidney) + + + + + + + + + pT3a (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3a (kidney) + + + + + + + + + pT3b (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3b (kidney) + + + + + + + + + pT3c (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3c (kidney) + + + + + + + + + pT4 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT4 (kidney) + + + + + + + + + pT0 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT0 (ovary) + + + + + + + + + pT1 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1 (ovary) + + + + + + + + + pT1a (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1a (ovary) + + + + + + + + + pT1b (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1b (ovary) + + + + + + + + + pT1c (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1c (ovary) + + + + + + + + + pT2 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2 (ovary) + + + + + + + + + pT2a (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2a (ovary) + + + + + + + + + pT2b (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2b (ovary) + + + + + + + + + pT2c (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2c (ovary) + + + + + + + + + pT3 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3 (ovary) + + + + + + + + + pT3a (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3a (ovary) + + + + + + + + + pT3b (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3b (ovary) + + + + + + + + + pT3c (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3c (ovary) + + + + + + + + + pN0 (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN0 (colon) + + + + + + + + + pN1 (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1 (colon) + + + + + + + + + pN1a (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1a (colon) + + + + + + + + + pN1b (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1b (colon) + + + + + + + + + pN1c (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1c (colon) + + + + + + + + + pN2 (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN2 (colon) + + + + + + + + + pN2a (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN2a (colon) + + + + + + + + + pN2b (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN2b (colon) + + + + + + + + + pN0 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN0 (lung) + + + + + + + + + pN1 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN1 (lung) + + + + + + + + + pN2 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN2 (lung) + + + + + + + + + pN3 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN3 (lung) + + + + + + + + + pN0 (kidney) + + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ + NCI BBRB + pN0 (kidney) + + + + + + + + + pN1 (kidney) + + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ + NCI BBRB + pN1 (kidney) + + + + + + + + + pN0 (ovary) + + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ + NCI BBRB + pN0 (ovary) + + + + + + + + + pN1 (ovary) + + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ + NCI BBRB + pN1 (ovary) + + + + + + + + + cM0 (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 + NCI BBRB + cM0 (colon) + + + + + + + + + cM1 (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 + NCI BBRB + cM1 (colon) + + + + + + + + + cM1a (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + cM1a (colon) + + + + + + + + + cM1b (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + cM1b (colon) + + + + + + + + + pM1 (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + pM1 (colon) + + + + + + + + + pM1a (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + pM1a (colon) + + + + + + + + + pM1b (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + pM1b (colon) + + + + + + + + + cM0 (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM0 (lung) + + + + + + + + + cM1 (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM1 (lung) + + + + + + + + + cM1a (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM1a (lung) + + + + + + + + + cM1b (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM1b (lung) + + + + + + + + + pM1 (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + pM1 (lung) + + + + + + + + + pM1a (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + pM1a (lung) + + + + + + + + + pM1b (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + pM1b (lung) + + + + + + + + + cM0 (kidney) + + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB + cM0 (kidney) + + + + + + + + + cM1 (kidney) + + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB + cM1 (kidney) + + + + + + + + + pM1 (kidney) + + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB + pM1 (kidney) + + + + + + + + + cM0 (ovary) + + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB + cM0 (ovary) + + + + + + + + + cM1 (ovary) + + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB + cM1 (ovary) + + + + + + + + + pM1 (ovary) + + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB + pM1 (ovary) + + + + + + + + + Occult Carcinoma (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. + Chris Stoeckert, Helena Ellis + Occult Carcinoma + http://www.medilexicon.com/dictionary/14371 + NCI BBRB + Occult Carcinoma (AJCC 7th) + + + + + + + + + Stage 0 (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. + Chris Stoeckert, Helena Ellis + Stage 0 + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage 0 (AJCC 7th) + + + + + + + + + Stage I (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. + Chris Stoeckert, Helena Ellis + Stage I + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage I (AJCC 7th) + + + + + + + + + Stage IIA (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. + Chris Stoeckert, Helena Ellis + Stage IIA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIA (AJCC 7th) + + + + + + + + + Stage IIB (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. + Chris Stoeckert, Helena Ellis + Stage IIB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIB (AJCC 7th) + + + + + + + + + Stage IIC (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. + Chris Stoeckert, Helena Ellis + Stage IIC + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIC (AJCC 7th) + + + + + + + + + Stage IIIA (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. + Chris Stoeckert, Helena Ellis + Stage IIIA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIIA (AJCC 7th) + + + + + + + + + Stage IIIB (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. + Chris Stoeckert, Helena Ellis + Stage IIIB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIIB (AJCC 7th) + + + + + + + + + Stage IIIC (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. + Chris Stoeckert, Helena Ellis + Stage IIIC + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIIC (AJCC 7th) + + + + + + + + + Stage IVA (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. + Chris Stoeckert, Helena Ellis + Stage IVA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IVA (AJCC 7th) + + + + + + + + + Stage IVB (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. + Chris Stoeckert, Helena Ellis + Stage IVB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IVB (AJCC 7th) + + + + + + + + + Stage IA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. + Chris Stoeckert, Helena Ellis + Stage IA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IA (FIGO) + + + + + + + + + Stage IA1 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. + Chris Stoeckert, Helena Ellis + Stage IA1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IA1 (FIGO) + + + + + + + + + Stage IA2 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. + Chris Stoeckert, Helena Ellis + Stage IA2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IA2 (FIGO) + + + + + + + + + Stage IB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA + Chris Stoeckert, Helena Ellis + Stage IB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IB (FIGO) + + + + + + + + + Stage IB1 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IB1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IB1 (FIGO) + + + + + + + + + Stage IB2 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IB2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IB2 (FIGO) + + + + + + + + + Stage IIA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. + Chris Stoeckert, Helena Ellis + Stage IIA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIA (FIGO) + + + + + + + + + Stage IIA1 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IIA1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIA1 (FIGO) + + + + + + + + + Stage IIA2 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IIA2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIA2 (FIGO) + + + + + + + + + Stage IIB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. + Chris Stoeckert, Helena Ellis + Stage IIB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIB (FIGO) + + + + + + + + + Stage IIIA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. + Chris Stoeckert, Helena Ellis + Stage IIIA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIIA (FIGO) + + + + + + + + + Stage IIIB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. + Chris Stoeckert, Helena Ellis + Stage IIIB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIIB (FIGO) + + + + + + + + + Stage IVA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. + Chris Stoeckert, Helena Ellis + Stage IVA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IVA (FIGO) + + + + + + + + + Stage IVB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. + Chris Stoeckert, Helena Ellis + Stage IVB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IVB (FIGO) + + + + + + + + + Stage 1 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1 (FIGO) + + + + + + + + + Stage 1A (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1A (FIGO) + + + + + + + + + Stage 1B (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1B (FIGO) + + + + + + + + + Stage 1C (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1C (FIGO) + + + + + + + + + Stage 2 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2 (FIGO) + + + + + + + + + Stage 2A (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2A (FIGO) + + + + + + + + + Stage 2B (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2B (FIGO) + + + + + + + + + Stage 2C (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2C (FIGO) + + + + + + + + + Stage 3 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). + Chris Stoeckert, Helena Ellis + Stage 3 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3 (FIGO) + + + + + + + + + Stage 3A (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . + Chris Stoeckert, Helena Ellis + Stage 3A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3A (FIGO) + + + + + + + + + Stage 3B (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . + Chris Stoeckert, Helena Ellis + Stage 3B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3B (FIGO) + + + + + + + + + Stage 3C (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). + Chris Stoeckert, Helena Ellis + Stage 3C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3C (FIGO) + + + + + + + + + Stage 4 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. + Chris Stoeckert, Helena Ellis + Stage 4 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 4 (FIGO) + + + + + + + + + Stage Unknown (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). + Chris Stoeckert, Helena Ellis + Stage Unknown + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage Unknown (FIGO) + + + + + + + + + 3: symptomatic in bed more than 50% of the day but not bed ridden + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 3: symptomatic in bed more than 50% of the day but not bed ridden + + + + + + + + + 2: symptomatic but in bed less than 50% of the day + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 2: symptomatic but in bed less than 50% of the day + + + + + + + + + 4: bed ridden + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 4: bed ridden + + + + + + + + + 0: asymptomatic + + An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 0: asymptomatic + + + + + + + + + 1: symptomatic but fully ambulatory + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 1: symptomatic but fully ambulatory + + + + + + + + + 100: asymptomatic + + A Karnofsky score vaue specification indicating that a patient is asymptomatic. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 100: asymptomatic + + + + + + + + + 80-90: symptomatic but fully ambulatory + + A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 80-90: symptomatic but fully ambulatory + + + + + + + + + 60-70: symptomatic but in bed less than 50% of the day + + A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 60-70: symptomatic but in bed less than 50% of the day + + + + + + + + + 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden + + A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden + + + + + + + + + meter + A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. + m + + meter + + + + + + + + + kilogram + A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. + kg + + kilogram + + + + + + + + + second + A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + s + sec + + second + + + + + + + + + centimeter + A length unit which is equal to one hundredth of a meter or 10^[-2] m. + cm + + centimeter + + + + + + + + + millimeter + A length unit which is equal to one thousandth of a meter or 10^[-3] m. + mm + + millimeter + + + + + + + + + micrometer + A length unit which is equal to one millionth of a meter or 10^[-6] m. + um + + micrometer + + + + + + + + + nanometer + A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. + nm + + nanometer + + + + + + + + + angstrom + A length unit which is equal to 10 [-10] m. + + angstrom + + + + + + + + + gram + A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. + g + + gram + + + + + + + + + milligram + A mass unit which is equal to one thousandth of a gram or 10^[-3] g. + mg + + milligram + + + + + + + + + microgram + A mass unit which is equal to one millionth of a gram or 10^[-6] g. + ug + + microgram + + + + + + + + + nanogram + A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. + ng + + nanogram + + + + + + + + + picogram + A mass unit which is equal to 10^[-12] g. + pg + + picogram + + + + + + + + + degree Celsius + A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. + C + degree C + + degree Celsius + + + + + + + + + minute + A time unit which is equal to 60 seconds. + min + + minute + + + + + + + + + hour + A time unit which is equal to 3600 seconds or 60 minutes. + h + hr + + hour + + + + + + + + + day + A time unit which is equal to 24 hours. + + day + + + + + + + + + week + A time unit which is equal to 7 days. + + week + + + + + + + + + month + A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. + + month + + + + + + + + + year + A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. + + year + + + + + + + + + micromole + A substance unit equal to a millionth of a mol or 10^[-6] mol. + umol + + micromole + + + + + + + + + nanomole + A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. + nmol + + nanomole + + + + + + + + + picomole + A substance unit equal to 10^[-12] mol. + pmol + + picomole + + + + + + + + + molar + A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). + M + + molar + + + + + + + + + millimolar + A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. + mM + + millimolar + + + + + + + + + micromolar + A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. + uM + + micromolar + + + + + + + + + nanomolar + A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. + nM + + nanomolar + + + + + + + + + picomolar + A unit of molarity which is equal to 10^[-12] M. + pM + + picomolar + + + + + + + + + cubic centimeter + A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. + cc + + cubic centimeter + + + + + + + + + milliliter + A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. + ml + + milliliter + + + + + + + + + liter + A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. + L + + liter + + + + + + + + + cubic decimeter + A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. + + cubic decimeter + + + + + + + + + microliter + A volume unit which is equal to one millionth of a liter or 10^[-6] L. + ul + + microliter + + + + + + + + + nanoliter + A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. + nl + + nanoliter + + + + + + + + + picoliter + A volume unit which is equal to 10^[-12] L. + pl + + picoliter + + + + + + + + + hertz + A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. + + hertz + + + + + + + + + mass percentage + A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. + % w/w + percent weight pr weight + + mass percentage + + + + + + + + + mass volume percentage + A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. + % w/v + percent vol per vol + + mass volume percentage + + + + + + + + + volume percentage + A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. + % v/v + percent vol per vol + + volume percentage + + + + + + + + + gram per liter + A mass unit density which is equal to mass of an object in grams divided by the volume in liters. + g per L + g/L + + gram per liter + + + + + + + + + milligram per milliliter + A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. + mg per ml + mg/ml + + milligram per milliliter + + + + + + + + + degree Fahrenheit + A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. + + degree Fahrenheit + + + + + + + + + pH + A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). + + pH + + + + + + + + + milliliter per liter + A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. + ml per L + ml/l + + milliliter per liter + + + + + + + + + gram per deciliter + A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. + g/dl + + gram per deciliter + + + + + + + + + colony forming unit per volume + A concentration unit which a measure of viable bacterial numbers in a given volume. + + colony forming unit per volume + + + + + + + + + microliters per minute + A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. + + microliters per minute + + + + + + + + + count per nanomolar second + A rate unit which is equal to one over one nanomolar second. + + count per nanomolar second + + + + + + + + + count per molar second + A rate unit which is equal to one over one molar second. + + count per molar second + + + + + + + + + count per nanomolar + A rate unit which is equal to one over one nanomolar. + + count per nanomolar + + + + + + + + + count per molar + A rate unit which is equal to one over one molar. + + count per molar + + + + + + + + + microgram per liter + A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. + ng/ml + ug/L + + microgram per liter + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/obi_terms.txt b/src/ontology/imports/obi_terms.txt new file mode 100644 index 0000000..553d177 --- /dev/null +++ b/src/ontology/imports/obi_terms.txt @@ -0,0 +1,2 @@ +OBI:0000011 + diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl new file mode 100644 index 0000000..b46f072 --- /dev/null +++ b/src/ontology/imports/pato_import.owl @@ -0,0 +1,14 @@ + + + + + + diff --git a/src/ontology/imports/pato_terms.txt b/src/ontology/imports/pato_terms.txt new file mode 100644 index 0000000..3b14895 --- /dev/null +++ b/src/ontology/imports/pato_terms.txt @@ -0,0 +1,2 @@ +PATO:0000001 + diff --git a/src/ontology/imports/pco_import.owl b/src/ontology/imports/pco_import.owl new file mode 100644 index 0000000..6bdfeae --- /dev/null +++ b/src/ontology/imports/pco_import.owl @@ -0,0 +1,14 @@ + + + + + + diff --git a/src/ontology/imports/pco_terms.txt b/src/ontology/imports/pco_terms.txt new file mode 100644 index 0000000..b0b46e1 --- /dev/null +++ b/src/ontology/imports/pco_terms.txt @@ -0,0 +1,4 @@ +PCO:0000000 +PCO:0000001 +PCO:0000002 + diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 328cb8e..3a0fb4a 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -17,7 +17,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -63,7 +63,6 @@ definition - definition @@ -106,10 +105,7 @@ - - - curator note - + @@ -124,35 +120,13 @@ - - expand expression to - - - - - - - - expand assertion to - - - - - - - - An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. - first order logic expression - + - - - OBO foundry unique label - + @@ -228,21 +202,9 @@ - - - - - - - + - - - - - - - + @@ -264,6 +226,12 @@ + + + + + + @@ -783,19 +751,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos - 2017-07-19T17:30:36Z - has ligand - - - - @@ -1034,10 +989,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - @@ -1267,36 +1218,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - x actively participates in y if and only if x participates in y and x realizes some active role - Chris Mungall - agent in - actively participates in - - - - - - - - - 'heart development' has active participant some Shh protein - - x has participant y if and only if x realizes some active role that inheres in y - This may be obsoleted and replaced by the original 'has agent' relation - Chris Mungall - has agent - - obsolete has active participant - true - - - - @@ -1639,7 +1560,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + @@ -2103,16 +2024,21 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + + + - Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall + Vasundra Touré molecularly controls - activity directly regulates activity of + directly regulates activity of @@ -2121,16 +2047,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + - Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall - inhibits + Vasundra Touré + directly inhibits molecularly decreases activity of - activity directly negatively regulates activity of + directly negatively regulates activity of @@ -2139,16 +2069,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + - Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall - activates + Vasundra Touré + directly activates molecularly increases activity of - activity directly positively regulates activity of + directly positively regulates activity of @@ -2240,13 +2174,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between material entities + causal relation between entities @@ -2397,7 +2331,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Chris Mungall - causally influenced by (material entity to material entity) + causally influenced by (entity-centric) causally influenced by @@ -2429,6 +2363,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + @@ -2439,10 +2375,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b + The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall + Vasundra Touré - causally influences (material entity to material entity) + causally influences (entity-centric) causally influences @@ -2887,6 +2824,19 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. + Vasundra Touré + regulates activity of + + + + @@ -3157,12 +3107,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - @@ -3205,12 +3149,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - - @@ -3300,15 +3238,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - ready for release - - - - @@ -3318,15 +3247,6 @@ Environmental exposures include those imposed by natural environments, experimen - - - - - requires discussion - - - - + diff --git a/src/ontology/imports/uberon_terms.txt b/src/ontology/imports/uberon_terms.txt new file mode 100644 index 0000000..7417ec8 --- /dev/null +++ b/src/ontology/imports/uberon_terms.txt @@ -0,0 +1,2 @@ +UBERON:0001062 + diff --git a/src/ontology/reports/geno-edit.owl-obo-report.tsv b/src/ontology/reports/geno-edit.owl-obo-report.tsv index 36fbb89..6312b9e 100644 --- a/src/ontology/reports/geno-edit.owl-obo-report.tsv +++ b/src/ontology/reports/geno-edit.owl-obo-report.tsv @@ -314,4 +314,3 @@ INFO missing_superclass GENO:0000885 rdfs:subClassOf INFO missing_superclass SO:0000804 rdfs:subClassOf INFO missing_superclass SO:0000830 rdfs:subClassOf INFO missing_superclass SO:0001059 rdfs:subClassOf -INFO missing_superclass oboInOwl:ObsoleteClass rdfs:subClassOf diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh new file mode 100644 index 0000000..cd72c8f --- /dev/null +++ b/src/scripts/update_repo.sh @@ -0,0 +1,22 @@ +echo "This (experimental) update script will create a new repo according to your config file. It will:" +echo "(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries wont be touched) and docker wrapper (run.sh)." +echo "(2) and add missing files, if any." + +set -e + +OID=geno +SRCDIR=../ +CONFIG=$OID"-odk.yaml" + +rm -rf target +mkdir target +/tools/odk.py seed -c -g False -C $CONFIG +ls -l target/$OID/src +ls -l $SRCDIR +rsync -r -u --ignore-existing --exclude 'patterns/data/default/example.tsv' --exclude 'patterns/dosdp-patterns/example.yaml' target/$OID/src/ $SRCDIR +cp target/$OID/src/scripts/update_repo.sh $SRCDIR/scripts/ +cp target/$OID/src/ontology/Makefile $SRCDIR/ontology/ +cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/ +cp -r target/$OID/src/sparql/* $SRCDIR/sparql/ +echo "WARNING: These files should be manually migrated: .gitignore, src/ontology/catalog.xml (if you added a new import or component)" +echo "Update successfully completed." \ No newline at end of file diff --git a/src/sparql/simple-seed.sparql b/src/sparql/simple-seed.sparql index e62d216..a96d263 100644 --- a/src/sparql/simple-seed.sparql +++ b/src/sparql/simple-seed.sparql @@ -3,6 +3,8 @@ prefix obo: SELECT DISTINCT ?cls WHERE { + {?cls a owl:AnnotationProperty .} + UNION {?cls a owl:ObjectProperty .} UNION {?x ?cls} diff --git a/src/sparql/subsets-labeled.sparql b/src/sparql/subsets-labeled.sparql index 9f8aca6..7bc992f 100644 --- a/src/sparql/subsets-labeled.sparql +++ b/src/sparql/subsets-labeled.sparql @@ -7,7 +7,7 @@ prefix rdfs: SELECT ?subset ?clsLabel WHERE { - ?cls a owl:Class . + ?cls a owl:Class ; inSubset: ?subset ; rdfs:label ?clsLabel } From f99b496a1137c2dbee0e5a4906e639e0da7620d1 Mon Sep 17 00:00:00 2001 From: matentzn Date: Sun, 8 Mar 2020 23:46:06 +0000 Subject: [PATCH 10/11] Properly depracted obsolete classes --- src/ontology/geno-edit.owl | 291 ++++++++++++++++++++++--------------- 1 file changed, 176 insertions(+), 115 deletions(-) diff --git a/src/ontology/geno-edit.owl b/src/ontology/geno-edit.owl index 3aa66d1..9198b23 100644 --- a/src/ontology/geno-edit.owl +++ b/src/ontology/geno-edit.owl @@ -99,6 +99,16 @@ Declaration(Class(obo:GENO_0000149)) Declaration(Class(obo:GENO_0000150)) Declaration(Class(obo:GENO_0000152)) Declaration(Class(obo:GENO_0000160)) +Declaration(Class(obo:GENO_0000164)) +Declaration(Class(obo:GENO_0000165)) +Declaration(Class(obo:GENO_0000166)) +Declaration(Class(obo:GENO_0000169)) +Declaration(Class(obo:GENO_0000170)) +Declaration(Class(obo:GENO_0000171)) +Declaration(Class(obo:GENO_0000172)) +Declaration(Class(obo:GENO_0000173)) +Declaration(Class(obo:GENO_0000174)) +Declaration(Class(obo:GENO_0000175)) Declaration(Class(obo:GENO_0000324)) Declaration(Class(obo:GENO_0000338)) Declaration(Class(obo:GENO_0000339)) @@ -405,7 +415,6 @@ Declaration(Class(obo:ZP_0000755)) Declaration(Class(obo:ZP_0005531)) Declaration(Class(obo:ZP_0005692)) Declaration(Class()) -Declaration(Class(oboInOwl:ObsoleteClass)) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1881,24 +1890,24 @@ AnnotationAssertion(rdfs:comment obo:GENO_0000017 "A reference sequence is one t AnnotationAssertion(rdfs:label obo:GENO_0000017 "reference sequence") EquivalentClasses(obo:GENO_0000017 ObjectIntersectionOf(obo:GENO_0000702 ObjectSomeValuesFrom(obo:GENO_0000968 obo:GENO_0000152))) -# Class: obo:GENO_0000019 (obsolete_sequence feature collection) +# Class: obo:GENO_0000019 (obsolete sequence feature collection) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000019 "a collection more than one sequence features (ie a collection of discontinuous sequence features)") AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000019 "perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one)") AnnotationAssertion(rdfs:comment obo:GENO_0000019 "1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions.") -AnnotationAssertion(rdfs:label obo:GENO_0000019 "obsolete_sequence feature collection") -SubClassOf(obo:GENO_0000019 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000019 "obsolete sequence feature collection"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000019 "true"^^xsd:boolean) -# Class: obo:GENO_0000022 (obsolete_genomic feature collection) +# Class: obo:GENO_0000022 (obsolete genomic feature collection) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000022 "A sequence feature collection comprised of discontiguous sequences from a single genome") AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000022 "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system.") AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000022 "genomic feature collection") AnnotationAssertion(rdfs:comment obo:GENO_0000022 "Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection.") -AnnotationAssertion(rdfs:label obo:GENO_0000022 "obsolete_genomic feature collection") -SubClassOf(obo:GENO_0000022 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000022 "obsolete genomic feature collection"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000022 "true"^^xsd:boolean) -# Class: obo:GENO_0000029 (obsolete_reference single locus complement) +# Class: obo:GENO_0000029 (obsolete reference single locus complement) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000029 "A single locus complement that serves as a standard against which 'variant' sequences are compared") AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000029 "reference allelic complement") @@ -1913,8 +1922,8 @@ SC axioms: 'has member' exactly 0 'variant allele' 'has member' only 'reference genomic feature' 'has member' some 'reference genomic feature'") -AnnotationAssertion(rdfs:label obo:GENO_0000029 "obsolete_reference single locus complement") -SubClassOf(obo:GENO_0000029 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000029 "obsolete reference single locus complement"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000029 "true"^^xsd:boolean) # Class: obo:GENO_0000030 (variant single locus complement) @@ -1943,7 +1952,7 @@ In model organism datasets, 'reference' alleles are typically (but not always) t AnnotationAssertion(rdfs:label obo:GENO_0000036 "reference allele") EquivalentClasses(obo:GENO_0000036 ObjectIntersectionOf(obo:GENO_0000512 ObjectSomeValuesFrom(obo:GENO_0000968 obo:GENO_0000152))) -# Class: obo:GENO_0000037 (obsolete_unspecified feature) +# Class: obo:GENO_0000037 (obsolete unspecified feature) AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000037 obo:GENO_0000484) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000037 "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus).") @@ -1953,10 +1962,10 @@ AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000037 "Not required at present fo Eq Class def: 'genomic feature' and (has_sequence_attribute some unspecified)") AnnotationAssertion(rdfs:comment obo:GENO_0000037 "An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele).") -AnnotationAssertion(rdfs:label obo:GENO_0000037 "obsolete_unspecified feature") -SubClassOf(obo:GENO_0000037 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000037 "obsolete unspecified feature"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000037 "true"^^xsd:boolean) -# Class: obo:GENO_0000042 (obsolete_reference junction) +# Class: obo:GENO_0000042 (obsolete reference junction) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000042 "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature.") AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000042 "hemizygous reference junction") @@ -1970,8 +1979,8 @@ is_variant_with some insertion") AnnotationAssertion(rdfs:comment obo:GENO_0000042 "In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation.") -AnnotationAssertion(rdfs:label obo:GENO_0000042 "obsolete_reference junction") -SubClassOf(obo:GENO_0000042 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000042 "obsolete reference junction"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000042 "true"^^xsd:boolean) # Class: obo:GENO_0000047 (danio rerio gene) @@ -1991,7 +2000,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000057 "A gene that originates fro AnnotationAssertion(rdfs:label obo:GENO_0000057 "mus musculus gene") EquivalentClasses(obo:GENO_0000057 ObjectIntersectionOf(obo:SO_0000704 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_10090))) -# Class: obo:GENO_0000060 (obsolete_reference gene allele) +# Class: obo:GENO_0000060 (obsolete reference gene allele) AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000060 "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development. http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690 @@ -2011,13 +2020,13 @@ is_reference_allele_of some gene") AnnotationAssertion(rdfs:comment obo:GENO_0000060 "Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared.") -AnnotationAssertion(rdfs:label obo:GENO_0000060 "obsolete_reference gene allele") -SubClassOf(obo:GENO_0000060 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000060 "obsolete reference gene allele"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000060 "true"^^xsd:boolean) -# Class: obo:GENO_0000091 (obsolete_experimental insertion) +# Class: obo:GENO_0000091 (obsolete experimental insertion) -AnnotationAssertion(rdfs:label obo:GENO_0000091 "obsolete_experimental insertion") -SubClassOf(obo:GENO_0000091 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000091 "obsolete experimental insertion"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000091 "true"^^xsd:boolean) # Class: obo:GENO_0000092 (gene trap insertion) @@ -2093,11 +2102,11 @@ SubClassOf(obo:GENO_0000119 obo:GENO_0000112) SubClassOf(obo:GENO_0000119 ObjectSomeValuesFrom(obo:RO_0002351 obo:NCBITaxon_7955)) SubClassOf(obo:GENO_0000119 ObjectAllValuesFrom(obo:RO_0002351 obo:NCBITaxon_7955)) -# Class: obo:GENO_0000125 (obsolete_sequence feature collection attribute) +# Class: obo:GENO_0000125 (obsolete sequence feature collection attribute) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000125 "sequence attribute that can inhere only in a collection of more than one sequence features") -AnnotationAssertion(rdfs:label obo:GENO_0000125 "obsolete_sequence feature collection attribute") -SubClassOf(obo:GENO_0000125 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000125 "obsolete sequence feature collection attribute"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000125 "true"^^xsd:boolean) # Class: obo:GENO_0000131 (in cis) @@ -2177,12 +2186,12 @@ These genetic and environmental \"interactions\" of alleles play out at the leve AnnotationAssertion(rdfs:label obo:GENO_0000141 "inheritance pattern") SubClassOf(obo:GENO_0000141 obo:BFO_0000016) -# Class: obo:GENO_0000142 (obsolete_dominant inheritance) +# Class: obo:GENO_0000142 (obsolete dominant inheritance) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000142 "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes") AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000142 "Triage until decide if want to define this as grouping class that would result in multiple-inheritance.") -AnnotationAssertion(rdfs:label obo:GENO_0000142 "obsolete_dominant inheritance") -SubClassOf(obo:GENO_0000142 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000142 "obsolete dominant inheritance"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000142 "true"^^xsd:boolean) # Class: obo:GENO_0000143 (co-dominant autosomal inheritance) @@ -2233,11 +2242,11 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000149 "http://purl.obolibrary. AnnotationAssertion(rdfs:label obo:GENO_0000149 "X-linked recessive inheritance"@en) SubClassOf(obo:GENO_0000149 obo:GENO_0000936) -# Class: obo:GENO_0000150 (obsolete_autosomal recessive inheritance) +# Class: obo:GENO_0000150 (obsolete autosomal recessive inheritance) AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000150 "duplicate term, use GENO:0000148") -AnnotationAssertion(rdfs:label obo:GENO_0000150 "obsolete_autosomal recessive inheritance") -SubClassOf(obo:GENO_0000150 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000150 "obsolete autosomal recessive inheritance"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000150 "true"^^xsd:boolean) # Class: obo:GENO_0000152 (reference) @@ -2251,11 +2260,61 @@ SubClassOf(obo:GENO_0000152 obo:GENO_0000773) AnnotationAssertion(rdfs:label obo:GENO_0000160 "unspecified life cycle stage") SubClassOf(obo:GENO_0000160 obo:UBERON_0000105) -# Class: obo:GENO_0000324 (obsolete_chromosome complement) +# Class: obo:GENO_0000164 (obsolete genetic insertion technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000164 "obsolete genetic insertion technique"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000164 "true"^^xsd:boolean) + +# Class: obo:GENO_0000165 (obsolete mutagen treatment technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000165 "obsolete mutagen treatment technique"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000165 "true"^^xsd:boolean) + +# Class: obo:GENO_0000166 (obsolete targeted gene mutation technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000166 "obsolete targeted gene mutation technique"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000166 "true"^^xsd:boolean) + +# Class: obo:GENO_0000169 (obsolete random genetic insertion technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000169 "obsolete random genetic insertion technique"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000169 "true"^^xsd:boolean) + +# Class: obo:GENO_0000170 (obsolete targeted genetic insertion technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000170 "obsolete targeted genetic insertion technique"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000170 "true"^^xsd:boolean) + +# Class: obo:GENO_0000171 (obsolete enhancer trapping technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000171 "obsolete enhancer trapping technique"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000171 "true"^^xsd:boolean) + +# Class: obo:GENO_0000172 (obsolete gene trapping technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000172 "obsolete gene trapping technique"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000172 "true"^^xsd:boolean) + +# Class: obo:GENO_0000173 (obsolete promoter trapping technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000173 "obsolete promoter trapping technique"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000173 "true"^^xsd:boolean) + +# Class: obo:GENO_0000174 (obsolete targeted knock-in technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000174 "obsolete targeted knock-in technique"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000174 "true"^^xsd:boolean) + +# Class: obo:GENO_0000175 (obsolete random transgene insertion technique) + +AnnotationAssertion(rdfs:label obo:GENO_0000175 "obsolete random transgene insertion technique"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000175 "true"^^xsd:boolean) + +# Class: obo:GENO_0000324 (obsolete chromosome complement) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000324 "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome") -AnnotationAssertion(rdfs:label obo:GENO_0000324 "obsolete_chromosome complement") -SubClassOf(obo:GENO_0000324 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000324 "obsolete chromosome complement"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000324 "true"^^xsd:boolean) # Class: obo:GENO_0000338 (gained aneusomic chromosome) @@ -2363,13 +2422,13 @@ AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000402 "trans-heterozygous") AnnotationAssertion(rdfs:label obo:GENO_0000402 "compound heterozygous") SubClassOf(obo:GENO_0000402 obo:GENO_0000135) -# Class: obo:GENO_0000415 (obsolete_reagent sequence feature) +# Class: obo:GENO_0000415 (obsolete reagent sequence feature) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000415 "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)") AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000415 "replaced with SO:engineered_region") AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000415 "extra-genomic sequence") -AnnotationAssertion(rdfs:label obo:GENO_0000415 "obsolete_reagent sequence feature") -SubClassOf(obo:GENO_0000415 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000415 "obsolete reagent sequence feature"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000415 "true"^^xsd:boolean) # Class: obo:GENO_0000458 (simple heterozygous) @@ -2424,7 +2483,7 @@ AnnotationAssertion(rdfs:comment obo:GENO_0000482 "This class is different from AnnotationAssertion(rdfs:label obo:GENO_0000482 "genetic material"@en) SubClassOf(obo:GENO_0000482 obo:CHEBI_33696) -# Class: obo:GENO_0000491 (obsolete_mutant allele) +# Class: obo:GENO_0000491 (obsolete mutant allele) AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000491 obo:GENO_0000484) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000491 "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain.") @@ -2435,8 +2494,8 @@ Eq class definition: allele and (mutation or ('has subsequence' some mutation))") AnnotationAssertion(rdfs:comment obo:GENO_0000491 "'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line.") -AnnotationAssertion(rdfs:label obo:GENO_0000491 "obsolete_mutant allele") -SubClassOf(obo:GENO_0000491 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000491 "obsolete mutant allele"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000491 "true"^^xsd:boolean) # Class: obo:GENO_0000492 (mutation) @@ -2955,15 +3014,15 @@ EquivalentClasses(obo:GENO_0000667 ObjectIntersectionOf(obo:SO_0000902 ObjectSom SubClassOf(obo:GENO_0000667 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GENO_0000640)) SubClassOf(obo:GENO_0000667 ObjectSomeValuesFrom(obo:GENO_0000207 obo:SO_0000783)) -# Class: obo:GENO_0000680 (obsolete_null feature) +# Class: obo:GENO_0000680 (obsolete null feature) AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000680 "A junction between bases, a deletion variant, a terminus at the end of a chromosome.") AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000680 "A genomic feature that has an extent of zero.") AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000680 "Former logical def: 'genomic feature' and (has_extent value 0)") -AnnotationAssertion(rdfs:label obo:GENO_0000680 "obsolete_null feature"@en) -SubClassOf(obo:GENO_0000680 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000680 "obsolete null feature"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000680 "true"^^xsd:boolean) # Class: obo:GENO_0000681 (novel extrachromosomal replicon) @@ -3084,15 +3143,15 @@ EquivalentClasses(obo:GENO_0000721 ObjectIntersectionOf(obo:GENO_0000702 ObjectS AnnotationAssertion(rdfs:label obo:GENO_0000722 "amino acid sequence"@en) EquivalentClasses(obo:GENO_0000722 ObjectIntersectionOf(obo:GENO_0000702 ObjectSomeValuesFrom(obo:GENO_0000783 obo:GENO_0000782) ObjectAllValuesFrom(obo:GENO_0000783 obo:GENO_0000782))) -# Class: obo:GENO_0000724 (obsolete_biological sequence or collection) +# Class: obo:GENO_0000724 (obsolete biological sequence or collection) -AnnotationAssertion(rdfs:label obo:GENO_0000724 "obsolete_biological sequence or collection"@en) -SubClassOf(obo:GENO_0000724 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000724 "obsolete biological sequence or collection"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000724 "true"^^xsd:boolean) -# Class: obo:GENO_0000725 (obsolete_biological sequence collection) +# Class: obo:GENO_0000725 (obsolete biological sequence collection) -AnnotationAssertion(rdfs:label obo:GENO_0000725 "obsolete_biological sequence collection"@en) -SubClassOf(obo:GENO_0000725 obo:GENO_0000724) +AnnotationAssertion(rdfs:label obo:GENO_0000725 "obsolete biological sequence collection"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000725 "true"^^xsd:boolean) # Class: obo:GENO_0000736 (location-qualified sequence feature) @@ -3108,14 +3167,14 @@ AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000737 "A sequence feature whose i AnnotationAssertion(rdfs:label obo:GENO_0000737 "expression-qualified sequence feature"@en) SubClassOf(obo:GENO_0000737 obo:GENO_0000714) -# Class: obo:GENO_0000768 (obsolete_genomic position) +# Class: obo:GENO_0000768 (obsolete genomic position) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000768 "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence.") AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000768 "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature.") AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000768 "genomic coordinates"@en) AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000768 "remodeling notion of sequence feature position around the idea of a 'genomic locus'") -AnnotationAssertion(rdfs:label obo:GENO_0000768 "obsolete_genomic position") -SubClassOf(obo:GENO_0000768 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000768 "obsolete genomic position"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000768 "true"^^xsd:boolean) # Class: obo:GENO_0000770 (phenotypic inheritance process) @@ -3123,11 +3182,11 @@ AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000770 obo:GENO_0000484) AnnotationAssertion(rdfs:label obo:GENO_0000770 "phenotypic inheritance process"@en) SubClassOf(obo:GENO_0000770 obo:GENO_0000351) -# Class: obo:GENO_0000772 (obsolete_unspecified) +# Class: obo:GENO_0000772 (obsolete unspecified) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000772 "A sequence attribute inhering in a feature whose identity is not specified.") -AnnotationAssertion(rdfs:label obo:GENO_0000772 "obsolete_unspecified"@en) -SubClassOf(obo:GENO_0000772 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000772 "obsolete unspecified"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000772 "true"^^xsd:boolean) # Class: obo:GENO_0000773 (variation attribute) @@ -3142,12 +3201,12 @@ AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000777 "An intrinsic genotype that AnnotationAssertion(rdfs:label obo:GENO_0000777 "variant genomic genotype"@en) EquivalentClasses(obo:GENO_0000777 ObjectIntersectionOf(obo:GENO_0000899 ObjectSomeValuesFrom(obo:IAO_0000219 obo:GENO_0000033))) -# Class: obo:GENO_0000778 (obsolete_sequence information entity) +# Class: obo:GENO_0000778 (obsolete sequence information entity) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000778 "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities.") AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000778 "eliminating classes that are not necessary or add uneeded complexity.") -AnnotationAssertion(rdfs:label obo:GENO_0000778 "obsolete_sequence information entity"@en) -SubClassOf(obo:GENO_0000778 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000778 "obsolete sequence information entity"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000778 "true"^^xsd:boolean) # Class: obo:GENO_0000779 (biological sequence unit) @@ -3237,14 +3296,14 @@ AnnotationAssertion(rdfs:label obo:GENO_0000839 "knockdown reagent targeted gene SubClassOf(obo:GENO_0000839 obo:GENO_0000527) SubClassOf(obo:GENO_0000839 ObjectSomeValuesFrom(obo:GENO_0000382 obo:GENO_0000504)) -# Class: obo:GENO_0000848 (obsolete_coding sequence alteration) +# Class: obo:GENO_0000848 (obsolete coding sequence alteration) AnnotationAssertion(obo:IAO_0000114 obo:GENO_0000848 obo:GENO_0000484) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000848 "A sequence alteration within the coding sequence of a gene.") AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000848 "Not required at this poitn, so marked exploratory and obsoleted. Asserted under sequence_alteration.") -AnnotationAssertion(rdfs:label obo:GENO_0000848 "obsolete_coding sequence alteration"@en) -SubClassOf(obo:GENO_0000848 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000848 "obsolete coding sequence alteration"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000848 "true"^^xsd:boolean) # Class: obo:GENO_0000850 (P-element construct) @@ -3269,12 +3328,12 @@ AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000861 "non-integrated transgene") AnnotationAssertion(rdfs:label obo:GENO_0000861 "extra-chromosomal transgene"@en) SubClassOf(obo:GENO_0000861 obo:SO_0000902) -# Class: obo:GENO_0000870 (obsolete_sequence feature collection) +# Class: obo:GENO_0000870 (obsolete sequence feature collection) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000870 "A collection of more than one sequence feature.") AnnotationAssertion(oboInOwl:hasDbXref obo:GENO_0000870 "http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection") -AnnotationAssertion(rdfs:label obo:GENO_0000870 "obsolete_sequence feature collection"@en) -SubClassOf(obo:GENO_0000870 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000870 "obsolete sequence feature collection"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000870 "true"^^xsd:boolean) # Class: obo:GENO_0000871 (haplotype) @@ -3324,7 +3383,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000875 "A quality inhering in an ' AnnotationAssertion(rdfs:label obo:GENO_0000875 "allelic state"@en) SubClassOf(obo:GENO_0000875 obo:GENO_0000788) -# Class: obo:GENO_0000876 (obsolete_genetic dosage) +# Class: obo:GENO_0000876 (obsolete genetic dosage) AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000876 "allelic dosage") AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000876 "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome.") @@ -3333,8 +3392,8 @@ AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000876 "Remodeled this concept as AnnotationAssertion(rdfs:comment obo:GENO_0000876 "Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found.") -AnnotationAssertion(rdfs:label obo:GENO_0000876 "obsolete_genetic dosage"@en) -SubClassOf(obo:GENO_0000876 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000876 "obsolete genetic dosage"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000876 "true"^^xsd:boolean) # Class: obo:GENO_0000877 (allele origin) @@ -3385,13 +3444,13 @@ These acquired mutations are called 'somatic' because they typically affect som AnnotationAssertion(rdfs:label obo:GENO_0000882 "somatic allele origin"@en) SubClassOf(obo:GENO_0000882 obo:GENO_0000877) -# Class: obo:GENO_0000883 (obsolete_gametic) +# Class: obo:GENO_0000883 (obsolete gametic) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000883 "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells).") AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000883 "germ-line") AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000883 "replaced by GENO:0000900 ! 'germline'") -AnnotationAssertion(rdfs:label obo:GENO_0000883 "obsolete_gametic"@en) -SubClassOf(obo:GENO_0000883 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000883 "obsolete gametic"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000883 "true"^^xsd:boolean) # Class: obo:GENO_0000885 (diplotype) @@ -3435,7 +3494,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000889 "unknown inheritance") AnnotationAssertion(rdfs:label obo:GENO_0000889 "undetermined inheritance") SubClassOf(obo:GENO_0000889 obo:GENO_0000141) -# Class: obo:GENO_0000890 (obsolete_canonical allele) +# Class: obo:GENO_0000890 (obsolete canonical allele) AnnotationAssertion(obo:IAO_0000112 obo:GENO_0000890 "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”.") AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000890 "One of a set of sequence features or haplotypes that exist at a particular genetic locus. ") @@ -3446,10 +3505,10 @@ AnnotationAssertion(dcterms:source obo:GENO_0000890 "ClinGen Allele Model (http: AnnotationAssertion(rdfs:comment obo:GENO_0000890 "As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references)") -AnnotationAssertion(rdfs:label obo:GENO_0000890 "obsolete_canonical allele") -SubClassOf(obo:GENO_0000890 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000890 "obsolete canonical allele"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000890 "true"^^xsd:boolean) -# Class: obo:GENO_0000891 (obsolete_contextual allele) +# Class: obo:GENO_0000891 (obsolete contextual allele) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000891 "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence.") AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000891 "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model.") @@ -3459,8 +3518,8 @@ AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000891 "No longer needed by ClinG Former axiom: denotes some 'obsolete_canonical allele'") AnnotationAssertion(dcterms:source obo:GENO_0000891 "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)") AnnotationAssertion(rdfs:comment obo:GENO_0000891 "The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene.") -AnnotationAssertion(rdfs:label obo:GENO_0000891 "obsolete_contextual allele") -SubClassOf(obo:GENO_0000891 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000891 "obsolete contextual allele"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000891 "true"^^xsd:boolean) # Class: obo:GENO_0000892 (heteroplasmic mitochondrial inheritance) @@ -3509,13 +3568,13 @@ AnnotationAssertion(rdfs:label obo:GENO_0000899 "genomic genotype"@en) EquivalentClasses(obo:GENO_0000899 ObjectIntersectionOf(obo:GENO_0000719 ObjectSomeValuesFrom(obo:IAO_0000219 obo:SO_0001026))) SubClassOf(obo:GENO_0000899 ObjectSomeValuesFrom(obo:GENO_0000385 obo:GENO_0000611)) -# Class: obo:GENO_0000901 (obsolete_allele cellular context) +# Class: obo:GENO_0000901 (obsolete allele cellular context) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000901 "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)") AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000901 "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin") AnnotationAssertion(rdfs:comment obo:GENO_0000901 "Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others.") -AnnotationAssertion(rdfs:label obo:GENO_0000901 "obsolete_allele cellular context") -SubClassOf(obo:GENO_0000901 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000901 "obsolete allele cellular context"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000901 "true"^^xsd:boolean) # Class: obo:GENO_0000902 (genomic feature location) @@ -3555,11 +3614,13 @@ SubClassOf(obo:GENO_0000907 obo:SO_0000110) # Class: obo:GENO_0000910 (reporter) +AnnotationAssertion(rdfs:label obo:GENO_0000910 "obsolete reporter role"@en) AnnotationAssertion(rdfs:label obo:GENO_0000910 "reporter"@en) SubClassOf(obo:GENO_0000910 obo:GENO_0000788) # Class: obo:GENO_0000911 (selectable marker) +AnnotationAssertion(rdfs:label obo:GENO_0000911 "obsolete selectable marker role"@en) AnnotationAssertion(rdfs:label obo:GENO_0000911 "selectable marker"@en) SubClassOf(obo:GENO_0000911 obo:GENO_0000788) @@ -3575,7 +3636,7 @@ AnnotationAssertion(rdfs:label obo:GENO_0000914 "reference genome"@en) SubClassOf(obo:GENO_0000914 obo:SO_0001026) SubClassOf(obo:GENO_0000914 ObjectSomeValuesFrom(obo:GENO_0000239 obo:SO_0001505)) -# Class: obo:GENO_0000915 (obsolete_haplotype) +# Class: obo:GENO_0000915 (obsolete haplotype) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000915 "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it.") AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000915 "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"") @@ -3598,10 +3659,10 @@ b. The second is a region containing multiple linked single nucleotide polymorph c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations.") -AnnotationAssertion(rdfs:label obo:GENO_0000915 "obsolete_haplotype"@en) -SubClassOf(obo:GENO_0000915 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000915 "obsolete haplotype"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000915 "true"^^xsd:boolean) -# Class: obo:GENO_0000916 (obsolete_haplotype block) +# Class: obo:GENO_0000916 (obsolete haplotype block) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000916 "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations.") AnnotationAssertion(obo:IAO_0000119 obo:GENO_0000916 "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block.") @@ -3613,8 +3674,8 @@ The boundaries of haplotype blocks are defined in efforts to identify haplotypes ----------------------- * One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces.") -AnnotationAssertion(rdfs:label obo:GENO_0000916 "obsolete_haplotype block"@en) -SubClassOf(obo:GENO_0000916 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000916 "obsolete haplotype block"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000916 "true"^^xsd:boolean) # Class: obo:GENO_0000918 (organellar plasmy) @@ -3660,7 +3721,7 @@ A set may also include multiple copies of the same sequence. For example, in a ' AnnotationAssertion(rdfs:label obo:GENO_0000922 "biological sequence set"@en) SubClassOf(obo:GENO_0000922 obo:GENO_0000921) -# Class: obo:GENO_0000923 (obsolete_functional copy number complement) +# Class: obo:GENO_0000923 (obsolete functional copy number complement) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000923 "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome.") AnnotationAssertion(obo:IAO_0000116 obo:GENO_0000923 "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"") @@ -3669,20 +3730,20 @@ AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000923 "genetic dosage"@en) AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000923 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963.") AnnotationAssertion(rdfs:comment obo:GENO_0000923 "As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage).") AnnotationAssertion(rdfs:comment obo:GENO_0000923 "The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage.") -AnnotationAssertion(rdfs:label obo:GENO_0000923 "obsolete_functional copy number complement") -SubClassOf(obo:GENO_0000923 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000923 "obsolete functional copy number complement"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000923 "true"^^xsd:boolean) -# Class: obo:GENO_0000924 (obsolete_intrinsic sequence feature attribute) +# Class: obo:GENO_0000924 (obsolete intrinsic sequence feature attribute) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000924 "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form.") -AnnotationAssertion(rdfs:label obo:GENO_0000924 "obsolete_intrinsic sequence feature attribute"@en) -SubClassOf(obo:GENO_0000924 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000924 "obsolete intrinsic sequence feature attribute"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000924 "true"^^xsd:boolean) -# Class: obo:GENO_0000925 (obsolete_extrinsic sequence feature attribute) +# Class: obo:GENO_0000925 (obsolete extrinsic sequence feature attribute) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000925 "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)") -AnnotationAssertion(rdfs:label obo:GENO_0000925 "obsolete_extrinsic sequence feature attribute"@en) -SubClassOf(obo:GENO_0000925 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000925 "obsolete extrinsic sequence feature attribute"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000925 "true"^^xsd:boolean) # Class: obo:GENO_0000926 (allelic cellular distribution) @@ -3865,7 +3926,7 @@ AnnotationAssertion(rdfs:comment obo:GENO_0000954 "'Sets' are used to model enti AnnotationAssertion(rdfs:label obo:GENO_0000954 "allele set"@en) SubClassOf(obo:GENO_0000954 obo:GENO_0000660) -# Class: obo:GENO_0000955 (obsolete_variant copy number complement) +# Class: obo:GENO_0000955 (obsolete variant copy number complement) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000955 "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s).") AnnotationAssertion(obo:IAO_0000118 obo:GENO_0000955 "copy number variation"@en) @@ -3873,10 +3934,10 @@ AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000955 "Decided to implement copy AnnotationAssertion(rdfs:comment obo:GENO_0000955 "In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class.") -AnnotationAssertion(rdfs:label obo:GENO_0000955 "obsolete_variant copy number complement") -SubClassOf(obo:GENO_0000955 obo:GENO_0000956) +AnnotationAssertion(rdfs:label obo:GENO_0000955 "obsolete variant copy number complement"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000955 "true"^^xsd:boolean) -# Class: obo:GENO_0000956 (obsolete_copy number complement) +# Class: obo:GENO_0000956 (obsolete copy number complement) AnnotationAssertion(obo:IAO_0000115 obo:GENO_0000956 "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger.") AnnotationAssertion(obo:IAO_0000231 obo:GENO_0000956 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961.") @@ -3885,8 +3946,8 @@ AnnotationAssertion(rdfs:comment obo:GENO_0000956 "1. Features described by 'cop 2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. 3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members.") -AnnotationAssertion(rdfs:label obo:GENO_0000956 "obsolete_copy number complement"@en) -SubClassOf(obo:GENO_0000956 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:GENO_0000956 "obsolete copy number complement"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:GENO_0000956 "true"^^xsd:boolean) # Class: obo:GENO_0000960 (genomic sequence) @@ -4069,13 +4130,13 @@ AnnotationAssertion(obo:IAO_0000116 obo:OBI_0100026 "Stub class to serve as root AnnotationAssertion(rdfs:label obo:OBI_0100026 "organism") SubClassOf(obo:OBI_0100026 obo:BFO_0000040) -# Class: obo:PATO_0000016 (obsolete_color brightness) +# Class: obo:PATO_0000016 (obsolete color brightness) AnnotationAssertion(obo:IAO_0000116 obo:PATO_0000016 "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html") AnnotationAssertion(obo:IAO_0000116 obo:PATO_0000016 "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute.") AnnotationAssertion(obo:IAO_0000118 obo:PATO_0000016 "color value") -AnnotationAssertion(rdfs:label obo:PATO_0000016 "obsolete_color brightness"@en) -SubClassOf(obo:PATO_0000016 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:PATO_0000016 "obsolete color brightness"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:PATO_0000016 "true"^^xsd:boolean) # Class: obo:PATO_0000383 (female) @@ -4139,17 +4200,17 @@ SubClassOf(obo:SO_0000110 obo:GENO_0000701) SubClassOf(Annotation(obo:GENO_0000834 "true"^^xsd:boolean) Annotation(rdfs:comment "Formalizes the first identity criteria for a sequence feature of its sequence.") obo:SO_0000110 ObjectSomeValuesFrom(obo:GENO_0000239 obo:GENO_0000702)) SubClassOf(Annotation(obo:GENO_0000834 "true"^^xsd:boolean) Annotation(rdfs:comment "Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property).") obo:SO_0000110 ObjectSomeValuesFrom(obo:GENO_0000903 obo:GENO_0000815)) -# Class: obo:SO_0000143 (obsolete_assembly_component) +# Class: obo:SO_0000143 (obsolete assembly_component) AnnotationAssertion(obo:IAO_0000115 obo:SO_0000143 "A region of known length which may be used to manufacture a longer region.") -AnnotationAssertion(rdfs:label obo:SO_0000143 "obsolete_assembly_component"@en) -SubClassOf(obo:SO_0000143 obo:SO_0001410) +AnnotationAssertion(rdfs:label obo:SO_0000143 "obsolete assembly_component"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:SO_0000143 "true"^^xsd:boolean) -# Class: obo:SO_0000149 (obsolete_contig) +# Class: obo:SO_0000149 (obsolete contig) AnnotationAssertion(obo:IAO_0000115 obo:SO_0000149 "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.") -AnnotationAssertion(rdfs:label obo:SO_0000149 "obsolete_contig"@en) -SubClassOf(obo:SO_0000149 obo:SO_0000143) +AnnotationAssertion(rdfs:label obo:SO_0000149 "obsolete contig"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:SO_0000149 "true"^^xsd:boolean) # Class: obo:SO_0000159 (deletion) @@ -4256,11 +4317,11 @@ SubClassOf(obo:SO_0000341 ObjectSomeValuesFrom(obo:GENO_0000207 obo:GENO_0000618 AnnotationAssertion(rdfs:label obo:SO_0000577 "centromere"@en) SubClassOf(obo:SO_0000577 obo:SO_0000830) -# Class: obo:SO_0000637 (obsolete_engineered_plasmid) +# Class: obo:SO_0000637 (obsolete engineered_plasmid) AnnotationAssertion(obo:IAO_0000116 obo:SO_0000637 "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct.") -AnnotationAssertion(rdfs:label obo:SO_0000637 "obsolete_engineered_plasmid"@en) -SubClassOf(obo:SO_0000637 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:SO_0000637 "obsolete engineered_plasmid"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:SO_0000637 "true"^^xsd:boolean) # Class: obo:SO_0000667 (insertion) @@ -4414,12 +4475,12 @@ AnnotationAssertion(rdfs:label obo:SO_0001218 "transgenic_insertion"^^xsd:string SubClassOf(obo:SO_0001218 obo:SO_0000667) SubClassOf(obo:SO_0001218 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GENO_0000093)) -# Class: obo:SO_0001410 (obsolete_experimental_feature) +# Class: obo:SO_0001410 (obsolete experimental_feature) AnnotationAssertion(obo:IAO_0000115 obo:SO_0001410 "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.") AnnotationAssertion(obo:IAO_0000231 obo:SO_0001410 "not currently needed to support modeling use cases. can re-introduce if becomes necessary.") -AnnotationAssertion(rdfs:label obo:SO_0001410 "obsolete_experimental_feature"@en) -SubClassOf(obo:SO_0001410 oboInOwl:ObsoleteClass) +AnnotationAssertion(rdfs:label obo:SO_0001410 "obsolete experimental_feature"^^xsd:string) +AnnotationAssertion(owl:deprecated obo:SO_0001410 "true"^^xsd:boolean) # Class: obo:SO_0001477 (gene_trap_construct) From 0c4220e348f4b2f2996c9fa6e3e09e01bf7c3849 Mon Sep 17 00:00:00 2001 From: matentzn Date: Sun, 8 Mar 2020 23:49:37 +0000 Subject: [PATCH 11/11] New release --- geno-base.json | 639 ++++++++++-------- geno-base.obo | 208 +++--- geno-base.owl | 252 ++++--- geno-full.json | 587 +++++++++------- geno-full.obo | 208 +++--- geno-full.owl | 252 ++++--- geno.json | 539 ++++++++------- geno.obo | 208 +++--- geno.owl | 252 ++++--- reports/geno-edit.owl-obo-report.tsv | 56 +- .../reports/geno-edit.owl-obo-report.tsv | 56 +- 11 files changed, 1910 insertions(+), 1347 deletions(-) diff --git a/geno-base.json b/geno-base.json index 14b0532..3615d9b 100644 --- a/geno-base.json +++ b/geno-base.json @@ -60,13 +60,16 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "reference gene" } ] }, "type" : "CLASS", - "lbl" : "obsolete_reference gene allele" + "lbl" : "obsolete reference gene allele" }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_10090", "type" : "CLASS", @@ -165,6 +168,36 @@ }, "type" : "CLASS", "lbl" : "SNV" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000173", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete promoter trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000172", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete gene trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000175", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete random transgene insertion technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000054", "meta" : { @@ -179,6 +212,9 @@ "id" : "http://purl.obolibrary.org/obo/PATO_0000016", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." }, { @@ -190,7 +226,17 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_color brightness" + "lbl" : "obsolete color brightness" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000174", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete targeted knock-in technique" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002162", "meta" : { @@ -201,6 +247,26 @@ }, "type" : "PROPERTY", "lbl" : "in taxon" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000171", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete enhancer trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000170", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete targeted genetic insertion technique" }, { "id" : "http://www.ncbi.nlm.nih.gov/gene/6469", "meta" : { @@ -214,6 +280,36 @@ }, "type" : "CLASS", "lbl" : "homo sapiens SHH gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000169", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete random genetic insertion technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000166", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete targeted gene mutation technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000165", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete mutagen treatment technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000047", "meta" : { @@ -266,10 +362,14 @@ "definition" : { "val" : "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_contig" + "lbl" : "obsolete contig" }, { "id" : "http://purl.obolibrary.org/obo/SO_0001479", "meta" : { @@ -486,8 +586,14 @@ "lbl" : "gene trap insertion" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000091", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, "type" : "CLASS", - "lbl" : "obsolete_experimental insertion" + "lbl" : "obsolete experimental insertion" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000093", "meta" : { @@ -883,13 +989,16 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype." } ] }, "type" : "CLASS", - "lbl" : "obsolete_haplotype" + "lbl" : "obsolete haplotype" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000914", "meta" : { @@ -937,6 +1046,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.\n\nThe boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.\n\n-----------------------\n\n* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces." @@ -946,7 +1058,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_haplotype block" + "lbl" : "obsolete haplotype block" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000911", "type" : "CLASS", @@ -1094,6 +1206,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others." }, { @@ -1102,7 +1217,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_allele cellular context" + "lbl" : "obsolete allele cellular context" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002525", "type" : "PROPERTY", @@ -1411,10 +1526,14 @@ "definition" : { "val" : "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_extrinsic sequence feature attribute" + "lbl" : "obsolete extrinsic sequence feature attribute" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000928", "meta" : { @@ -1469,10 +1588,14 @@ "definition" : { "val" : "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form.", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_intrinsic sequence feature attribute" + "lbl" : "obsolete intrinsic sequence feature attribute" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000923", "meta" : { @@ -1495,13 +1618,16 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage)." } ] }, "type" : "CLASS", - "lbl" : "obsolete_functional copy number complement" + "lbl" : "obsolete functional copy number complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000953", "meta" : { @@ -1626,10 +1752,13 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_variant copy number complement" + "lbl" : "obsolete variant copy number complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000713", "meta" : { @@ -1712,13 +1841,16 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members." } ] }, "type" : "CLASS", - "lbl" : "obsolete_copy number complement" + "lbl" : "obsolete copy number complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000714", "meta" : { @@ -2633,13 +2765,16 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/GENO_0000484" } ] }, "type" : "CLASS", - "lbl" : "obsolete_coding sequence alteration" + "lbl" : "obsolete coding sequence alteration" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000606", "type" : "CLASS", @@ -2723,8 +2858,14 @@ "lbl" : "has_interval" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000724", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, "type" : "CLASS", - "lbl" : "obsolete_biological sequence or collection" + "lbl" : "obsolete biological sequence or collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000965", "meta" : { @@ -2853,6 +2994,16 @@ }, "type" : "PROPERTY", "lbl" : "has_qualifying_process" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000725", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete biological sequence collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000967", "meta" : { @@ -2863,10 +3014,6 @@ }, "type" : "PROPERTY", "lbl" : "has_reference_sequence" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000725", - "type" : "CLASS", - "lbl" : "obsolete_biological sequence collection" }, { "id" : "http://purl.obolibrary.org/obo/SO_1000036", "meta" : { @@ -2974,24 +3121,13 @@ }, "type" : "CLASS", "lbl" : "microsatellite alteration" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000634", - "meta" : { - "definition" : { - "val" : "relation between an molecular agent and its molecular target", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant." - } ] - }, - "type" : "PROPERTY", - "lbl" : "is_targeted_by" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000876", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "allelic dosage" }, { @@ -3009,7 +3145,21 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_genetic dosage" + "lbl" : "obsolete genetic dosage" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000634", + "meta" : { + "definition" : { + "val" : "relation between an molecular agent and its molecular target", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is_targeted_by" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000513", "meta" : { @@ -3067,10 +3217,14 @@ }, "xrefs" : [ { "val" : "http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence feature collection" + "lbl" : "obsolete sequence feature collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000872", "meta" : { @@ -3852,6 +4006,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." @@ -3864,7 +4021,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_contextual allele" + "lbl" : "obsolete contextual allele" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000894", "meta" : { @@ -3933,6 +4090,20 @@ "id" : "http://purl.obolibrary.org/obo/ZP_0005692", "type" : "CLASS", "lbl" : "abnormal(ly) absent adaxial cell" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000772", + "meta" : { + "definition" : { + "val" : "A sequence attribute inhering in a feature whose identity is not specified.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete unspecified" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000651", "meta" : { @@ -3943,26 +4114,19 @@ }, "type" : "PROPERTY", "lbl" : "is_mutant_allele_of" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000772", - "meta" : { - "definition" : { - "val" : "A sequence attribute inhering in a feature whose identity is not specified.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "obsolete_unspecified" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000637", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." } ] }, "type" : "CLASS", - "lbl" : "obsolete_engineered_plasmid" + "lbl" : "obsolete engineered_plasmid" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000779", "meta" : { @@ -3977,42 +4141,45 @@ "type" : "CLASS", "lbl" : "biological sequence unit" }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000536", + "id" : "http://purl.obolibrary.org/obo/GENO_0000415", "meta" : { "definition" : { - "val" : "A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference.", + "val" : "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)", "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "1. Scope of 'Genetic State': \n'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs.\n\n2. Genotype Subtypes:\nIn GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. \n\nTwo more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features.\n\n3. The Genotype Partonomy: \n'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype \"fgf8a; fgf3[AB]\", described at zfin.org/ZDB-FISH-150901-9362, include the following elements:\n\n - GVC: fgf8a; fgf3 (total intrinsic variation in the genome)\n - Genomic Background: AB (the reference against which the GVC is variant)\n - VSLC1: fgf8a (homozygous complement of gene alleles at one known variant locus)\n - VSLC2: fgf3 (heterozygous complement of gene alleles at another known variant locus)\n - Allele 1: fgf8a (variant version of the fgf8a gene, present in two copies)\n - Allele 2: fgf3 (variant version of the fgf3 gene, present in one copy)\n - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy)\n - Sequence Alteration1: (the specific mutation within the fgf8a gene that makes it variant)\n - Sequence Alteration2: (the specific mutation within the fgf3 gene that makes it variant)\n\nA graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md\n\nOne reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to \"propagate phenotypes\" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "replaced with SO:engineered_region" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). \nNote however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "extra-genomic sequence" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above." + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "genotype" + "lbl" : "obsolete reagent sequence feature" }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000415", + "id" : "http://purl.obolibrary.org/obo/GENO_0000536", "meta" : { "definition" : { - "val" : "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)", + "val" : "A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference.", "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "replaced with SO:engineered_region" + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "1. Scope of 'Genetic State': \n'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs.\n\n2. Genotype Subtypes:\nIn GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. \n\nTwo more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features.\n\n3. The Genotype Partonomy: \n'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype \"fgf8a; fgf3[AB]\", described at zfin.org/ZDB-FISH-150901-9362, include the following elements:\n\n - GVC: fgf8a; fgf3 (total intrinsic variation in the genome)\n - Genomic Background: AB (the reference against which the GVC is variant)\n - VSLC1: fgf8a (homozygous complement of gene alleles at one known variant locus)\n - VSLC2: fgf3 (heterozygous complement of gene alleles at another known variant locus)\n - Allele 1: fgf8a (variant version of the fgf8a gene, present in two copies)\n - Allele 2: fgf3 (variant version of the fgf3 gene, present in one copy)\n - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy)\n - Sequence Alteration1: (the specific mutation within the fgf8a gene that makes it variant)\n - Sequence Alteration2: (the specific mutation within the fgf3 gene that makes it variant)\n\nA graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md\n\nOne reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to \"propagate phenotypes\" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "extra-genomic sequence" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). \nNote however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above." } ] }, "type" : "CLASS", - "lbl" : "obsolete_reagent sequence feature" + "lbl" : "genotype" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000778", "meta" : { @@ -4023,10 +4190,13 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "eliminating classes that are not necessary or add uneeded complexity." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence information entity" + "lbl" : "obsolete sequence information entity" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000899", "meta" : { @@ -4110,13 +4280,16 @@ }, { "pred" : "http://purl.org/dc/terms/source", "val" : "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs." } ] }, "type" : "CLASS", - "lbl" : "obsolete_canonical allele" + "lbl" : "obsolete canonical allele" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000885", "meta" : { @@ -4288,10 +4461,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "germ-line" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_gametic" + "lbl" : "obsolete gametic" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000882", "meta" : { @@ -4431,10 +4607,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "remodeling notion of sequence feature position around the idea of a 'genomic locus'" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_genomic position" + "lbl" : "obsolete genomic position" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000647", "meta" : { @@ -4599,6 +4778,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Former logical def: \n'genomic feature'\n and (has_extent value 0)" }, { @@ -4607,7 +4789,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_null feature" + "lbl" : "obsolete null feature" }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", "type" : "CLASS", @@ -4987,10 +5169,6 @@ }, "type" : "PROPERTY", "lbl" : "has_sequence_unit" - }, { - "id" : "http://biohackathon.org/resource/faldo#location", - "type" : "PROPERTY", - "lbl" : "location" }, { "id" : "http://purl.obolibrary.org/obo/SO_0001410", "meta" : { @@ -4999,12 +5177,19 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "not currently needed to support modeling use cases. can re-introduce if becomes necessary." } ] }, "type" : "CLASS", - "lbl" : "obsolete_experimental_feature" + "lbl" : "obsolete experimental_feature" + }, { + "id" : "http://biohackathon.org/resource/faldo#location", + "type" : "PROPERTY", + "lbl" : "location" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000580", "meta" : { @@ -5154,10 +5339,14 @@ "definition" : { "val" : "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_chromosome complement" + "lbl" : "obsolete chromosome complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000447", "meta" : { @@ -6072,12 +6261,15 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." } ] }, "type" : "CLASS", - "lbl" : "obsolete_dominant inheritance" + "lbl" : "obsolete dominant inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000141", "meta" : { @@ -6305,10 +6497,13 @@ "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence feature collection" + "lbl" : "obsolete sequence feature collection" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000110", "meta" : { @@ -6362,10 +6557,10 @@ "val" : "a chair" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a molecule" + "val" : "an organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an organism" + "val" : "a molecule" } ] }, "type" : "CLASS", @@ -6388,6 +6583,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Not required for any specific use case at this point so removed for simplicity. \nFormely asserted as allele and inferred as varaint allele. \nEq class definition:\nallele\n and (mutation or ('has subsequence' some mutation))" }, { @@ -6402,7 +6600,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_mutant allele" + "lbl" : "obsolete mutant allele" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000010", "meta" : { @@ -6497,10 +6695,14 @@ "definition" : { "val" : "sequence attribute that can inhere only in a collection of more than one sequence features", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence feature collection attribute" + "lbl" : "obsolete sequence feature collection attribute" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000488", "meta" : { @@ -6779,10 +6981,24 @@ "definition" : { "val" : "A region of known length which may be used to manufacture a longer region.", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_assembly_component" + "lbl" : "obsolete assembly_component" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000164", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete genetic insertion technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000042", "meta" : { @@ -6791,6 +7007,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" }, { @@ -6802,7 +7021,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_reference junction" + "lbl" : "obsolete reference junction" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000160", "type" : "CLASS", @@ -6817,6 +7036,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class def: 'genomic feature'\n and (has_sequence_attribute some unspecified)" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/GENO_0000484" @@ -6829,7 +7051,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_unspecified feature" + "lbl" : "obsolete unspecified feature" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000033", "meta" : { @@ -6922,12 +7144,15 @@ "id" : "http://purl.obolibrary.org/obo/GENO_0000150", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "duplicate term, use GENO:0000148" } ] }, "type" : "CLASS", - "lbl" : "obsolete_autosomal recessive inheritance" + "lbl" : "obsolete autosomal recessive inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000394", "type" : "CLASS", @@ -6985,6 +7210,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "reference allelic complement" }, { @@ -6996,7 +7224,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_reference single locus complement" + "lbl" : "obsolete reference single locus complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000149", "meta" : { @@ -7040,10 +7268,13 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_genomic feature collection" + "lbl" : "obsolete genomic feature collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000143", "meta" : { @@ -7282,10 +7513,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000145", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000147" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000890", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000930", "pred" : "is_a", @@ -7306,10 +7533,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000010" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000016", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_8090", "pred" : "is_a", @@ -7362,10 +7585,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0003303", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003302" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000125", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001785", "pred" : "is_a", @@ -7374,14 +7593,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000231", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000818", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000577", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000830" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000818", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000492", "pred" : "http://purl.obolibrary.org/obo/GENO_0000683", @@ -7510,10 +7729,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000391", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000876", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000619", "pred" : "is_a", @@ -7526,10 +7741,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000902", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000815" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000778", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000014", "pred" : "http://purl.obolibrary.org/obo/GENO_0000408", @@ -7578,10 +7789,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000339", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000346" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000142", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000118", "pred" : "is_a", @@ -7678,10 +7885,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000501", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000512" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000680", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000146", "pred" : "is_a", @@ -7786,10 +7989,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000956", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000659", "pred" : "is_a", @@ -7818,10 +8017,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000022", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://biohackathon.org/resource/faldo#begin", "pred" : "subPropertyOf", @@ -7854,10 +8049,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000486", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000925", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000714", "pred" : "is_a", @@ -7934,14 +8125,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000846", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000580" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000781", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000779" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001742", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001019" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000781", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000779" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000338", "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", @@ -7966,10 +8157,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000910", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000916", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000525", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -7998,10 +8185,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000411", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0000143", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0001410" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000629", "pred" : "is_a", @@ -8014,10 +8197,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000392", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000324", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/MP_0000001", "pred" : "is_a", @@ -8074,14 +8253,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000840", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003303" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000482", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CHEBI_33696" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000963", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000872" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000482", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CHEBI_33696" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000904", "pred" : "is_a", @@ -8090,14 +8269,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000502", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000704" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000893", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000949" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000939", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000146" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000893", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000949" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000337", "pred" : "is_a", @@ -8158,10 +8337,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000147", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000934" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000150", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/ZP_0000755", "pred" : "is_a", @@ -8174,10 +8349,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000965", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000725", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000724" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000660", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -8214,10 +8385,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000948", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000935" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000768", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000501", "pred" : "http://purl.obolibrary.org/obo/GENO_0000683", @@ -8290,10 +8457,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000027", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000724", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://www.ncbi.nlm.nih.gov/gene/399483", "pred" : "is_a", @@ -8314,18 +8477,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000625", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000619" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000848", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000032", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000955", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000956" }, { "sub" : "http://purl.obolibrary.org/obo/PCO_0000020", "pred" : "is_a", @@ -8334,10 +8489,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000242", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0000637", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000248", "pred" : "is_a", @@ -8370,10 +8521,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000138", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000016" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000029", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000515", "pred" : "http://purl.obolibrary.org/obo/GENO_0000382", @@ -8394,22 +8541,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000684", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000924", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/ENVO_01000254", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000915", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000870", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000009", "pred" : "is_a", @@ -8418,10 +8553,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000093", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000902" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000772", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/HsapDv_0000000", "pred" : "is_a", @@ -8458,10 +8589,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000014", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000009" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000091", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000621", "pred" : "is_a", @@ -8470,14 +8597,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000850", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000856" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000529", - "pred" : "http://purl.obolibrary.org/obo/GENO_0000443", - "obj" : "http://purl.obolibrary.org/obo/SO_0000704" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000715", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000529", + "pred" : "http://purl.obolibrary.org/obo/GENO_0000443", + "obj" : "http://purl.obolibrary.org/obo/SO_0000704" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000920", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -8510,10 +8637,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000022", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000018" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000883", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000252", "pred" : "inverseOf", @@ -8590,10 +8713,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000911", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000060", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000949", "pred" : "is_a", @@ -8694,10 +8813,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000878", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000888" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000042", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002526", "pred" : "subPropertyOf", @@ -8710,10 +8825,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_0005836", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000666" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000491", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000715", "pred" : "is_a", @@ -8758,14 +8869,14 @@ "sub" : "http://purl.obolibrary.org/obo/SO_0000704", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000481" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000160", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000105" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000736", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000160", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000105" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000702", "pred" : "is_a", @@ -8798,10 +8909,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000026", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000923", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000108", "pred" : "is_a", @@ -8830,10 +8937,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000112", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000113" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000891", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000394", "pred" : "is_a", @@ -8902,10 +9005,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000231", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000248" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000901", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000685", "pred" : "is_a", @@ -8966,10 +9065,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_0000341", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GENO_0000614" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000037", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://biohackathon.org/resource/faldo#reference", "pred" : "subPropertyOf", @@ -8994,10 +9089,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000719", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000536" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0000149", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0000143" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000368", "pred" : "subPropertyOf", @@ -9042,14 +9133,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000359", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000000", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000343", "pred" : "http://purl.obolibrary.org/obo/GENO_0000248", "obj" : "http://purl.obolibrary.org/obo/SO_0000340" + }, { + "sub" : "http://purl.obolibrary.org/obo/PCO_0000000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000616", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -9098,10 +9189,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002234", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002353" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000019", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000341", "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", @@ -9210,14 +9297,14 @@ "sub" : "http://purl.obolibrary.org/obo/SO_0000341", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000830" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000737", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000338", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000346" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000737", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000897", "pred" : "is_a", @@ -9242,10 +9329,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000649", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000611" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000415", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000086", "pred" : "subPropertyOf", @@ -9318,10 +9401,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000219", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/IAO_0000136" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0001410", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000253", "pred" : "subPropertyOf", @@ -9396,7 +9475,7 @@ "pred" : "http://purl.org/dc/terms/license", "val" : "Unspecified" } ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2020-03-07/geno-base.json" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2020-03-08/geno-base.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { @@ -9577,13 +9656,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" - }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000368", diff --git a/geno-base.obo b/geno-base.obo index cbe9fbe..6c24ed2 100644 --- a/geno-base.obo +++ b/geno-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: geno/releases/2020-03-07/geno-base.owl +data-version: geno/releases/2020-03-08/geno-base.owl ontology: geno/geno-base property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string @@ -290,29 +290,29 @@ property_value: IAO:0000118 "reference sequence" xsd:string [Term] id: GENO:0000019 -name: obsolete_sequence feature collection +name: obsolete sequence feature collection def: "a collection more than one sequence features (ie a collection of discontinuous sequence features)" [] comment: 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. xref: perhaps not same as SO:sequence collection\, as here we explicitly include features that can have an extent of zero (and SO\:sequence collection is a collection of regions that have an extent of at least one) -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000022 -name: obsolete_genomic feature collection +name: obsolete genomic feature collection def: "A sequence feature collection comprised of discontiguous sequences from a single genome" [] comment: Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. -is_a: ObsoleteClass property_value: IAO:0000116 "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system." xsd:string property_value: IAO:0000118 "genomic feature collection" xsd:string +is_obsolete: true [Term] id: GENO:0000029 -name: obsolete_reference single locus complement +name: obsolete reference single locus complement def: "A single locus complement that serves as a standard against which 'variant' sequences are compared" [] -is_a: ObsoleteClass property_value: IAO:0000118 "reference allelic complement" xsd:string property_value: IAO:0000118 "reference single locus feature complement" xsd:string property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'single locus complement'\n and (has_sequence_attribute some reference)\n\nSC axioms:\n'has member' exactly 0 'variant allele'\n'has member' only 'reference genomic feature'\n'has member' some 'reference genomic feature'" xsd:string +is_obsolete: true [Term] id: GENO:0000030 @@ -342,22 +342,22 @@ intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference [Term] id: GENO:0000037 -name: obsolete_unspecified feature +name: obsolete unspecified feature def: "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus)." [] comment: An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). -is_a: ObsoleteClass property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000116 "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '." xsd:string property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class def: 'genomic feature'\n and (has_sequence_attribute some unspecified)" xsd:string +is_obsolete: true [Term] id: GENO:0000042 -name: obsolete_reference junction +name: obsolete reference junction def: "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature." [] comment: In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction.\n\nThe junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. -is_a: ObsoleteClass property_value: IAO:0000118 "hemizygous reference junction" xsd:string property_value: IAO:0000231 "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" xsd:string +is_obsolete: true [Term] id: GENO:0000047 @@ -382,18 +382,18 @@ intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus [Term] id: GENO:0000060 -name: obsolete_reference gene allele +name: obsolete reference gene allele def: "A version/allele of a gene that serves as a standard against which variant genes are compared." [] comment: Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. -is_a: ObsoleteClass property_value: IAO:0000112 "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development.\nhttp://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690\n\nNote that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469" xsd:string property_value: IAO:0000118 "reference gene" xsd:string property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" xsd:string +is_obsolete: true [Term] id: GENO:0000091 -name: obsolete_experimental insertion -is_a: ObsoleteClass +name: obsolete experimental insertion +is_obsolete: true [Term] id: GENO:0000092 @@ -463,9 +463,9 @@ relationship: RO:0002351 NCBITaxon:7955 ! has member Danio rerio [Term] id: GENO:0000125 -name: obsolete_sequence feature collection attribute +name: obsolete sequence feature collection attribute def: "sequence attribute that can inhere only in a collection of more than one sequence features" [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000131 @@ -543,10 +543,10 @@ property_value: IAO:0000118 "phenotypic inheritance pattern" xsd:string [Term] id: GENO:0000142 -name: obsolete_dominant inheritance +name: obsolete dominant inheritance def: "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes" [] -is_a: ObsoleteClass property_value: IAO:0000231 "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." xsd:string +is_obsolete: true [Term] id: GENO:0000143 @@ -599,9 +599,9 @@ is_a: GENO:0000936 ! X-linked inheritance [Term] id: GENO:0000150 -name: obsolete_autosomal recessive inheritance -is_a: ObsoleteClass +name: obsolete autosomal recessive inheritance property_value: IAO:0000231 "duplicate term, use GENO:0000148" xsd:string +is_obsolete: true [Term] id: GENO:0000152 @@ -615,11 +615,61 @@ id: GENO:0000160 name: unspecified life cycle stage is_a: UBERON:0000105 ! life cycle stage +[Term] +id: GENO:0000164 +name: obsolete genetic insertion technique +is_obsolete: true + +[Term] +id: GENO:0000165 +name: obsolete mutagen treatment technique +is_obsolete: true + +[Term] +id: GENO:0000166 +name: obsolete targeted gene mutation technique +is_obsolete: true + +[Term] +id: GENO:0000169 +name: obsolete random genetic insertion technique +is_obsolete: true + +[Term] +id: GENO:0000170 +name: obsolete targeted genetic insertion technique +is_obsolete: true + +[Term] +id: GENO:0000171 +name: obsolete enhancer trapping technique +is_obsolete: true + +[Term] +id: GENO:0000172 +name: obsolete gene trapping technique +is_obsolete: true + +[Term] +id: GENO:0000173 +name: obsolete promoter trapping technique +is_obsolete: true + +[Term] +id: GENO:0000174 +name: obsolete targeted knock-in technique +is_obsolete: true + +[Term] +id: GENO:0000175 +name: obsolete random transgene insertion technique +is_obsolete: true + [Term] id: GENO:0000324 -name: obsolete_chromosome complement +name: obsolete chromosome complement def: "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome" [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000338 @@ -723,11 +773,11 @@ property_value: IAO:0000118 "trans-heterozygous" xsd:string [Term] id: GENO:0000415 -name: obsolete_reagent sequence feature +name: obsolete reagent sequence feature def: "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)" [] -is_a: ObsoleteClass property_value: IAO:0000116 "replaced with SO:engineered_region" xsd:string property_value: IAO:0000118 "extra-genomic sequence" xsd:string +is_obsolete: true [Term] id: GENO:0000458 @@ -782,13 +832,13 @@ property_value: IAO:0000114 GENO:0000484 [Term] id: GENO:0000491 -name: obsolete_mutant allele +name: obsolete mutant allele def: "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain." [] comment: 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. -is_a: ObsoleteClass property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000119 "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" xsd:string property_value: IAO:0000231 "Not required for any specific use case at this point so removed for simplicity. \nFormely asserted as allele and inferred as varaint allele. \nEq class definition:\nallele\n and (mutation or ('has subsequence' some mutation))" xsd:string +is_obsolete: true [Term] id: GENO:0000492 @@ -1226,11 +1276,11 @@ relationship: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered [Term] id: GENO:0000680 -name: obsolete_null feature +name: obsolete null feature def: "A genomic feature that has an extent of zero." [] -is_a: ObsoleteClass property_value: IAO:0000112 "A junction between bases, a deletion variant, a terminus at the end of a chromosome." xsd:string property_value: IAO:0000116 "Former logical def: \n'genomic feature'\n and (has_extent value 0)" xsd:string +is_obsolete: true [Term] id: GENO:0000681 @@ -1346,13 +1396,13 @@ intersection_of: GENO:0000783 GENO:0000782 {all_only="true"} ! has_sequence_unit [Term] id: GENO:0000724 -name: obsolete_biological sequence or collection -is_a: ObsoleteClass +name: obsolete biological sequence or collection +is_obsolete: true [Term] id: GENO:0000725 -name: obsolete_biological sequence collection -is_a: GENO:0000724 ! obsolete_biological sequence or collection +name: obsolete biological sequence collection +is_obsolete: true [Term] id: GENO:0000736 @@ -1370,12 +1420,12 @@ is_a: GENO:0000714 ! qualified genomic feature [Term] id: GENO:0000768 -name: obsolete_genomic position +name: obsolete genomic position def: "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence." [] -is_a: ObsoleteClass property_value: IAO:0000116 "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature." xsd:string property_value: IAO:0000118 "genomic coordinates" xsd:string property_value: IAO:0000231 "remodeling notion of sequence feature position around the idea of a 'genomic locus'" xsd:string +is_obsolete: true [Term] id: GENO:0000770 @@ -1385,9 +1435,9 @@ property_value: IAO:0000114 GENO:0000484 [Term] id: GENO:0000772 -name: obsolete_unspecified +name: obsolete unspecified def: "A sequence attribute inhering in a feature whose identity is not specified." [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000773 @@ -1405,10 +1455,10 @@ intersection_of: IAO:0000219 GENO:0000033 ! denotes variant genome [Term] id: GENO:0000778 -name: obsolete_sequence information entity +name: obsolete sequence information entity def: "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities." [] -is_a: ObsoleteClass property_value: IAO:0000231 "eliminating classes that are not necessary or add uneeded complexity." xsd:string +is_obsolete: true [Term] id: GENO:0000779 @@ -1483,11 +1533,11 @@ relationship: GENO:0000382 GENO:0000504 ! has_variant_part reagent targeted gene [Term] id: GENO:0000848 -name: obsolete_coding sequence alteration +name: obsolete coding sequence alteration def: "A sequence alteration within the coding sequence of a gene." [] -is_a: ObsoleteClass property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000231 "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." xsd:string +is_obsolete: true [Term] id: GENO:0000850 @@ -1512,10 +1562,10 @@ property_value: IAO:0000118 "non-integrated transgene" xsd:string [Term] id: GENO:0000870 -name: obsolete_sequence feature collection +name: obsolete sequence feature collection def: "A collection of more than one sequence feature." [] xref: http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000871 @@ -1555,13 +1605,13 @@ is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000876 -name: obsolete_genetic dosage +name: obsolete genetic dosage comment: Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. -is_a: ObsoleteClass property_value: IAO:0000118 "allelic dosage" xsd:string property_value: IAO:0000118 "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome." xsd:string property_value: IAO:0000118 "gene dosage" xsd:string property_value: IAO:0000231 "Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute." xsd:string +is_obsolete: true [Term] id: GENO:0000877 @@ -1610,11 +1660,11 @@ property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/di [Term] id: GENO:0000883 -name: obsolete_gametic +name: obsolete gametic def: "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells)." [] -is_a: ObsoleteClass property_value: IAO:0000118 "germ-line" xsd:string property_value: IAO:0000231 "replaced by GENO:0000900 ! 'germline'" xsd:string +is_obsolete: true [Term] id: GENO:0000885 @@ -1655,26 +1705,26 @@ property_value: IAO:0000118 "unknown inheritance" xsd:string [Term] id: GENO:0000890 -name: obsolete_canonical allele +name: obsolete canonical allele def: "One of a set of sequence features or haplotypes that exist at a particular genetic locus. " [] comment: As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand.\n\nIn the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) -is_a: ObsoleteClass property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string property_value: IAO:0000112 "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." xsd:string property_value: IAO:0000116 "The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/ xsd:string property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs." xsd:string +is_obsolete: true [Term] id: GENO:0000891 -name: obsolete_contextual allele +name: obsolete contextual allele def: "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence." [] comment: The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. -is_a: ObsoleteClass property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string property_value: IAO:0000116 "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ xsd:string property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.\n\nFormer axiom: denotes some 'obsolete_canonical allele'" xsd:string +is_obsolete: true [Term] id: GENO:0000892 @@ -1719,11 +1769,11 @@ property_value: IAO:0000118 "complete genotype" xsd:string [Term] id: GENO:0000901 -name: obsolete_allele cellular context +name: obsolete allele cellular context def: "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)" [] comment: Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. -is_a: ObsoleteClass property_value: IAO:0000231 "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin" xsd:string +is_obsolete: true [Term] id: GENO:0000902 @@ -1754,11 +1804,13 @@ is_a: SO:0000110 ! sequence_feature [Term] id: GENO:0000910 +name: obsolete reporter role name: reporter is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000911 +name: obsolete selectable marker role name: selectable marker is_a: GENO:0000788 ! sequence feature attribute @@ -1776,22 +1828,22 @@ relationship: GENO:0000239 SO:0001505 ! has_sequence reference genome sequence [Term] id: GENO:0000915 -name: obsolete_haplotype +name: obsolete haplotype def: "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it." [] comment: 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. -is_a: ObsoleteClass property_value: IAO:0000116 "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"" xsd:string property_value: IAO:0000119 "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype." xsd:string property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" xsd:string +is_obsolete: true [Term] id: GENO:0000916 -name: obsolete_haplotype block +name: obsolete haplotype block def: "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations." [] comment: A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.\n\nThe boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.\n\n-----------------------\n\n* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. -is_a: ObsoleteClass property_value: IAO:0000119 "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." xsd:string property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets." xsd:string +is_obsolete: true [Term] id: GENO:0000918 @@ -1834,27 +1886,27 @@ is_a: GENO:0000921 ! biological sequence or set [Term] id: GENO:0000923 -name: obsolete_functional copy number complement +name: obsolete functional copy number complement def: "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome." [] comment: As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). comment: The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. -is_a: ObsoleteClass property_value: IAO:0000116 "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"" xsd:string property_value: IAO:0000118 "functional feature complement" xsd:string property_value: IAO:0000118 "genetic dosage" xsd:string property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." xsd:string +is_obsolete: true [Term] id: GENO:0000924 -name: obsolete_intrinsic sequence feature attribute +name: obsolete intrinsic sequence feature attribute def: "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form." [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000925 -name: obsolete_extrinsic sequence feature attribute +name: obsolete extrinsic sequence feature attribute def: "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)" [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000926 @@ -2039,20 +2091,20 @@ is_a: GENO:0000660 ! genomic feature set [Term] id: GENO:0000955 -name: obsolete_variant copy number complement +name: obsolete variant copy number complement def: "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s)." [] comment: In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. -is_a: GENO:0000956 ! obsolete_copy number complement property_value: IAO:0000118 "copy number variation" xsd:string property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level." xsd:string +is_obsolete: true [Term] id: GENO:0000956 -name: obsolete_copy number complement +name: obsolete copy number complement def: "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger." [] comment: 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. -is_a: ObsoleteClass property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." xsd:string +is_obsolete: true [Term] id: GENO:0000960 @@ -2221,11 +2273,11 @@ property_value: IAO:0000116 "Stub class to serve as root of hierarchy for import [Term] id: PATO:0000016 -name: obsolete_color brightness -is_a: ObsoleteClass +name: obsolete color brightness property_value: IAO:0000116 "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html" xsd:string property_value: IAO:0000116 "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." xsd:string property_value: IAO:0000118 "color value" xsd:string +is_obsolete: true [Term] id: PATO:0000383 @@ -2306,15 +2358,15 @@ property_value: IAO:0000116 "GENO defines three levels of sequence-related artif [Term] id: SO:0000143 -name: obsolete_assembly_component +name: obsolete assembly_component def: "A region of known length which may be used to manufacture a longer region." [] -is_a: SO:0001410 ! obsolete_experimental_feature +is_obsolete: true [Term] id: SO:0000149 -name: obsolete_contig +name: obsolete contig def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [] -is_a: SO:0000143 ! obsolete_assembly_component +is_obsolete: true [Term] id: SO:0000159 @@ -2411,9 +2463,9 @@ is_a: SO:0000830 ! chromosome part [Term] id: SO:0000637 -name: obsolete_engineered_plasmid -is_a: ObsoleteClass +name: obsolete engineered_plasmid property_value: IAO:0000116 "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." xsd:string +is_obsolete: true [Term] id: SO:0000667 @@ -2544,10 +2596,10 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl [Term] id: SO:0001410 -name: obsolete_experimental_feature +name: obsolete experimental_feature def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [] -is_a: ObsoleteClass property_value: IAO:0000231 "not currently needed to support modeling use cases. can re-introduce if becomes necessary." xsd:string +is_obsolete: true [Term] id: SO:0001477 @@ -3316,7 +3368,7 @@ inverse_of: GENO:0000661 ! is_sex_agnostic_part_of id: GENO:0000651 name: is_mutant_allele_of comment: A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of. -domain: GENO:0000491 ! obsolete_mutant allele +domain: GENO:0000491 ! obsolete mutant allele is_a: GENO:0000641 ! is_variant_allele_of [Typedef] diff --git a/geno-base.owl b/geno-base.owl index 5b21b14..2af65e4 100644 --- a/geno-base.owl +++ b/geno-base.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 @@ -2630,11 +2630,11 @@ A genomic feature being an allele_of a gene is based on its location in a host g - a collection more than one sequence features (ie a collection of discontinuous sequence features) perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one) 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. - obsolete_sequence feature collection + obsolete sequence feature collection + true @@ -2642,12 +2642,12 @@ A genomic feature being an allele_of a gene is based on its location in a host g - A sequence feature collection comprised of discontiguous sequences from a single genome Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system. genomic feature collection Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. - obsolete_genomic feature collection + obsolete genomic feature collection + true @@ -2655,7 +2655,6 @@ A genomic feature being an allele_of a gene is based on its location in a host g - A single locus complement that serves as a standard against which 'variant' sequences are compared reference allelic complement reference single locus feature complement @@ -2669,7 +2668,8 @@ SC axioms: 'has member' exactly 0 'variant allele' 'has member' only 'reference genomic feature' 'has member' some 'reference genomic feature' - obsolete_reference single locus complement + obsolete reference single locus complement + true @@ -2751,7 +2751,6 @@ In model organism datasets, 'reference' alleles are typically (but not - A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus). Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '. @@ -2760,7 +2759,8 @@ In model organism datasets, 'reference' alleles are typically (but not Eq Class def: 'genomic feature' and (has_sequence_attribute some unspecified) An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). - obsolete_unspecified feature + obsolete unspecified feature + true @@ -2768,7 +2768,6 @@ Eq Class def: 'genomic feature' - A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature. hemizygous reference junction Eliminating unecessary defined/organizational classes. Former logical def: @@ -2781,7 +2780,8 @@ is_variant_with some insertion In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. - obsolete_reference junction + obsolete reference junction + true @@ -2849,7 +2849,6 @@ The junction-insertion pair represents the allelic complement at that locus, whi - A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development. http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690 @@ -2868,7 +2867,8 @@ is_reference_allele_of some gene Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. - obsolete_reference gene allele + obsolete reference gene allele + true @@ -2876,8 +2876,8 @@ In model organism datasets, 'reference' genes are typically the ' - - obsolete_experimental insertion + obsolete experimental insertion + true @@ -3020,9 +3020,9 @@ Note that at present, a material genome and genetic material are necessarily par - sequence attribute that can inhere only in a collection of more than one sequence features - obsolete_sequence feature collection attribute + obsolete sequence feature collection attribute + true @@ -3169,10 +3169,10 @@ These genetic and environmental "interactions" of alleles play out at - disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes Triage until decide if want to define this as grouping class that would result in multiple-inheritance. - obsolete_dominant inheritance + obsolete dominant inheritance + true @@ -3257,9 +3257,9 @@ These genetic and environmental "interactions" of alleles play out at - duplicate term, use GENO:0000148 - obsolete_autosomal recessive inheritance + obsolete autosomal recessive inheritance + true @@ -3284,12 +3284,102 @@ These genetic and environmental "interactions" of alleles play out at + + + + obsolete genetic insertion technique + true + + + + + + + + obsolete mutagen treatment technique + true + + + + + + + + obsolete targeted gene mutation technique + true + + + + + + + + obsolete random genetic insertion technique + true + + + + + + + + obsolete targeted genetic insertion technique + true + + + + + + + + obsolete enhancer trapping technique + true + + + + + + + + obsolete gene trapping technique + true + + + + + + + + obsolete promoter trapping technique + true + + + + + + + + obsolete targeted knock-in technique + true + + + + + + + + obsolete random transgene insertion technique + true + + + + - A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome - obsolete_chromosome complement + obsolete chromosome complement + true @@ -3481,11 +3571,11 @@ Similarly, large sequence features lost from genome are akin to deletions and th - A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe) replaced with SO:engineered_region extra-genomic sequence - obsolete_reagent sequence feature + obsolete reagent sequence feature + true @@ -3609,7 +3699,6 @@ Similarly, large sequence features lost from genome are akin to deletions and th - An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain. Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines @@ -3619,7 +3708,8 @@ Eq class definition: allele and (mutation or ('has subsequence' some mutation)) 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. - obsolete_mutant allele + obsolete mutant allele + true @@ -4596,13 +4686,13 @@ The notion of a 'genomic feature set' differs from that of a 'gen - A junction between bases, a deletion variant, a terminus at the end of a chromosome. A genomic feature that has an extent of zero. Former logical def: 'genomic feature' and (has_extent value 0) - obsolete_null feature + obsolete null feature + true @@ -4942,8 +5032,8 @@ A complements may contain 0, 1, or more than one members. For example, the compl - - obsolete_biological sequence or collection + obsolete biological sequence or collection + true @@ -4951,8 +5041,8 @@ A complements may contain 0, 1, or more than one members. For example, the compl - - obsolete_biological sequence collection + obsolete biological sequence collection + true @@ -4982,12 +5072,12 @@ A complements may contain 0, 1, or more than one members. For example, the compl - A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence. This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature. genomic coordinates remodeling notion of sequence feature position around the idea of a 'genomic locus' - obsolete_genomic position + obsolete genomic position + true @@ -5005,9 +5095,9 @@ A complements may contain 0, 1, or more than one members. For example, the compl - A sequence attribute inhering in a feature whose identity is not specified. - obsolete_unspecified + obsolete unspecified + true @@ -5046,10 +5136,10 @@ A complements may contain 0, 1, or more than one members. For example, the compl - An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities. eliminating classes that are not necessary or add uneeded complexity. - obsolete_sequence information entity + obsolete sequence information entity + true @@ -5330,12 +5420,12 @@ This contrasts to the use of the term 'genotype in model orgnaism communiti - A sequence alteration within the coding sequence of a gene. Not required at this poitn, so marked exploratory and obsoleted. Asserted under sequence_alteration. - obsolete_coding sequence alteration + obsolete coding sequence alteration + true @@ -5378,10 +5468,10 @@ Constructs are typically packaged as part of delivery systems such as plasmids - A collection of more than one sequence feature. http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection - obsolete_sequence feature collection + obsolete sequence feature collection + true @@ -5462,7 +5552,6 @@ Each of these more specific definition serves a purpose for a particular type of - allelic dosage an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome. gene dosage @@ -5470,7 +5559,8 @@ Each of these more specific definition serves a purpose for a particular type of Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. - obsolete_genetic dosage + obsolete genetic dosage + true @@ -5551,11 +5641,11 @@ These acquired mutations are called 'somatic' because they typically a - a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells). germ-line replaced by GENO:0000900 ! 'germline' - obsolete_gametic + obsolete gametic + true @@ -5656,7 +5746,6 @@ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/< - The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”. One of a set of sequence features or haplotypes that exist at a particular genetic locus. <see ClinGen Allele Model> The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. @@ -5666,7 +5755,8 @@ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/< As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) - obsolete_canonical allele + obsolete canonical allele + true @@ -5674,7 +5764,6 @@ In the ClinGen allele model, 'canonical alleles are contrasted with ' - An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence. The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ @@ -5683,7 +5772,8 @@ In the ClinGen allele model, 'canonical alleles are contrasted with ' Former axiom: denotes some 'obsolete_canonical allele' ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. - obsolete_contextual allele + obsolete contextual allele + true @@ -5811,11 +5901,11 @@ A genomic genotype is an information artifact with a representational syntax tha - A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells) decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. - obsolete_allele cellular context + obsolete allele cellular context + true @@ -5886,6 +5976,7 @@ For example, we would define an 'HLA gene block' as a subclass of &ap + obsolete reporter role reporter @@ -5895,6 +5986,7 @@ For example, we would define an 'HLA gene block' as a subclass of &ap + obsolete selectable marker role selectable marker @@ -5928,7 +6020,6 @@ For example, we would define an 'HLA gene block' as a subclass of &ap - A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it. Former comment: "Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project." Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype. @@ -5950,7 +6041,8 @@ b. The second is a region containing multiple linked single nucleotide polymorph c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. - obsolete_haplotype + obsolete haplotype + true @@ -5958,7 +6050,6 @@ The GENO definition of 'haplotype' is broadly inclusive of these and a - A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations. Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block. Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. @@ -5969,7 +6060,8 @@ The boundaries of haplotype blocks are defined in efforts to identify haplotypes ----------------------- * One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. - obsolete_haplotype block + obsolete haplotype block + true @@ -6051,7 +6143,6 @@ A set may also include multiple copies of the same sequence. For example, in a & - A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome. Formerly considered modeling this as an informational entity, defined as "An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome." functional feature complement @@ -6059,7 +6150,8 @@ A set may also include multiple copies of the same sequence. For example, in a & Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963. As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. - obsolete_functional copy number complement + obsolete functional copy number complement + true @@ -6067,9 +6159,9 @@ A set may also include multiple copies of the same sequence. For example, in a & - A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form. - obsolete_intrinsic sequence feature attribute + obsolete intrinsic sequence feature attribute + true @@ -6077,9 +6169,9 @@ A set may also include multiple copies of the same sequence. For example, in a & - A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.) - obsolete_extrinsic sequence feature attribute + obsolete extrinsic sequence feature attribute + true @@ -6372,14 +6464,14 @@ A set may also include multiple copies of the same sequence. For example, in a & - A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s). copy number variation Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. - obsolete_variant copy number complement + obsolete variant copy number complement + true @@ -6387,7 +6479,6 @@ Note that the 'copy number variation' class in GENO is related to but - A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger. Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961. 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. @@ -6395,7 +6486,8 @@ Note that the 'copy number variation' class in GENO is related to but 2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. 3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. - obsolete_copy number complement + obsolete copy number complement + true @@ -6689,11 +6781,11 @@ Previous. An information content entity is a non-realizable information entity t - 'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute. color value - obsolete_color brightness + obsolete color brightness + true @@ -6839,9 +6931,9 @@ chromosome > arm > band > sub-band > sub-sub-band - A region of known length which may be used to manufacture a longer region. - obsolete_assembly_component + obsolete assembly_component + true @@ -6849,9 +6941,9 @@ chromosome > arm > band > sub-band > sub-sub-band - A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. - obsolete_contig + obsolete contig + true @@ -7032,9 +7124,9 @@ chromosome > arm > band > sub-band > sub-sub-band - Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct. - obsolete_engineered_plasmid + obsolete engineered_plasmid + true @@ -7290,10 +7382,10 @@ For a particular instance of a sequence alteration, howver, we may in some cases - A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. not currently needed to support modeling use cases. can re-introduce if becomes necessary. - obsolete_experimental_feature + obsolete experimental_feature + true @@ -7973,12 +8065,6 @@ For a particular instance of a sequence alteration, howver, we may in some cases - - - - - - diff --git a/geno-full.json b/geno-full.json index 52c783f..242db90 100644 --- a/geno-full.json +++ b/geno-full.json @@ -57,6 +57,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared." @@ -66,7 +69,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_reference gene allele" + "lbl" : "obsolete reference gene allele" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000057", "meta" : { @@ -165,6 +168,36 @@ }, "type" : "CLASS", "lbl" : "SNV" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000173", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete promoter trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000172", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete gene trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000175", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete random transgene insertion technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000054", "meta" : { @@ -175,6 +208,16 @@ }, "type" : "CLASS", "lbl" : "homo sapiens gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000174", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete targeted knock-in technique" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000016", "meta" : { @@ -184,13 +227,16 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "color value" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." } ] }, "type" : "CLASS", - "lbl" : "obsolete_color brightness" + "lbl" : "obsolete color brightness" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002162", "meta" : { @@ -201,6 +247,26 @@ }, "type" : "PROPERTY", "lbl" : "in taxon" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000171", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete enhancer trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000170", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete targeted genetic insertion technique" }, { "id" : "http://www.ncbi.nlm.nih.gov/gene/6469", "meta" : { @@ -214,6 +280,36 @@ }, "type" : "CLASS", "lbl" : "homo sapiens SHH gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000169", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete random genetic insertion technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000166", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete targeted gene mutation technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000165", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete mutagen treatment technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000047", "meta" : { @@ -266,10 +362,14 @@ "definition" : { "val" : "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_contig" + "lbl" : "obsolete contig" }, { "id" : "http://purl.obolibrary.org/obo/SO_0001479", "meta" : { @@ -1143,8 +1243,14 @@ "lbl" : "gene trap insertion" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000091", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, "type" : "CLASS", - "lbl" : "obsolete_experimental insertion" + "lbl" : "obsolete experimental insertion" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000093", "meta" : { @@ -2067,6 +2173,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations." @@ -2076,7 +2185,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_haplotype" + "lbl" : "obsolete haplotype" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000914", "meta" : { @@ -2130,10 +2239,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_haplotype block" + "lbl" : "obsolete haplotype block" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000911", "type" : "CLASS", @@ -2285,6 +2397,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others." }, { @@ -2293,7 +2408,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_allele cellular context" + "lbl" : "obsolete allele cellular context" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", "meta" : { @@ -2671,10 +2786,14 @@ "definition" : { "val" : "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_extrinsic sequence feature attribute" + "lbl" : "obsolete extrinsic sequence feature attribute" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000928", "meta" : { @@ -2729,10 +2848,14 @@ "definition" : { "val" : "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form.", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_intrinsic sequence feature attribute" + "lbl" : "obsolete intrinsic sequence feature attribute" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000923", "meta" : { @@ -2758,10 +2881,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_functional copy number complement" + "lbl" : "obsolete functional copy number complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000953", "meta" : { @@ -2873,13 +2999,16 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "copy number variation" } ] }, "type" : "CLASS", - "lbl" : "obsolete_variant copy number complement" + "lbl" : "obsolete variant copy number complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000713", "meta" : { @@ -2972,13 +3101,16 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members." } ] }, "type" : "CLASS", - "lbl" : "obsolete_copy number complement" + "lbl" : "obsolete copy number complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000714", "meta" : { @@ -4035,13 +4167,16 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/GENO_0000484" } ] }, "type" : "CLASS", - "lbl" : "obsolete_coding sequence alteration" + "lbl" : "obsolete coding sequence alteration" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000606", "type" : "CLASS", @@ -4113,10 +4248,6 @@ }, "type" : "PROPERTY", "lbl" : "has_interval" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000724", - "type" : "CLASS", - "lbl" : "obsolete_biological sequence or collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000603", "meta" : { @@ -4127,6 +4258,16 @@ }, "type" : "CLASS", "lbl" : "heteroplasmic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000724", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete biological sequence or collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000602", "meta" : { @@ -4241,6 +4382,16 @@ }, "type" : "PROPERTY", "lbl" : "sequence role" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000725", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete biological sequence collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000967", "meta" : { @@ -4251,10 +4402,6 @@ }, "type" : "PROPERTY", "lbl" : "has_reference_sequence" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000725", - "type" : "CLASS", - "lbl" : "obsolete_biological sequence collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000604", "type" : "CLASS", @@ -4410,6 +4557,9 @@ "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "allelic dosage" @@ -4425,7 +4575,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_genetic dosage" + "lbl" : "obsolete genetic dosage" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000875", "meta" : { @@ -4469,10 +4619,14 @@ }, "xrefs" : [ { "val" : "http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence feature collection" + "lbl" : "obsolete sequence feature collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000872", "meta" : { @@ -5257,6 +5411,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." @@ -5266,7 +5423,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_contextual allele" + "lbl" : "obsolete contextual allele" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000410", "meta" : { @@ -5331,6 +5488,20 @@ }, "type" : "CLASS", "lbl" : "homoplasmic mitochondrial inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000772", + "meta" : { + "definition" : { + "val" : "A sequence attribute inhering in a feature whose identity is not specified.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete unspecified" }, { "id" : "http://purl.obolibrary.org/obo/ZP_0005692", "type" : "CLASS", @@ -5345,26 +5516,19 @@ }, "type" : "PROPERTY", "lbl" : "is_mutant_allele_of" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000772", - "meta" : { - "definition" : { - "val" : "A sequence attribute inhering in a feature whose identity is not specified.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "obsolete_unspecified" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000637", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." } ] }, "type" : "CLASS", - "lbl" : "obsolete_engineered_plasmid" + "lbl" : "obsolete engineered_plasmid" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000779", "meta" : { @@ -5388,13 +5552,16 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "replaced with SO:engineered_region" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "extra-genomic sequence" } ] }, "type" : "CLASS", - "lbl" : "obsolete_reagent sequence feature" + "lbl" : "obsolete reagent sequence feature" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000778", "meta" : { @@ -5405,10 +5572,13 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "eliminating classes that are not necessary or add uneeded complexity." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence information entity" + "lbl" : "obsolete sequence information entity" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000536", "meta" : { @@ -5503,6 +5673,9 @@ }, { "pred" : "http://purl.org/dc/terms/source", "val" : "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." @@ -5518,7 +5691,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_canonical allele" + "lbl" : "obsolete canonical allele" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000885", "meta" : { @@ -5680,10 +5853,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "germ-line" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_gametic" + "lbl" : "obsolete gametic" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000641", "meta" : { @@ -5803,6 +5979,16 @@ }, "type" : "PROPERTY", "lbl" : "is_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000647", + "meta" : { + "definition" : { + "val" : "A genomic genotype here the genomic background specifies a female sex chromosome complement.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "female intrinsic genotype" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000768", "meta" : { @@ -5816,23 +6002,16 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "remodeling notion of sequence feature position around the idea of a 'genomic locus'" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "genomic coordinates" } ] }, "type" : "CLASS", - "lbl" : "obsolete_genomic position" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000647", - "meta" : { - "definition" : { - "val" : "A genomic genotype here the genomic background specifies a female sex chromosome complement.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "female intrinsic genotype" + "lbl" : "obsolete genomic position" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000889", "meta" : { @@ -6001,6 +6180,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Former logical def: \n'genomic feature'\n and (has_extent value 0)" }, { @@ -6009,7 +6191,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_null feature" + "lbl" : "obsolete null feature" }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", "type" : "CLASS", @@ -6400,12 +6582,15 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "not currently needed to support modeling use cases. can re-introduce if becomes necessary." } ] }, "type" : "CLASS", - "lbl" : "obsolete_experimental_feature" + "lbl" : "obsolete experimental_feature" }, { "id" : "http://biohackathon.org/resource/faldo#location", "type" : "PROPERTY", @@ -6559,10 +6744,14 @@ "definition" : { "val" : "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_chromosome complement" + "lbl" : "obsolete chromosome complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000447", "meta" : { @@ -7494,12 +7683,15 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." } ] }, "type" : "CLASS", - "lbl" : "obsolete_dominant inheritance" + "lbl" : "obsolete dominant inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000141", "meta" : { @@ -7725,12 +7917,15 @@ "val" : "perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one)" } ], "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions." } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence feature collection" + "lbl" : "obsolete sequence feature collection" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000110", "meta" : { @@ -7810,6 +8005,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" }, { @@ -7824,7 +8022,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_mutant allele" + "lbl" : "obsolete mutant allele" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000010", "meta" : { @@ -7919,10 +8117,14 @@ "definition" : { "val" : "sequence attribute that can inhere only in a collection of more than one sequence features", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence feature collection attribute" + "lbl" : "obsolete sequence feature collection attribute" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000488", "meta" : { @@ -8201,10 +8403,24 @@ "definition" : { "val" : "A region of known length which may be used to manufacture a longer region.", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete assembly_component" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000164", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_assembly_component" + "lbl" : "obsolete genetic insertion technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000042", "meta" : { @@ -8213,6 +8429,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" }, { @@ -8224,7 +8443,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_reference junction" + "lbl" : "obsolete reference junction" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000160", "type" : "CLASS", @@ -8242,6 +8461,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/GENO_0000484" @@ -8251,7 +8473,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_unspecified feature" + "lbl" : "obsolete unspecified feature" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000033", "meta" : { @@ -8344,12 +8566,15 @@ "id" : "http://purl.obolibrary.org/obo/GENO_0000150", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "duplicate term, use GENO:0000148" } ] }, "type" : "CLASS", - "lbl" : "obsolete_autosomal recessive inheritance" + "lbl" : "obsolete autosomal recessive inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000394", "type" : "CLASS", @@ -8407,6 +8632,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "reference allelic complement" }, { @@ -8418,7 +8646,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_reference single locus complement" + "lbl" : "obsolete reference single locus complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000149", "meta" : { @@ -8462,10 +8690,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_genomic feature collection" + "lbl" : "obsolete genomic feature collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000143", "meta" : { @@ -8704,10 +8935,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000343", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000830" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000016", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000721", "pred" : "is_a", @@ -8832,10 +9059,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000391", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000876", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000619", "pred" : "is_a", @@ -8944,14 +9167,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000845", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000790" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000343", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0001059" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_8000006" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000343", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/SO_0001059" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000525", "pred" : "is_a", @@ -9124,10 +9347,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_8000009", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_8000006" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000916", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000242", "pred" : "inverseOf", @@ -9136,10 +9355,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000640", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000638" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0000143", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0001410" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000629", "pred" : "is_a", @@ -9152,10 +9367,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000392", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000324", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000402", "pred" : "is_a", @@ -9240,10 +9451,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000147", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000934" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000150", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/ZP_0000755", "pred" : "is_a", @@ -9252,14 +9459,14 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000036", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000121", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0000121", + "pred" : "type", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000626", "pred" : "subPropertyOf", @@ -9276,10 +9483,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000948", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000935" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000768", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000645", "pred" : "http://purl.obolibrary.org/obo/GENO_0000650", @@ -9320,10 +9523,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000018" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000724", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "is_a", @@ -9368,10 +9567,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000823", "pred" : "http://purl.obolibrary.org/obo/IAO_0000219", "obj" : "http://purl.obolibrary.org/obo/GENO_0000516" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000029", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000393", "pred" : "is_a", @@ -9380,14 +9575,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000684", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000924", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000870", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000642", "pred" : "is_a", @@ -9440,10 +9627,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000410", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000883", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000794", "pred" : "subPropertyOf", @@ -9456,14 +9639,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000408", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000413" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0001745", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0001744" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000500", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000497" + }, { + "sub" : "http://purl.obolibrary.org/obo/SO_0001745", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/SO_0001744" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000953", "pred" : "is_a", @@ -9636,10 +9819,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000026", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000923", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000108", "pred" : "is_a", @@ -9896,14 +10075,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000743", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002200" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000737", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000338", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000346" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000737", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000714" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000110", "pred" : "http://purl.obolibrary.org/obo/GENO_0000239", @@ -9912,10 +10091,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000654", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000415", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000054", "pred" : "is_a", @@ -10024,10 +10199,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000652", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000641" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000890", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000930", "pred" : "is_a", @@ -10080,10 +10251,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0003303", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003302" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000125", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000030", "pred" : "http://purl.obolibrary.org/obo/GENO_0000382", @@ -10184,10 +10351,6 @@ "sub" : "http://purl.org/oban/association", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000778", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000741", "pred" : "subPropertyOf", @@ -10224,10 +10387,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000339", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000346" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000142", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000841", "pred" : "subPropertyOf", @@ -10268,10 +10427,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000777", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000899" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000680", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000650", "pred" : "inverseOf", @@ -10304,14 +10459,14 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000016", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000014" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000057", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_10090" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000344", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000343" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000057", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_10090" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000614", "pred" : "is_a", @@ -10324,10 +10479,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000969", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000956", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0100026", "pred" : "is_a", @@ -10344,10 +10495,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000899" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000022", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000494", "pred" : "is_a", @@ -10360,10 +10507,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000486", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000925", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000005", "pred" : "is_a", @@ -10528,10 +10671,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000965", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000725", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000724" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000660", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -10600,22 +10739,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000943", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000942" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000848", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000032", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000955", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000956" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0000637", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000248", "pred" : "is_a", @@ -10664,10 +10791,6 @@ "sub" : "http://purl.obolibrary.org/obo/ENVO_01000254", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000915", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000009", "pred" : "is_a", @@ -10676,10 +10799,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000093", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000902" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000772", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/HsapDv_0000000", "pred" : "is_a", @@ -10704,10 +10823,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000410", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/IAO_0000409" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000091", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000621", "pred" : "is_a", @@ -10784,10 +10899,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000911", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000060", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://biohackathon.org/resource/faldo#BothStrandsPosition", "pred" : "is_a", @@ -10832,18 +10943,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000928", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000926" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000042", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000529", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000491", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000418", "pred" : "inverseOf", @@ -10896,10 +10999,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000914", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001026" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000891", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000604", "pred" : "is_a", @@ -10916,14 +11015,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000919", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000713" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000720", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001059", "pred" : "http://purl.obolibrary.org/obo/GENO_0000784", @@ -10940,10 +11039,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000091", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000053" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000901", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000144", "pred" : "is_a", @@ -10984,10 +11079,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_0000341", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GENO_0000614" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000037", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://biohackathon.org/resource/faldo#reference", "pred" : "subPropertyOf", @@ -11000,10 +11091,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000761", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000655" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0000149", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0000143" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000368", "pred" : "subPropertyOf", @@ -11044,10 +11131,6 @@ "sub" : "http://biohackathon.org/resource/faldo#ForwardStrandPosition", "pred" : "is_a", "obj" : "http://biohackathon.org/resource/faldo#StrandedPosition" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000019", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000341", "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", @@ -11060,14 +11143,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000784", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000683" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000036", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000512" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000017", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000036", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000512" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000165", "pred" : "is_a", @@ -11172,10 +11255,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000646", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000645" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0001410", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000253", "pred" : "subPropertyOf", @@ -11219,7 +11298,7 @@ "pred" : "http://purl.org/dc/terms/license", "val" : "Unspecified" } ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2020-03-07/geno-full.json" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2020-03-08/geno-full.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { @@ -11400,13 +11479,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000368", diff --git a/geno-full.obo b/geno-full.obo index 37b050d..7bae5b3 100644 --- a/geno-full.obo +++ b/geno-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: geno/releases/2020-03-07/geno-full.owl +data-version: geno/releases/2020-03-08/geno-full.owl ontology: geno/geno-full property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string @@ -303,29 +303,29 @@ property_value: IAO:0000118 "reference sequence" xsd:string [Term] id: GENO:0000019 -name: obsolete_sequence feature collection +name: obsolete sequence feature collection def: "a collection more than one sequence features (ie a collection of discontinuous sequence features)" [] comment: 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. xref: perhaps not same as SO:sequence collection\, as here we explicitly include features that can have an extent of zero (and SO\:sequence collection is a collection of regions that have an extent of at least one) -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000022 -name: obsolete_genomic feature collection +name: obsolete genomic feature collection def: "A sequence feature collection comprised of discontiguous sequences from a single genome" [] comment: Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. -is_a: ObsoleteClass property_value: IAO:0000116 "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system." xsd:string property_value: IAO:0000118 "genomic feature collection" xsd:string +is_obsolete: true [Term] id: GENO:0000029 -name: obsolete_reference single locus complement +name: obsolete reference single locus complement def: "A single locus complement that serves as a standard against which 'variant' sequences are compared" [] -is_a: ObsoleteClass property_value: IAO:0000118 "reference allelic complement" xsd:string property_value: IAO:0000118 "reference single locus feature complement" xsd:string property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'single locus complement'\n and (has_sequence_attribute some reference)\n\nSC axioms:\n'has member' exactly 0 'variant allele'\n'has member' only 'reference genomic feature'\n'has member' some 'reference genomic feature'" xsd:string +is_obsolete: true [Term] id: GENO:0000030 @@ -361,22 +361,22 @@ relationship: GENO:0000968 GENO:0000152 ! sequence role reference [Term] id: GENO:0000037 -name: obsolete_unspecified feature +name: obsolete unspecified feature def: "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus)." [] comment: An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). -is_a: ObsoleteClass property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000116 "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '." xsd:string property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class def: 'genomic feature'\n and (has_sequence_attribute some unspecified)" xsd:string +is_obsolete: true [Term] id: GENO:0000042 -name: obsolete_reference junction +name: obsolete reference junction def: "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature." [] comment: In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction.\n\nThe junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. -is_a: ObsoleteClass property_value: IAO:0000118 "hemizygous reference junction" xsd:string property_value: IAO:0000231 "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" xsd:string +is_obsolete: true [Term] id: GENO:0000047 @@ -407,18 +407,18 @@ relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus [Term] id: GENO:0000060 -name: obsolete_reference gene allele +name: obsolete reference gene allele def: "A version/allele of a gene that serves as a standard against which variant genes are compared." [] comment: Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. -is_a: ObsoleteClass property_value: IAO:0000112 "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development.\nhttp://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690\n\nNote that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469" xsd:string property_value: IAO:0000118 "reference gene" xsd:string property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" xsd:string +is_obsolete: true [Term] id: GENO:0000091 -name: obsolete_experimental insertion -is_a: ObsoleteClass +name: obsolete experimental insertion +is_obsolete: true [Term] id: GENO:0000092 @@ -488,9 +488,9 @@ relationship: RO:0002351 NCBITaxon:7955 ! has member Danio rerio [Term] id: GENO:0000125 -name: obsolete_sequence feature collection attribute +name: obsolete sequence feature collection attribute def: "sequence attribute that can inhere only in a collection of more than one sequence features" [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000131 @@ -568,10 +568,10 @@ property_value: IAO:0000118 "phenotypic inheritance pattern" xsd:string [Term] id: GENO:0000142 -name: obsolete_dominant inheritance +name: obsolete dominant inheritance def: "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes" [] -is_a: ObsoleteClass property_value: IAO:0000231 "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." xsd:string +is_obsolete: true [Term] id: GENO:0000143 @@ -624,9 +624,9 @@ is_a: GENO:0000936 ! X-linked inheritance [Term] id: GENO:0000150 -name: obsolete_autosomal recessive inheritance -is_a: ObsoleteClass +name: obsolete autosomal recessive inheritance property_value: IAO:0000231 "duplicate term, use GENO:0000148" xsd:string +is_obsolete: true [Term] id: GENO:0000152 @@ -640,11 +640,61 @@ id: GENO:0000160 name: unspecified life cycle stage is_a: UBERON:0000105 ! life cycle stage +[Term] +id: GENO:0000164 +name: obsolete genetic insertion technique +is_obsolete: true + +[Term] +id: GENO:0000165 +name: obsolete mutagen treatment technique +is_obsolete: true + +[Term] +id: GENO:0000166 +name: obsolete targeted gene mutation technique +is_obsolete: true + +[Term] +id: GENO:0000169 +name: obsolete random genetic insertion technique +is_obsolete: true + +[Term] +id: GENO:0000170 +name: obsolete targeted genetic insertion technique +is_obsolete: true + +[Term] +id: GENO:0000171 +name: obsolete enhancer trapping technique +is_obsolete: true + +[Term] +id: GENO:0000172 +name: obsolete gene trapping technique +is_obsolete: true + +[Term] +id: GENO:0000173 +name: obsolete promoter trapping technique +is_obsolete: true + +[Term] +id: GENO:0000174 +name: obsolete targeted knock-in technique +is_obsolete: true + +[Term] +id: GENO:0000175 +name: obsolete random transgene insertion technique +is_obsolete: true + [Term] id: GENO:0000324 -name: obsolete_chromosome complement +name: obsolete chromosome complement def: "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome" [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000338 @@ -748,11 +798,11 @@ property_value: IAO:0000118 "trans-heterozygous" xsd:string [Term] id: GENO:0000415 -name: obsolete_reagent sequence feature +name: obsolete reagent sequence feature def: "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)" [] -is_a: ObsoleteClass property_value: IAO:0000116 "replaced with SO:engineered_region" xsd:string property_value: IAO:0000118 "extra-genomic sequence" xsd:string +is_obsolete: true [Term] id: GENO:0000458 @@ -811,13 +861,13 @@ property_value: IAO:0000114 GENO:0000484 [Term] id: GENO:0000491 -name: obsolete_mutant allele +name: obsolete mutant allele def: "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain." [] comment: 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. -is_a: ObsoleteClass property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000119 "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" xsd:string property_value: IAO:0000231 "Not required for any specific use case at this point so removed for simplicity. \nFormely asserted as allele and inferred as varaint allele. \nEq class definition:\nallele\n and (mutation or ('has subsequence' some mutation))" xsd:string +is_obsolete: true [Term] id: GENO:0000492 @@ -1266,11 +1316,11 @@ relationship: GENO:0000207 GENO:0000910 ! has_sequence_attribute reporter [Term] id: GENO:0000680 -name: obsolete_null feature +name: obsolete null feature def: "A genomic feature that has an extent of zero." [] -is_a: ObsoleteClass property_value: IAO:0000112 "A junction between bases, a deletion variant, a terminus at the end of a chromosome." xsd:string property_value: IAO:0000116 "Former logical def: \n'genomic feature'\n and (has_extent value 0)" xsd:string +is_obsolete: true [Term] id: GENO:0000681 @@ -1391,13 +1441,13 @@ relationship: GENO:0000783 GENO:0000782 ! has_sequence_unit amino acid residue [Term] id: GENO:0000724 -name: obsolete_biological sequence or collection -is_a: ObsoleteClass +name: obsolete biological sequence or collection +is_obsolete: true [Term] id: GENO:0000725 -name: obsolete_biological sequence collection -is_a: GENO:0000724 ! obsolete_biological sequence or collection +name: obsolete biological sequence collection +is_obsolete: true [Term] id: GENO:0000736 @@ -1415,12 +1465,12 @@ is_a: GENO:0000714 ! qualified genomic feature [Term] id: GENO:0000768 -name: obsolete_genomic position +name: obsolete genomic position def: "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence." [] -is_a: ObsoleteClass property_value: IAO:0000116 "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature." xsd:string property_value: IAO:0000118 "genomic coordinates" xsd:string property_value: IAO:0000231 "remodeling notion of sequence feature position around the idea of a 'genomic locus'" xsd:string +is_obsolete: true [Term] id: GENO:0000770 @@ -1430,9 +1480,9 @@ property_value: IAO:0000114 GENO:0000484 [Term] id: GENO:0000772 -name: obsolete_unspecified +name: obsolete unspecified def: "A sequence attribute inhering in a feature whose identity is not specified." [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000773 @@ -1452,10 +1502,10 @@ relationship: IAO:0000219 GENO:0000033 ! denotes variant genome [Term] id: GENO:0000778 -name: obsolete_sequence information entity +name: obsolete sequence information entity def: "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities." [] -is_a: ObsoleteClass property_value: IAO:0000231 "eliminating classes that are not necessary or add uneeded complexity." xsd:string +is_obsolete: true [Term] id: GENO:0000779 @@ -1534,11 +1584,11 @@ relationship: GENO:0000382 GENO:0000504 ! has_variant_part reagent targeted gene [Term] id: GENO:0000848 -name: obsolete_coding sequence alteration +name: obsolete coding sequence alteration def: "A sequence alteration within the coding sequence of a gene." [] -is_a: ObsoleteClass property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000231 "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." xsd:string +is_obsolete: true [Term] id: GENO:0000850 @@ -1563,10 +1613,10 @@ property_value: IAO:0000118 "non-integrated transgene" xsd:string [Term] id: GENO:0000870 -name: obsolete_sequence feature collection +name: obsolete sequence feature collection def: "A collection of more than one sequence feature." [] xref: http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000871 @@ -1606,13 +1656,13 @@ is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000876 -name: obsolete_genetic dosage +name: obsolete genetic dosage comment: Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. -is_a: ObsoleteClass property_value: IAO:0000118 "allelic dosage" xsd:string property_value: IAO:0000118 "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome." xsd:string property_value: IAO:0000118 "gene dosage" xsd:string property_value: IAO:0000231 "Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute." xsd:string +is_obsolete: true [Term] id: GENO:0000877 @@ -1661,11 +1711,11 @@ property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/di [Term] id: GENO:0000883 -name: obsolete_gametic +name: obsolete gametic def: "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells)." [] -is_a: ObsoleteClass property_value: IAO:0000118 "germ-line" xsd:string property_value: IAO:0000231 "replaced by GENO:0000900 ! 'germline'" xsd:string +is_obsolete: true [Term] id: GENO:0000885 @@ -1707,26 +1757,26 @@ property_value: IAO:0000118 "unknown inheritance" xsd:string [Term] id: GENO:0000890 -name: obsolete_canonical allele +name: obsolete canonical allele def: "One of a set of sequence features or haplotypes that exist at a particular genetic locus. " [] comment: As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand.\n\nIn the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) -is_a: ObsoleteClass property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string property_value: IAO:0000112 "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." xsd:string property_value: IAO:0000116 "The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/ xsd:string property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs." xsd:string +is_obsolete: true [Term] id: GENO:0000891 -name: obsolete_contextual allele +name: obsolete contextual allele def: "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence." [] comment: The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. -is_a: ObsoleteClass property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string property_value: IAO:0000116 "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ xsd:string property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.\n\nFormer axiom: denotes some 'obsolete_canonical allele'" xsd:string +is_obsolete: true [Term] id: GENO:0000892 @@ -1774,11 +1824,11 @@ property_value: IAO:0000118 "complete genotype" xsd:string [Term] id: GENO:0000901 -name: obsolete_allele cellular context +name: obsolete allele cellular context def: "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)" [] comment: Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. -is_a: ObsoleteClass property_value: IAO:0000231 "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin" xsd:string +is_obsolete: true [Term] id: GENO:0000902 @@ -1809,11 +1859,13 @@ is_a: SO:0000110 ! sequence_feature [Term] id: GENO:0000910 +name: obsolete reporter role name: reporter is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000911 +name: obsolete selectable marker role name: selectable marker is_a: GENO:0000788 ! sequence feature attribute @@ -1831,22 +1883,22 @@ relationship: GENO:0000239 SO:0001505 ! has_sequence reference genome sequence [Term] id: GENO:0000915 -name: obsolete_haplotype +name: obsolete haplotype def: "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it." [] comment: 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. -is_a: ObsoleteClass property_value: IAO:0000116 "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"" xsd:string property_value: IAO:0000119 "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype." xsd:string property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" xsd:string +is_obsolete: true [Term] id: GENO:0000916 -name: obsolete_haplotype block +name: obsolete haplotype block def: "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations." [] comment: A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.\n\nThe boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.\n\n-----------------------\n\n* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. -is_a: ObsoleteClass property_value: IAO:0000119 "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." xsd:string property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets." xsd:string +is_obsolete: true [Term] id: GENO:0000918 @@ -1889,27 +1941,27 @@ is_a: GENO:0000921 ! biological sequence or set [Term] id: GENO:0000923 -name: obsolete_functional copy number complement +name: obsolete functional copy number complement def: "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome." [] comment: As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). comment: The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. -is_a: ObsoleteClass property_value: IAO:0000116 "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"" xsd:string property_value: IAO:0000118 "functional feature complement" xsd:string property_value: IAO:0000118 "genetic dosage" xsd:string property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." xsd:string +is_obsolete: true [Term] id: GENO:0000924 -name: obsolete_intrinsic sequence feature attribute +name: obsolete intrinsic sequence feature attribute def: "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form." [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000925 -name: obsolete_extrinsic sequence feature attribute +name: obsolete extrinsic sequence feature attribute def: "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)" [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000926 @@ -2094,20 +2146,20 @@ is_a: GENO:0000660 ! genomic feature set [Term] id: GENO:0000955 -name: obsolete_variant copy number complement +name: obsolete variant copy number complement def: "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s)." [] comment: In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. -is_a: GENO:0000956 ! obsolete_copy number complement property_value: IAO:0000118 "copy number variation" xsd:string property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level." xsd:string +is_obsolete: true [Term] id: GENO:0000956 -name: obsolete_copy number complement +name: obsolete copy number complement def: "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger." [] comment: 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. -is_a: ObsoleteClass property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." xsd:string +is_obsolete: true [Term] id: GENO:0000960 @@ -2504,11 +2556,11 @@ property_value: IAO:0000116 "Stub class to serve as root of hierarchy for import [Term] id: PATO:0000016 -name: obsolete_color brightness -is_a: ObsoleteClass +name: obsolete color brightness property_value: IAO:0000116 "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html" xsd:string property_value: IAO:0000116 "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." xsd:string property_value: IAO:0000118 "color value" xsd:string +is_obsolete: true [Term] id: PATO:0000383 @@ -2589,15 +2641,15 @@ property_value: IAO:0000116 "GENO defines three levels of sequence-related artif [Term] id: SO:0000143 -name: obsolete_assembly_component +name: obsolete assembly_component def: "A region of known length which may be used to manufacture a longer region." [] -is_a: SO:0001410 ! obsolete_experimental_feature +is_obsolete: true [Term] id: SO:0000149 -name: obsolete_contig +name: obsolete contig def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [] -is_a: SO:0000143 ! obsolete_assembly_component +is_obsolete: true [Term] id: SO:0000159 @@ -2694,9 +2746,9 @@ is_a: SO:0000830 ! chromosome part [Term] id: SO:0000637 -name: obsolete_engineered_plasmid -is_a: ObsoleteClass +name: obsolete engineered_plasmid property_value: IAO:0000116 "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." xsd:string +is_obsolete: true [Term] id: SO:0000667 @@ -2832,10 +2884,10 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl [Term] id: SO:0001410 -name: obsolete_experimental_feature +name: obsolete experimental_feature def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [] -is_a: ObsoleteClass property_value: IAO:0000231 "not currently needed to support modeling use cases. can re-introduce if becomes necessary." xsd:string +is_obsolete: true [Term] id: SO:0001477 @@ -3615,7 +3667,7 @@ inverse_of: GENO:0000661 ! is_sex_agnostic_part_of id: GENO:0000651 name: is_mutant_allele_of comment: A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of. -domain: GENO:0000491 ! obsolete_mutant allele +domain: GENO:0000491 ! obsolete mutant allele is_a: GENO:0000641 ! is_variant_allele_of [Typedef] diff --git a/geno-full.owl b/geno-full.owl index 76a3d66..94be182 100644 --- a/geno-full.owl +++ b/geno-full.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 @@ -3141,11 +3141,11 @@ A genomic feature being an allele_of a gene is based on its location in a host g - a collection more than one sequence features (ie a collection of discontinuous sequence features) perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one) 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. - obsolete_sequence feature collection + obsolete sequence feature collection + true @@ -3153,12 +3153,12 @@ A genomic feature being an allele_of a gene is based on its location in a host g - A sequence feature collection comprised of discontiguous sequences from a single genome Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system. genomic feature collection Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. - obsolete_genomic feature collection + obsolete genomic feature collection + true @@ -3166,7 +3166,6 @@ A genomic feature being an allele_of a gene is based on its location in a host g - A single locus complement that serves as a standard against which 'variant' sequences are compared reference allelic complement reference single locus feature complement @@ -3180,7 +3179,8 @@ SC axioms: 'has member' exactly 0 'variant allele' 'has member' only 'reference genomic feature' 'has member' some 'reference genomic feature' - obsolete_reference single locus complement + obsolete reference single locus complement + true @@ -3283,7 +3283,6 @@ In model organism datasets, 'reference' alleles are typically (but not - A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus). Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '. @@ -3292,7 +3291,8 @@ In model organism datasets, 'reference' alleles are typically (but not Eq Class def: 'genomic feature' and (has_sequence_attribute some unspecified) An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). - obsolete_unspecified feature + obsolete unspecified feature + true @@ -3300,7 +3300,6 @@ Eq Class def: 'genomic feature' - A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature. hemizygous reference junction Eliminating unecessary defined/organizational classes. Former logical def: @@ -3313,7 +3312,8 @@ is_variant_with some insertion In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. - obsolete_reference junction + obsolete reference junction + true @@ -3402,7 +3402,6 @@ The junction-insertion pair represents the allelic complement at that locus, whi - A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development. http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690 @@ -3421,7 +3420,8 @@ is_reference_allele_of some gene Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. - obsolete_reference gene allele + obsolete reference gene allele + true @@ -3429,8 +3429,8 @@ In model organism datasets, 'reference' genes are typically the ' - - obsolete_experimental insertion + obsolete experimental insertion + true @@ -3573,9 +3573,9 @@ Note that at present, a material genome and genetic material are necessarily par - sequence attribute that can inhere only in a collection of more than one sequence features - obsolete_sequence feature collection attribute + obsolete sequence feature collection attribute + true @@ -3722,10 +3722,10 @@ These genetic and environmental "interactions" of alleles play out at - disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes Triage until decide if want to define this as grouping class that would result in multiple-inheritance. - obsolete_dominant inheritance + obsolete dominant inheritance + true @@ -3810,9 +3810,9 @@ These genetic and environmental "interactions" of alleles play out at - duplicate term, use GENO:0000148 - obsolete_autosomal recessive inheritance + obsolete autosomal recessive inheritance + true @@ -3837,12 +3837,102 @@ These genetic and environmental "interactions" of alleles play out at + + + + obsolete genetic insertion technique + true + + + + + + + + obsolete mutagen treatment technique + true + + + + + + + + obsolete targeted gene mutation technique + true + + + + + + + + obsolete random genetic insertion technique + true + + + + + + + + obsolete targeted genetic insertion technique + true + + + + + + + + obsolete enhancer trapping technique + true + + + + + + + + obsolete gene trapping technique + true + + + + + + + + obsolete promoter trapping technique + true + + + + + + + + obsolete targeted knock-in technique + true + + + + + + + + obsolete random transgene insertion technique + true + + + + - A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome - obsolete_chromosome complement + obsolete chromosome complement + true @@ -4029,11 +4119,11 @@ Similarly, large sequence features lost from genome are akin to deletions and th - A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe) replaced with SO:engineered_region extra-genomic sequence - obsolete_reagent sequence feature + obsolete reagent sequence feature + true @@ -4166,7 +4256,6 @@ Similarly, large sequence features lost from genome are akin to deletions and th - An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain. Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines @@ -4176,7 +4265,8 @@ Eq class definition: allele and (mutation or ('has subsequence' some mutation)) 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. - obsolete_mutant allele + obsolete mutant allele + true @@ -5159,13 +5249,13 @@ The notion of a 'genomic feature set' differs from that of a 'gen - A junction between bases, a deletion variant, a terminus at the end of a chromosome. A genomic feature that has an extent of zero. Former logical def: 'genomic feature' and (has_extent value 0) - obsolete_null feature + obsolete null feature + true @@ -5505,8 +5595,8 @@ A complements may contain 0, 1, or more than one members. For example, the compl - - obsolete_biological sequence or collection + obsolete biological sequence or collection + true @@ -5514,8 +5604,8 @@ A complements may contain 0, 1, or more than one members. For example, the compl - - obsolete_biological sequence collection + obsolete biological sequence collection + true @@ -5545,12 +5635,12 @@ A complements may contain 0, 1, or more than one members. For example, the compl - A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence. This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature. genomic coordinates remodeling notion of sequence feature position around the idea of a 'genomic locus' - obsolete_genomic position + obsolete genomic position + true @@ -5568,9 +5658,9 @@ A complements may contain 0, 1, or more than one members. For example, the compl - A sequence attribute inhering in a feature whose identity is not specified. - obsolete_unspecified + obsolete unspecified + true @@ -5616,10 +5706,10 @@ A complements may contain 0, 1, or more than one members. For example, the compl - An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities. eliminating classes that are not necessary or add uneeded complexity. - obsolete_sequence information entity + obsolete sequence information entity + true @@ -5909,12 +5999,12 @@ This contrasts to the use of the term 'genotype in model orgnaism communiti - A sequence alteration within the coding sequence of a gene. Not required at this poitn, so marked exploratory and obsoleted. Asserted under sequence_alteration. - obsolete_coding sequence alteration + obsolete coding sequence alteration + true @@ -5957,10 +6047,10 @@ Constructs are typically packaged as part of delivery systems such as plasmids - A collection of more than one sequence feature. http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection - obsolete_sequence feature collection + obsolete sequence feature collection + true @@ -6041,7 +6131,6 @@ Each of these more specific definition serves a purpose for a particular type of - allelic dosage an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome. gene dosage @@ -6049,7 +6138,8 @@ Each of these more specific definition serves a purpose for a particular type of Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. - obsolete_genetic dosage + obsolete genetic dosage + true @@ -6130,11 +6220,11 @@ These acquired mutations are called 'somatic' because they typically a - a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells). germ-line replaced by GENO:0000900 ! 'germline' - obsolete_gametic + obsolete gametic + true @@ -6253,7 +6343,6 @@ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/< - The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”. One of a set of sequence features or haplotypes that exist at a particular genetic locus. <see ClinGen Allele Model> The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. @@ -6263,7 +6352,8 @@ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/< As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) - obsolete_canonical allele + obsolete canonical allele + true @@ -6271,7 +6361,6 @@ In the ClinGen allele model, 'canonical alleles are contrasted with ' - An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence. The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ @@ -6280,7 +6369,8 @@ In the ClinGen allele model, 'canonical alleles are contrasted with ' Former axiom: denotes some 'obsolete_canonical allele' ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. - obsolete_contextual allele + obsolete contextual allele + true @@ -6416,11 +6506,11 @@ A genomic genotype is an information artifact with a representational syntax tha - A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells) decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. - obsolete_allele cellular context + obsolete allele cellular context + true @@ -6491,6 +6581,7 @@ For example, we would define an 'HLA gene block' as a subclass of &ap + obsolete reporter role reporter @@ -6500,6 +6591,7 @@ For example, we would define an 'HLA gene block' as a subclass of &ap + obsolete selectable marker role selectable marker @@ -6533,7 +6625,6 @@ For example, we would define an 'HLA gene block' as a subclass of &ap - A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it. Former comment: "Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project." Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype. @@ -6555,7 +6646,8 @@ b. The second is a region containing multiple linked single nucleotide polymorph c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. - obsolete_haplotype + obsolete haplotype + true @@ -6563,7 +6655,6 @@ The GENO definition of 'haplotype' is broadly inclusive of these and a - A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations. Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block. Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. @@ -6574,7 +6665,8 @@ The boundaries of haplotype blocks are defined in efforts to identify haplotypes ----------------------- * One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. - obsolete_haplotype block + obsolete haplotype block + true @@ -6656,7 +6748,6 @@ A set may also include multiple copies of the same sequence. For example, in a & - A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome. Formerly considered modeling this as an informational entity, defined as "An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome." functional feature complement @@ -6664,7 +6755,8 @@ A set may also include multiple copies of the same sequence. For example, in a & Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963. As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. - obsolete_functional copy number complement + obsolete functional copy number complement + true @@ -6672,9 +6764,9 @@ A set may also include multiple copies of the same sequence. For example, in a & - A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form. - obsolete_intrinsic sequence feature attribute + obsolete intrinsic sequence feature attribute + true @@ -6682,9 +6774,9 @@ A set may also include multiple copies of the same sequence. For example, in a & - A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.) - obsolete_extrinsic sequence feature attribute + obsolete extrinsic sequence feature attribute + true @@ -6977,14 +7069,14 @@ A set may also include multiple copies of the same sequence. For example, in a & - A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s). copy number variation Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. - obsolete_variant copy number complement + obsolete variant copy number complement + true @@ -6992,7 +7084,6 @@ Note that the 'copy number variation' class in GENO is related to but - A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger. Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961. 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. @@ -7000,7 +7091,8 @@ Note that the 'copy number variation' class in GENO is related to but 2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. 3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. - obsolete_copy number complement + obsolete copy number complement + true @@ -7678,11 +7770,11 @@ No imports - 'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute. color value - obsolete_color brightness + obsolete color brightness + true @@ -7828,9 +7920,9 @@ chromosome > arm > band > sub-band > sub-sub-band - A region of known length which may be used to manufacture a longer region. - obsolete_assembly_component + obsolete assembly_component + true @@ -7838,9 +7930,9 @@ chromosome > arm > band > sub-band > sub-sub-band - A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. - obsolete_contig + obsolete contig + true @@ -8016,9 +8108,9 @@ chromosome > arm > band > sub-band > sub-sub-band - Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct. - obsolete_engineered_plasmid + obsolete engineered_plasmid + true @@ -8289,10 +8381,10 @@ For a particular instance of a sequence alteration, howver, we may in some cases - A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. not currently needed to support modeling use cases. can re-introduce if becomes necessary. - obsolete_experimental_feature + obsolete experimental_feature + true @@ -8982,12 +9074,6 @@ For a particular instance of a sequence alteration, howver, we may in some cases - - - - - - diff --git a/geno.json b/geno.json index 17c0383..44da360 100644 --- a/geno.json +++ b/geno.json @@ -57,6 +57,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared." @@ -66,7 +69,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_reference gene allele" + "lbl" : "obsolete reference gene allele" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000057", "meta" : { @@ -165,6 +168,36 @@ }, "type" : "CLASS", "lbl" : "SNV" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000173", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete promoter trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000172", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete gene trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000175", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete random transgene insertion technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000054", "meta" : { @@ -175,6 +208,16 @@ }, "type" : "CLASS", "lbl" : "homo sapiens gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000174", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete targeted knock-in technique" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000016", "meta" : { @@ -184,13 +227,16 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "color value" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." } ] }, "type" : "CLASS", - "lbl" : "obsolete_color brightness" + "lbl" : "obsolete color brightness" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002162", "meta" : { @@ -201,6 +247,26 @@ }, "type" : "PROPERTY", "lbl" : "in taxon" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000171", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete enhancer trapping technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000170", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete targeted genetic insertion technique" }, { "id" : "http://www.ncbi.nlm.nih.gov/gene/6469", "meta" : { @@ -214,6 +280,36 @@ }, "type" : "CLASS", "lbl" : "homo sapiens SHH gene" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000169", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete random genetic insertion technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000166", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete targeted gene mutation technique" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000165", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete mutagen treatment technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000047", "meta" : { @@ -266,10 +362,14 @@ "definition" : { "val" : "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_contig" + "lbl" : "obsolete contig" }, { "id" : "http://purl.obolibrary.org/obo/SO_0001479", "meta" : { @@ -1143,8 +1243,14 @@ "lbl" : "gene trap insertion" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000091", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, "type" : "CLASS", - "lbl" : "obsolete_experimental insertion" + "lbl" : "obsolete experimental insertion" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000093", "meta" : { @@ -2067,6 +2173,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations." @@ -2076,7 +2185,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_haplotype" + "lbl" : "obsolete haplotype" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000914", "meta" : { @@ -2130,10 +2239,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_haplotype block" + "lbl" : "obsolete haplotype block" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000911", "type" : "CLASS", @@ -2285,6 +2397,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others." }, { @@ -2293,7 +2408,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_allele cellular context" + "lbl" : "obsolete allele cellular context" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", "meta" : { @@ -2671,10 +2786,14 @@ "definition" : { "val" : "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_extrinsic sequence feature attribute" + "lbl" : "obsolete extrinsic sequence feature attribute" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000928", "meta" : { @@ -2729,10 +2848,14 @@ "definition" : { "val" : "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form.", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_intrinsic sequence feature attribute" + "lbl" : "obsolete intrinsic sequence feature attribute" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000923", "meta" : { @@ -2758,10 +2881,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_functional copy number complement" + "lbl" : "obsolete functional copy number complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000953", "meta" : { @@ -2873,13 +2999,16 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "copy number variation" } ] }, "type" : "CLASS", - "lbl" : "obsolete_variant copy number complement" + "lbl" : "obsolete variant copy number complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000713", "meta" : { @@ -2972,13 +3101,16 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members." } ] }, "type" : "CLASS", - "lbl" : "obsolete_copy number complement" + "lbl" : "obsolete copy number complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000714", "meta" : { @@ -4035,13 +4167,16 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/GENO_0000484" } ] }, "type" : "CLASS", - "lbl" : "obsolete_coding sequence alteration" + "lbl" : "obsolete coding sequence alteration" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000606", "type" : "CLASS", @@ -4113,10 +4248,6 @@ }, "type" : "PROPERTY", "lbl" : "has_interval" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000724", - "type" : "CLASS", - "lbl" : "obsolete_biological sequence or collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000603", "meta" : { @@ -4127,6 +4258,16 @@ }, "type" : "CLASS", "lbl" : "heteroplasmic" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000724", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete biological sequence or collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000602", "meta" : { @@ -4241,6 +4382,16 @@ }, "type" : "PROPERTY", "lbl" : "sequence role" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000725", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete biological sequence collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000967", "meta" : { @@ -4251,10 +4402,6 @@ }, "type" : "PROPERTY", "lbl" : "has_reference_sequence" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000725", - "type" : "CLASS", - "lbl" : "obsolete_biological sequence collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000604", "type" : "CLASS", @@ -4410,6 +4557,9 @@ "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "allelic dosage" @@ -4425,7 +4575,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_genetic dosage" + "lbl" : "obsolete genetic dosage" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000875", "meta" : { @@ -4469,10 +4619,14 @@ }, "xrefs" : [ { "val" : "http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence feature collection" + "lbl" : "obsolete sequence feature collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000872", "meta" : { @@ -5257,6 +5411,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." @@ -5266,7 +5423,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_contextual allele" + "lbl" : "obsolete contextual allele" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000410", "meta" : { @@ -5331,6 +5488,20 @@ }, "type" : "CLASS", "lbl" : "homoplasmic mitochondrial inheritance" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000772", + "meta" : { + "definition" : { + "val" : "A sequence attribute inhering in a feature whose identity is not specified.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete unspecified" }, { "id" : "http://purl.obolibrary.org/obo/ZP_0005692", "type" : "CLASS", @@ -5345,26 +5516,19 @@ }, "type" : "PROPERTY", "lbl" : "is_mutant_allele_of" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000772", - "meta" : { - "definition" : { - "val" : "A sequence attribute inhering in a feature whose identity is not specified.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "obsolete_unspecified" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000637", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." } ] }, "type" : "CLASS", - "lbl" : "obsolete_engineered_plasmid" + "lbl" : "obsolete engineered_plasmid" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000779", "meta" : { @@ -5388,13 +5552,16 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "replaced with SO:engineered_region" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "extra-genomic sequence" } ] }, "type" : "CLASS", - "lbl" : "obsolete_reagent sequence feature" + "lbl" : "obsolete reagent sequence feature" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000778", "meta" : { @@ -5405,10 +5572,13 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "eliminating classes that are not necessary or add uneeded complexity." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence information entity" + "lbl" : "obsolete sequence information entity" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000536", "meta" : { @@ -5503,6 +5673,9 @@ }, { "pred" : "http://purl.org/dc/terms/source", "val" : "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." @@ -5518,7 +5691,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_canonical allele" + "lbl" : "obsolete canonical allele" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000885", "meta" : { @@ -5680,10 +5853,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "germ-line" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_gametic" + "lbl" : "obsolete gametic" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000641", "meta" : { @@ -5803,6 +5979,16 @@ }, "type" : "PROPERTY", "lbl" : "is_allele_of" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000647", + "meta" : { + "definition" : { + "val" : "A genomic genotype here the genomic background specifies a female sex chromosome complement.", + "xrefs" : [ ] + } + }, + "type" : "CLASS", + "lbl" : "female intrinsic genotype" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000768", "meta" : { @@ -5816,23 +6002,16 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "remodeling notion of sequence feature position around the idea of a 'genomic locus'" + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "genomic coordinates" } ] }, "type" : "CLASS", - "lbl" : "obsolete_genomic position" - }, { - "id" : "http://purl.obolibrary.org/obo/GENO_0000647", - "meta" : { - "definition" : { - "val" : "A genomic genotype here the genomic background specifies a female sex chromosome complement.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "female intrinsic genotype" + "lbl" : "obsolete genomic position" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000889", "meta" : { @@ -6001,6 +6180,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Former logical def: \n'genomic feature'\n and (has_extent value 0)" }, { @@ -6009,7 +6191,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_null feature" + "lbl" : "obsolete null feature" }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", "type" : "CLASS", @@ -6400,12 +6582,15 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "not currently needed to support modeling use cases. can re-introduce if becomes necessary." } ] }, "type" : "CLASS", - "lbl" : "obsolete_experimental_feature" + "lbl" : "obsolete experimental_feature" }, { "id" : "http://biohackathon.org/resource/faldo#location", "type" : "PROPERTY", @@ -6559,10 +6744,14 @@ "definition" : { "val" : "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_chromosome complement" + "lbl" : "obsolete chromosome complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000447", "meta" : { @@ -7494,12 +7683,15 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." } ] }, "type" : "CLASS", - "lbl" : "obsolete_dominant inheritance" + "lbl" : "obsolete dominant inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000141", "meta" : { @@ -7725,12 +7917,15 @@ "val" : "perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one)" } ], "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions." } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence feature collection" + "lbl" : "obsolete sequence feature collection" }, { "id" : "http://purl.obolibrary.org/obo/SO_0000110", "meta" : { @@ -7810,6 +8005,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" }, { @@ -7824,7 +8022,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_mutant allele" + "lbl" : "obsolete mutant allele" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000010", "meta" : { @@ -7919,10 +8117,14 @@ "definition" : { "val" : "sequence attribute that can inhere only in a collection of more than one sequence features", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_sequence feature collection attribute" + "lbl" : "obsolete sequence feature collection attribute" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000488", "meta" : { @@ -8201,10 +8403,24 @@ "definition" : { "val" : "A region of known length which may be used to manufacture a longer region.", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] + }, + "type" : "CLASS", + "lbl" : "obsolete assembly_component" + }, { + "id" : "http://purl.obolibrary.org/obo/GENO_0000164", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + } ] }, "type" : "CLASS", - "lbl" : "obsolete_assembly_component" + "lbl" : "obsolete genetic insertion technique" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000042", "meta" : { @@ -8213,6 +8429,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" }, { @@ -8224,7 +8443,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_reference junction" + "lbl" : "obsolete reference junction" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000160", "type" : "CLASS", @@ -8242,6 +8461,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/GENO_0000484" @@ -8251,7 +8473,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_unspecified feature" + "lbl" : "obsolete unspecified feature" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000033", "meta" : { @@ -8344,12 +8566,15 @@ "id" : "http://purl.obolibrary.org/obo/GENO_0000150", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "duplicate term, use GENO:0000148" } ] }, "type" : "CLASS", - "lbl" : "obsolete_autosomal recessive inheritance" + "lbl" : "obsolete autosomal recessive inheritance" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000394", "type" : "CLASS", @@ -8407,6 +8632,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "reference allelic complement" }, { @@ -8418,7 +8646,7 @@ } ] }, "type" : "CLASS", - "lbl" : "obsolete_reference single locus complement" + "lbl" : "obsolete reference single locus complement" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000149", "meta" : { @@ -8462,10 +8690,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system." + }, { + "pred" : "http://www.w3.org/2002/07/owl#deprecated", + "val" : "true" } ] }, "type" : "CLASS", - "lbl" : "obsolete_genomic feature collection" + "lbl" : "obsolete genomic feature collection" }, { "id" : "http://purl.obolibrary.org/obo/GENO_0000143", "meta" : { @@ -8704,10 +8935,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000343", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000830" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000016", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000721", "pred" : "is_a", @@ -8832,10 +9059,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000391", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000876", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000619", "pred" : "is_a", @@ -9124,10 +9347,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_8000009", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_8000006" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000916", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000242", "pred" : "inverseOf", @@ -9136,10 +9355,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000640", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000638" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0000143", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0001410" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000629", "pred" : "is_a", @@ -9152,10 +9367,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000392", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000133" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000324", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000402", "pred" : "is_a", @@ -9240,10 +9451,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000147", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000934" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000150", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/ZP_0000755", "pred" : "is_a", @@ -9276,10 +9483,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000948", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000935" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000768", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000645", "pred" : "http://purl.obolibrary.org/obo/GENO_0000650", @@ -9320,10 +9523,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000018" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000724", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "is_a", @@ -9368,10 +9567,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000823", "pred" : "http://purl.obolibrary.org/obo/IAO_0000219", "obj" : "http://purl.obolibrary.org/obo/GENO_0000516" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000029", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000393", "pred" : "is_a", @@ -9380,14 +9575,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000684", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000924", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000870", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000642", "pred" : "is_a", @@ -9440,10 +9627,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000410", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000883", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000794", "pred" : "subPropertyOf", @@ -9636,10 +9819,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_1000026", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_1000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000923", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000108", "pred" : "is_a", @@ -9912,10 +10091,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000654", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000415", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000054", "pred" : "is_a", @@ -10024,10 +10199,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000652", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000641" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000890", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000930", "pred" : "is_a", @@ -10080,10 +10251,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0003303", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003302" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000125", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000030", "pred" : "http://purl.obolibrary.org/obo/GENO_0000382", @@ -10184,10 +10351,6 @@ "sub" : "http://purl.org/oban/association", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000778", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000741", "pred" : "subPropertyOf", @@ -10224,10 +10387,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000339", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000346" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000142", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000841", "pred" : "subPropertyOf", @@ -10264,10 +10423,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000383", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000655" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000680", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000777", "pred" : "is_a", @@ -10324,10 +10479,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000969", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000141" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000956", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0100026", "pred" : "is_a", @@ -10344,10 +10495,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000899" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000022", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000494", "pred" : "is_a", @@ -10360,10 +10507,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000486", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000925", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000005", "pred" : "is_a", @@ -10528,10 +10671,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000965", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000725", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000724" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000660", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -10600,22 +10739,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000943", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000942" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000848", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000955", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000956" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000032", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001059" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0000637", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000248", "pred" : "is_a", @@ -10664,10 +10791,6 @@ "sub" : "http://purl.obolibrary.org/obo/ENVO_01000254", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000915", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_1000009", "pred" : "is_a", @@ -10676,10 +10799,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000093", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0000902" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000772", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/HsapDv_0000000", "pred" : "is_a", @@ -10704,10 +10823,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000410", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/IAO_0000409" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000091", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000621", "pred" : "is_a", @@ -10784,10 +10899,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000911", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000788" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000060", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://biohackathon.org/resource/faldo#BothStrandsPosition", "pred" : "is_a", @@ -10832,18 +10943,10 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000928", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000926" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000042", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000529", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000737" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000491", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000418", "pred" : "inverseOf", @@ -10896,10 +10999,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000914", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/SO_0001026" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000891", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000604", "pred" : "is_a", @@ -10916,14 +11015,14 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000919", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000713" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000720", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000720", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GENO_0000702" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0001059", "pred" : "http://purl.obolibrary.org/obo/GENO_0000784", @@ -10940,10 +11039,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000091", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000053" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000901", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000144", "pred" : "is_a", @@ -10984,10 +11079,6 @@ "sub" : "http://purl.obolibrary.org/obo/SO_0000341", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GENO_0000614" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000037", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://biohackathon.org/resource/faldo#reference", "pred" : "subPropertyOf", @@ -11000,10 +11091,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000761", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/GENO_0000655" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0000149", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/SO_0000143" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000368", "pred" : "subPropertyOf", @@ -11044,10 +11131,6 @@ "sub" : "http://biohackathon.org/resource/faldo#ForwardStrandPosition", "pred" : "is_a", "obj" : "http://biohackathon.org/resource/faldo#StrandedPosition" - }, { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000019", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/SO_0000341", "pred" : "http://purl.obolibrary.org/obo/GENO_0000207", @@ -11172,10 +11255,6 @@ "sub" : "http://purl.obolibrary.org/obo/GENO_0000646", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GENO_0000645" - }, { - "sub" : "http://purl.obolibrary.org/obo/SO_0001410", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000253", "pred" : "subPropertyOf", @@ -11219,7 +11298,7 @@ "pred" : "http://purl.org/dc/terms/license", "val" : "Unspecified" } ], - "version" : "http://purl.obolibrary.org/obo/geno/releases/2020-03-07/geno.json" + "version" : "http://purl.obolibrary.org/obo/geno/releases/2020-03-08/geno.json" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { @@ -11400,13 +11479,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { "sub" : "http://purl.obolibrary.org/obo/GENO_0000887", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_8090" + }, { + "sub" : "http://purl.obolibrary.org/obo/GENO_0000119", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/GENO_0000368", diff --git a/geno.obo b/geno.obo index 3b47a98..4fcd049 100644 --- a/geno.obo +++ b/geno.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2020-03-07 +data-version: releases/2020-03-08 ontology: geno property_value: http://purl.org/dc/elements/1.1/description "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" xsd:string property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string @@ -303,29 +303,29 @@ property_value: IAO:0000118 "reference sequence" xsd:string [Term] id: GENO:0000019 -name: obsolete_sequence feature collection +name: obsolete sequence feature collection def: "a collection more than one sequence features (ie a collection of discontinuous sequence features)" [] comment: 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. xref: perhaps not same as SO:sequence collection\, as here we explicitly include features that can have an extent of zero (and SO\:sequence collection is a collection of regions that have an extent of at least one) -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000022 -name: obsolete_genomic feature collection +name: obsolete genomic feature collection def: "A sequence feature collection comprised of discontiguous sequences from a single genome" [] comment: Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. -is_a: ObsoleteClass property_value: IAO:0000116 "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system." xsd:string property_value: IAO:0000118 "genomic feature collection" xsd:string +is_obsolete: true [Term] id: GENO:0000029 -name: obsolete_reference single locus complement +name: obsolete reference single locus complement def: "A single locus complement that serves as a standard against which 'variant' sequences are compared" [] -is_a: ObsoleteClass property_value: IAO:0000118 "reference allelic complement" xsd:string property_value: IAO:0000118 "reference single locus feature complement" xsd:string property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'single locus complement'\n and (has_sequence_attribute some reference)\n\nSC axioms:\n'has member' exactly 0 'variant allele'\n'has member' only 'reference genomic feature'\n'has member' some 'reference genomic feature'" xsd:string +is_obsolete: true [Term] id: GENO:0000030 @@ -361,22 +361,22 @@ relationship: GENO:0000968 GENO:0000152 ! sequence role reference [Term] id: GENO:0000037 -name: obsolete_unspecified feature +name: obsolete unspecified feature def: "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus)." [] comment: An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). -is_a: ObsoleteClass property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000116 "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '." xsd:string property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class def: 'genomic feature'\n and (has_sequence_attribute some unspecified)" xsd:string +is_obsolete: true [Term] id: GENO:0000042 -name: obsolete_reference junction +name: obsolete reference junction def: "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature." [] comment: In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction.\n\nThe junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. -is_a: ObsoleteClass property_value: IAO:0000118 "hemizygous reference junction" xsd:string property_value: IAO:0000231 "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion" xsd:string +is_obsolete: true [Term] id: GENO:0000047 @@ -407,18 +407,18 @@ relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus [Term] id: GENO:0000060 -name: obsolete_reference gene allele +name: obsolete reference gene allele def: "A version/allele of a gene that serves as a standard against which variant genes are compared." [] comment: Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. -is_a: ObsoleteClass property_value: IAO:0000112 "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development.\nhttp://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690\n\nNote that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469" xsd:string property_value: IAO:0000118 "reference gene" xsd:string property_value: IAO:0000231 "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene" xsd:string +is_obsolete: true [Term] id: GENO:0000091 -name: obsolete_experimental insertion -is_a: ObsoleteClass +name: obsolete experimental insertion +is_obsolete: true [Term] id: GENO:0000092 @@ -488,9 +488,9 @@ relationship: RO:0002351 NCBITaxon:7955 ! has member Danio rerio [Term] id: GENO:0000125 -name: obsolete_sequence feature collection attribute +name: obsolete sequence feature collection attribute def: "sequence attribute that can inhere only in a collection of more than one sequence features" [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000131 @@ -568,10 +568,10 @@ property_value: IAO:0000118 "phenotypic inheritance pattern" xsd:string [Term] id: GENO:0000142 -name: obsolete_dominant inheritance +name: obsolete dominant inheritance def: "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes" [] -is_a: ObsoleteClass property_value: IAO:0000231 "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." xsd:string +is_obsolete: true [Term] id: GENO:0000143 @@ -624,9 +624,9 @@ is_a: GENO:0000936 ! X-linked inheritance [Term] id: GENO:0000150 -name: obsolete_autosomal recessive inheritance -is_a: ObsoleteClass +name: obsolete autosomal recessive inheritance property_value: IAO:0000231 "duplicate term, use GENO:0000148" xsd:string +is_obsolete: true [Term] id: GENO:0000152 @@ -640,11 +640,61 @@ id: GENO:0000160 name: unspecified life cycle stage is_a: UBERON:0000105 ! life cycle stage +[Term] +id: GENO:0000164 +name: obsolete genetic insertion technique +is_obsolete: true + +[Term] +id: GENO:0000165 +name: obsolete mutagen treatment technique +is_obsolete: true + +[Term] +id: GENO:0000166 +name: obsolete targeted gene mutation technique +is_obsolete: true + +[Term] +id: GENO:0000169 +name: obsolete random genetic insertion technique +is_obsolete: true + +[Term] +id: GENO:0000170 +name: obsolete targeted genetic insertion technique +is_obsolete: true + +[Term] +id: GENO:0000171 +name: obsolete enhancer trapping technique +is_obsolete: true + +[Term] +id: GENO:0000172 +name: obsolete gene trapping technique +is_obsolete: true + +[Term] +id: GENO:0000173 +name: obsolete promoter trapping technique +is_obsolete: true + +[Term] +id: GENO:0000174 +name: obsolete targeted knock-in technique +is_obsolete: true + +[Term] +id: GENO:0000175 +name: obsolete random transgene insertion technique +is_obsolete: true + [Term] id: GENO:0000324 -name: obsolete_chromosome complement +name: obsolete chromosome complement def: "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome" [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000338 @@ -748,11 +798,11 @@ property_value: IAO:0000118 "trans-heterozygous" xsd:string [Term] id: GENO:0000415 -name: obsolete_reagent sequence feature +name: obsolete reagent sequence feature def: "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)" [] -is_a: ObsoleteClass property_value: IAO:0000116 "replaced with SO:engineered_region" xsd:string property_value: IAO:0000118 "extra-genomic sequence" xsd:string +is_obsolete: true [Term] id: GENO:0000458 @@ -811,13 +861,13 @@ property_value: IAO:0000114 GENO:0000484 [Term] id: GENO:0000491 -name: obsolete_mutant allele +name: obsolete mutant allele def: "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain." [] comment: 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. -is_a: ObsoleteClass property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000119 "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" xsd:string property_value: IAO:0000231 "Not required for any specific use case at this point so removed for simplicity. \nFormely asserted as allele and inferred as varaint allele. \nEq class definition:\nallele\n and (mutation or ('has subsequence' some mutation))" xsd:string +is_obsolete: true [Term] id: GENO:0000492 @@ -1266,11 +1316,11 @@ relationship: GENO:0000207 GENO:0000910 ! has_sequence_attribute reporter [Term] id: GENO:0000680 -name: obsolete_null feature +name: obsolete null feature def: "A genomic feature that has an extent of zero." [] -is_a: ObsoleteClass property_value: IAO:0000112 "A junction between bases, a deletion variant, a terminus at the end of a chromosome." xsd:string property_value: IAO:0000116 "Former logical def: \n'genomic feature'\n and (has_extent value 0)" xsd:string +is_obsolete: true [Term] id: GENO:0000681 @@ -1391,13 +1441,13 @@ relationship: GENO:0000783 GENO:0000782 ! has_sequence_unit amino acid residue [Term] id: GENO:0000724 -name: obsolete_biological sequence or collection -is_a: ObsoleteClass +name: obsolete biological sequence or collection +is_obsolete: true [Term] id: GENO:0000725 -name: obsolete_biological sequence collection -is_a: GENO:0000724 ! obsolete_biological sequence or collection +name: obsolete biological sequence collection +is_obsolete: true [Term] id: GENO:0000736 @@ -1415,12 +1465,12 @@ is_a: GENO:0000714 ! qualified genomic feature [Term] id: GENO:0000768 -name: obsolete_genomic position +name: obsolete genomic position def: "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence." [] -is_a: ObsoleteClass property_value: IAO:0000116 "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature." xsd:string property_value: IAO:0000118 "genomic coordinates" xsd:string property_value: IAO:0000231 "remodeling notion of sequence feature position around the idea of a 'genomic locus'" xsd:string +is_obsolete: true [Term] id: GENO:0000770 @@ -1430,9 +1480,9 @@ property_value: IAO:0000114 GENO:0000484 [Term] id: GENO:0000772 -name: obsolete_unspecified +name: obsolete unspecified def: "A sequence attribute inhering in a feature whose identity is not specified." [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000773 @@ -1452,10 +1502,10 @@ relationship: IAO:0000219 GENO:0000033 ! denotes variant genome [Term] id: GENO:0000778 -name: obsolete_sequence information entity +name: obsolete sequence information entity def: "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities." [] -is_a: ObsoleteClass property_value: IAO:0000231 "eliminating classes that are not necessary or add uneeded complexity." xsd:string +is_obsolete: true [Term] id: GENO:0000779 @@ -1534,11 +1584,11 @@ relationship: GENO:0000382 GENO:0000504 ! has_variant_part reagent targeted gene [Term] id: GENO:0000848 -name: obsolete_coding sequence alteration +name: obsolete coding sequence alteration def: "A sequence alteration within the coding sequence of a gene." [] -is_a: ObsoleteClass property_value: IAO:0000114 GENO:0000484 property_value: IAO:0000231 "Not required at this poitn, so marked exploratory and obsoleted. \nAsserted under sequence_alteration." xsd:string +is_obsolete: true [Term] id: GENO:0000850 @@ -1563,10 +1613,10 @@ property_value: IAO:0000118 "non-integrated transgene" xsd:string [Term] id: GENO:0000870 -name: obsolete_sequence feature collection +name: obsolete sequence feature collection def: "A collection of more than one sequence feature." [] xref: http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000871 @@ -1606,13 +1656,13 @@ is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000876 -name: obsolete_genetic dosage +name: obsolete genetic dosage comment: Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. -is_a: ObsoleteClass property_value: IAO:0000118 "allelic dosage" xsd:string property_value: IAO:0000118 "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome." xsd:string property_value: IAO:0000118 "gene dosage" xsd:string property_value: IAO:0000231 "Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute." xsd:string +is_obsolete: true [Term] id: GENO:0000877 @@ -1661,11 +1711,11 @@ property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/di [Term] id: GENO:0000883 -name: obsolete_gametic +name: obsolete gametic def: "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells)." [] -is_a: ObsoleteClass property_value: IAO:0000118 "germ-line" xsd:string property_value: IAO:0000231 "replaced by GENO:0000900 ! 'germline'" xsd:string +is_obsolete: true [Term] id: GENO:0000885 @@ -1707,26 +1757,26 @@ property_value: IAO:0000118 "unknown inheritance" xsd:string [Term] id: GENO:0000890 -name: obsolete_canonical allele +name: obsolete canonical allele def: "One of a set of sequence features or haplotypes that exist at a particular genetic locus. " [] comment: As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand.\n\nIn the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) -is_a: ObsoleteClass property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string property_value: IAO:0000112 "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." xsd:string property_value: IAO:0000116 "The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/ xsd:string property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs." xsd:string +is_obsolete: true [Term] id: GENO:0000891 -name: obsolete_contextual allele +name: obsolete contextual allele def: "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence." [] comment: The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. -is_a: ObsoleteClass property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string property_value: IAO:0000116 "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string property_value: IAO:0000119 http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ xsd:string property_value: IAO:0000231 "No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.\n\nFormer axiom: denotes some 'obsolete_canonical allele'" xsd:string +is_obsolete: true [Term] id: GENO:0000892 @@ -1774,11 +1824,11 @@ property_value: IAO:0000118 "complete genotype" xsd:string [Term] id: GENO:0000901 -name: obsolete_allele cellular context +name: obsolete allele cellular context def: "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)" [] comment: Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. -is_a: ObsoleteClass property_value: IAO:0000231 "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin" xsd:string +is_obsolete: true [Term] id: GENO:0000902 @@ -1809,11 +1859,13 @@ is_a: SO:0000110 ! sequence_feature [Term] id: GENO:0000910 +name: obsolete reporter role name: reporter is_a: GENO:0000788 ! sequence feature attribute [Term] id: GENO:0000911 +name: obsolete selectable marker role name: selectable marker is_a: GENO:0000788 ! sequence feature attribute @@ -1831,22 +1883,22 @@ relationship: GENO:0000239 SO:0001505 ! has_sequence reference genome sequence [Term] id: GENO:0000915 -name: obsolete_haplotype +name: obsolete haplotype def: "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it." [] comment: 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. -is_a: ObsoleteClass property_value: IAO:0000116 "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"" xsd:string property_value: IAO:0000119 "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype." xsd:string property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" xsd:string +is_obsolete: true [Term] id: GENO:0000916 -name: obsolete_haplotype block +name: obsolete haplotype block def: "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations." [] comment: A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.\n\nThe boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.\n\n-----------------------\n\n* One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. -is_a: ObsoleteClass property_value: IAO:0000119 "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." xsd:string property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets." xsd:string +is_obsolete: true [Term] id: GENO:0000918 @@ -1889,27 +1941,27 @@ is_a: GENO:0000921 ! biological sequence or set [Term] id: GENO:0000923 -name: obsolete_functional copy number complement +name: obsolete functional copy number complement def: "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome." [] comment: As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). comment: The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. -is_a: ObsoleteClass property_value: IAO:0000116 "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"" xsd:string property_value: IAO:0000118 "functional feature complement" xsd:string property_value: IAO:0000118 "genetic dosage" xsd:string property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." xsd:string +is_obsolete: true [Term] id: GENO:0000924 -name: obsolete_intrinsic sequence feature attribute +name: obsolete intrinsic sequence feature attribute def: "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form." [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000925 -name: obsolete_extrinsic sequence feature attribute +name: obsolete extrinsic sequence feature attribute def: "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)" [] -is_a: ObsoleteClass +is_obsolete: true [Term] id: GENO:0000926 @@ -2094,20 +2146,20 @@ is_a: GENO:0000660 ! genomic feature set [Term] id: GENO:0000955 -name: obsolete_variant copy number complement +name: obsolete variant copy number complement def: "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s)." [] comment: In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. -is_a: GENO:0000956 ! obsolete_copy number complement property_value: IAO:0000118 "copy number variation" xsd:string property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level." xsd:string +is_obsolete: true [Term] id: GENO:0000956 -name: obsolete_copy number complement +name: obsolete copy number complement def: "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger." [] comment: 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. -is_a: ObsoleteClass property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." xsd:string +is_obsolete: true [Term] id: GENO:0000960 @@ -2504,11 +2556,11 @@ property_value: IAO:0000116 "Stub class to serve as root of hierarchy for import [Term] id: PATO:0000016 -name: obsolete_color brightness -is_a: ObsoleteClass +name: obsolete color brightness property_value: IAO:0000116 "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html" xsd:string property_value: IAO:0000116 "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." xsd:string property_value: IAO:0000118 "color value" xsd:string +is_obsolete: true [Term] id: PATO:0000383 @@ -2589,15 +2641,15 @@ property_value: IAO:0000116 "GENO defines three levels of sequence-related artif [Term] id: SO:0000143 -name: obsolete_assembly_component +name: obsolete assembly_component def: "A region of known length which may be used to manufacture a longer region." [] -is_a: SO:0001410 ! obsolete_experimental_feature +is_obsolete: true [Term] id: SO:0000149 -name: obsolete_contig +name: obsolete contig def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [] -is_a: SO:0000143 ! obsolete_assembly_component +is_obsolete: true [Term] id: SO:0000159 @@ -2694,9 +2746,9 @@ is_a: SO:0000830 ! chromosome part [Term] id: SO:0000637 -name: obsolete_engineered_plasmid -is_a: ObsoleteClass +name: obsolete engineered_plasmid property_value: IAO:0000116 "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." xsd:string +is_obsolete: true [Term] id: SO:0000667 @@ -2832,10 +2884,10 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl [Term] id: SO:0001410 -name: obsolete_experimental_feature +name: obsolete experimental_feature def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [] -is_a: ObsoleteClass property_value: IAO:0000231 "not currently needed to support modeling use cases. can re-introduce if becomes necessary." xsd:string +is_obsolete: true [Term] id: SO:0001477 @@ -3615,7 +3667,7 @@ inverse_of: GENO:0000661 ! is_sex_agnostic_part_of id: GENO:0000651 name: is_mutant_allele_of comment: A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of. -domain: GENO:0000491 ! obsolete_mutant allele +domain: GENO:0000491 ! obsolete mutant allele is_a: GENO:0000641 ! is_variant_allele_of [Typedef] diff --git a/geno.owl b/geno.owl index 8064b49..ebbd4a4 100644 --- a/geno.owl +++ b/geno.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 @@ -3141,11 +3141,11 @@ A genomic feature being an allele_of a gene is based on its location in a host g - a collection more than one sequence features (ie a collection of discontinuous sequence features) perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one) 1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions. - obsolete_sequence feature collection + obsolete sequence feature collection + true @@ -3153,12 +3153,12 @@ A genomic feature being an allele_of a gene is based on its location in a host g - A sequence feature collection comprised of discontiguous sequences from a single genome Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system. genomic feature collection Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection. - obsolete_genomic feature collection + obsolete genomic feature collection + true @@ -3166,7 +3166,6 @@ A genomic feature being an allele_of a gene is based on its location in a host g - A single locus complement that serves as a standard against which 'variant' sequences are compared reference allelic complement reference single locus feature complement @@ -3180,7 +3179,8 @@ SC axioms: 'has member' exactly 0 'variant allele' 'has member' only 'reference genomic feature' 'has member' some 'reference genomic feature' - obsolete_reference single locus complement + obsolete reference single locus complement + true @@ -3283,7 +3283,6 @@ In model organism datasets, 'reference' alleles are typically (but not - A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus). Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '. @@ -3292,7 +3291,8 @@ In model organism datasets, 'reference' alleles are typically (but not Eq Class def: 'genomic feature' and (has_sequence_attribute some unspecified) An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele). - obsolete_unspecified feature + obsolete unspecified feature + true @@ -3300,7 +3300,6 @@ Eq Class def: 'genomic feature' - A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature. hemizygous reference junction Eliminating unecessary defined/organizational classes. Former logical def: @@ -3313,7 +3312,8 @@ is_variant_with some insertion In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation. - obsolete_reference junction + obsolete reference junction + true @@ -3402,7 +3402,6 @@ The junction-insertion pair represents the allelic complement at that locus, whi - A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development. http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690 @@ -3421,7 +3420,8 @@ is_reference_allele_of some gene Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared. - obsolete_reference gene allele + obsolete reference gene allele + true @@ -3429,8 +3429,8 @@ In model organism datasets, 'reference' genes are typically the ' - - obsolete_experimental insertion + obsolete experimental insertion + true @@ -3573,9 +3573,9 @@ Note that at present, a material genome and genetic material are necessarily par - sequence attribute that can inhere only in a collection of more than one sequence features - obsolete_sequence feature collection attribute + obsolete sequence feature collection attribute + true @@ -3722,10 +3722,10 @@ These genetic and environmental "interactions" of alleles play out at - disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes Triage until decide if want to define this as grouping class that would result in multiple-inheritance. - obsolete_dominant inheritance + obsolete dominant inheritance + true @@ -3810,9 +3810,9 @@ These genetic and environmental "interactions" of alleles play out at - duplicate term, use GENO:0000148 - obsolete_autosomal recessive inheritance + obsolete autosomal recessive inheritance + true @@ -3837,12 +3837,102 @@ These genetic and environmental "interactions" of alleles play out at + + + + obsolete genetic insertion technique + true + + + + + + + + obsolete mutagen treatment technique + true + + + + + + + + obsolete targeted gene mutation technique + true + + + + + + + + obsolete random genetic insertion technique + true + + + + + + + + obsolete targeted genetic insertion technique + true + + + + + + + + obsolete enhancer trapping technique + true + + + + + + + + obsolete gene trapping technique + true + + + + + + + + obsolete promoter trapping technique + true + + + + + + + + obsolete targeted knock-in technique + true + + + + + + + + obsolete random transgene insertion technique + true + + + + - A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome - obsolete_chromosome complement + obsolete chromosome complement + true @@ -4029,11 +4119,11 @@ Similarly, large sequence features lost from genome are akin to deletions and th - A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe) replaced with SO:engineered_region extra-genomic sequence - obsolete_reagent sequence feature + obsolete reagent sequence feature + true @@ -4166,7 +4256,6 @@ Similarly, large sequence features lost from genome are akin to deletions and th - An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain. Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines @@ -4176,7 +4265,8 @@ Eq class definition: allele and (mutation or ('has subsequence' some mutation)) 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line. - obsolete_mutant allele + obsolete mutant allele + true @@ -5159,13 +5249,13 @@ The notion of a 'genomic feature set' differs from that of a 'gen - A junction between bases, a deletion variant, a terminus at the end of a chromosome. A genomic feature that has an extent of zero. Former logical def: 'genomic feature' and (has_extent value 0) - obsolete_null feature + obsolete null feature + true @@ -5505,8 +5595,8 @@ A complements may contain 0, 1, or more than one members. For example, the compl - - obsolete_biological sequence or collection + obsolete biological sequence or collection + true @@ -5514,8 +5604,8 @@ A complements may contain 0, 1, or more than one members. For example, the compl - - obsolete_biological sequence collection + obsolete biological sequence collection + true @@ -5545,12 +5635,12 @@ A complements may contain 0, 1, or more than one members. For example, the compl - A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence. This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature. genomic coordinates remodeling notion of sequence feature position around the idea of a 'genomic locus' - obsolete_genomic position + obsolete genomic position + true @@ -5568,9 +5658,9 @@ A complements may contain 0, 1, or more than one members. For example, the compl - A sequence attribute inhering in a feature whose identity is not specified. - obsolete_unspecified + obsolete unspecified + true @@ -5616,10 +5706,10 @@ A complements may contain 0, 1, or more than one members. For example, the compl - An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities. eliminating classes that are not necessary or add uneeded complexity. - obsolete_sequence information entity + obsolete sequence information entity + true @@ -5909,12 +5999,12 @@ This contrasts to the use of the term 'genotype in model orgnaism communiti - A sequence alteration within the coding sequence of a gene. Not required at this poitn, so marked exploratory and obsoleted. Asserted under sequence_alteration. - obsolete_coding sequence alteration + obsolete coding sequence alteration + true @@ -5957,10 +6047,10 @@ Constructs are typically packaged as part of delivery systems such as plasmids - A collection of more than one sequence feature. http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection - obsolete_sequence feature collection + obsolete sequence feature collection + true @@ -6041,7 +6131,6 @@ Each of these more specific definition serves a purpose for a particular type of - allelic dosage an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome. gene dosage @@ -6049,7 +6138,8 @@ Each of these more specific definition serves a purpose for a particular type of Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found. - obsolete_genetic dosage + obsolete genetic dosage + true @@ -6130,11 +6220,11 @@ These acquired mutations are called 'somatic' because they typically a - a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells). germ-line replaced by GENO:0000900 ! 'germline' - obsolete_gametic + obsolete gametic + true @@ -6253,7 +6343,6 @@ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/< - The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”. One of a set of sequence features or haplotypes that exist at a particular genetic locus. <see ClinGen Allele Model> The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. @@ -6263,7 +6352,8 @@ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/< As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references) - obsolete_canonical allele + obsolete canonical allele + true @@ -6271,7 +6361,6 @@ In the ClinGen allele model, 'canonical alleles are contrasted with ' - An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence. The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/). It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model. http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/ @@ -6280,7 +6369,8 @@ In the ClinGen allele model, 'canonical alleles are contrasted with ' Former axiom: denotes some 'obsolete_canonical allele' ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/) The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene. - obsolete_contextual allele + obsolete contextual allele + true @@ -6416,11 +6506,11 @@ A genomic genotype is an information artifact with a representational syntax tha - A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells) decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others. - obsolete_allele cellular context + obsolete allele cellular context + true @@ -6491,6 +6581,7 @@ For example, we would define an 'HLA gene block' as a subclass of &ap + obsolete reporter role reporter @@ -6500,6 +6591,7 @@ For example, we would define an 'HLA gene block' as a subclass of &ap + obsolete selectable marker role selectable marker @@ -6533,7 +6625,6 @@ For example, we would define an 'HLA gene block' as a subclass of &ap - A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it. Former comment: "Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project." Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype. @@ -6555,7 +6646,8 @@ b. The second is a region containing multiple linked single nucleotide polymorph c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations. - obsolete_haplotype + obsolete haplotype + true @@ -6563,7 +6655,6 @@ The GENO definition of 'haplotype' is broadly inclusive of these and a - A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations. Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block. Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. @@ -6574,7 +6665,8 @@ The boundaries of haplotype blocks are defined in efforts to identify haplotypes ----------------------- * One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces. - obsolete_haplotype block + obsolete haplotype block + true @@ -6656,7 +6748,6 @@ A set may also include multiple copies of the same sequence. For example, in a & - A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome. Formerly considered modeling this as an informational entity, defined as "An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome." functional feature complement @@ -6664,7 +6755,8 @@ A set may also include multiple copies of the same sequence. For example, in a & Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963. As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage). The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage. - obsolete_functional copy number complement + obsolete functional copy number complement + true @@ -6672,9 +6764,9 @@ A set may also include multiple copies of the same sequence. For example, in a & - A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, but are independent of how it may be concretized in physical form. - obsolete_intrinsic sequence feature attribute + obsolete intrinsic sequence feature attribute + true @@ -6682,9 +6774,9 @@ A set may also include multiple copies of the same sequence. For example, in a & - A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.) - obsolete_extrinsic sequence feature attribute + obsolete extrinsic sequence feature attribute + true @@ -6977,14 +7069,14 @@ A set may also include multiple copies of the same sequence. For example, in a & - A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s). copy number variation Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class. - obsolete_variant copy number complement + obsolete variant copy number complement + true @@ -6992,7 +7084,6 @@ Note that the 'copy number variation' class in GENO is related to but - A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome. Such features are typically on the scale of complete genes or larger. Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961. 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. @@ -7000,7 +7091,8 @@ Note that the 'copy number variation' class in GENO is related to but 2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. 3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members. - obsolete_copy number complement + obsolete copy number complement + true @@ -7678,11 +7770,11 @@ No imports - 'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute. color value - obsolete_color brightness + obsolete color brightness + true @@ -7828,9 +7920,9 @@ chromosome > arm > band > sub-band > sub-sub-band - A region of known length which may be used to manufacture a longer region. - obsolete_assembly_component + obsolete assembly_component + true @@ -7838,9 +7930,9 @@ chromosome > arm > band > sub-band > sub-sub-band - A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. - obsolete_contig + obsolete contig + true @@ -8016,9 +8108,9 @@ chromosome > arm > band > sub-band > sub-sub-band - Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct. - obsolete_engineered_plasmid + obsolete engineered_plasmid + true @@ -8289,10 +8381,10 @@ For a particular instance of a sequence alteration, howver, we may in some cases - A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. not currently needed to support modeling use cases. can re-introduce if becomes necessary. - obsolete_experimental_feature + obsolete experimental_feature + true @@ -8982,12 +9074,6 @@ For a particular instance of a sequence alteration, howver, we may in some cases - - - - - - diff --git a/reports/geno-edit.owl-obo-report.tsv b/reports/geno-edit.owl-obo-report.tsv index 6312b9e..5ec2453 100644 --- a/reports/geno-edit.owl-obo-report.tsv +++ b/reports/geno-edit.owl-obo-report.tsv @@ -5,59 +5,23 @@ ERROR duplicate_definition GENO:0000846 IAO:0000115 A relation used to describe ERROR duplicate_definition GENO:0000874 IAO:0000115 A relation used to describe a process contextualizing the identity of an entity. ERROR duplicate_definition GENO:0000719 IAO:0000115 A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. ERROR duplicate_definition GENO:0000899 IAO:0000115 A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. -ERROR misused_obsolete_label GENO:0000019 rdfs:label obsolete_sequence feature collection -ERROR misused_obsolete_label GENO:0000022 rdfs:label obsolete_genomic feature collection -ERROR misused_obsolete_label GENO:0000029 rdfs:label obsolete_reference single locus complement -ERROR misused_obsolete_label GENO:0000037 rdfs:label obsolete_unspecified feature -ERROR misused_obsolete_label GENO:0000042 rdfs:label obsolete_reference junction -ERROR misused_obsolete_label GENO:0000060 rdfs:label obsolete_reference gene allele -ERROR misused_obsolete_label GENO:0000091 rdfs:label obsolete_experimental insertion -ERROR misused_obsolete_label GENO:0000125 rdfs:label obsolete_sequence feature collection attribute -ERROR misused_obsolete_label GENO:0000142 rdfs:label obsolete_dominant inheritance -ERROR misused_obsolete_label GENO:0000150 rdfs:label obsolete_autosomal recessive inheritance ERROR misused_obsolete_label GENO:0000242 rdfs:label obsolete_specifies ERROR misused_obsolete_label GENO:0000243 rdfs:label obsolete_approximates_sequence ERROR misused_obsolete_label GENO:0000244 rdfs:label obsolete_resolves_to_sequence ERROR misused_obsolete_label GENO:0000253 rdfs:label obsolete_is_specified_by -ERROR misused_obsolete_label GENO:0000324 rdfs:label obsolete_chromosome complement ERROR misused_obsolete_label GENO:0000359 rdfs:label obsolete_is_phenotype_of_genotype ERROR misused_obsolete_label GENO:0000368 rdfs:label obsolete_participates_in_inheritance_process ERROR misused_obsolete_label GENO:0000410 rdfs:label obsolete_is_genetic_variant_of ERROR misused_obsolete_label GENO:0000411 rdfs:label obsolete_has_genetic_variant -ERROR misused_obsolete_label GENO:0000415 rdfs:label obsolete_reagent sequence feature ERROR misused_obsolete_label GENO:0000486 rdfs:label obsolete_is_variant_with@en ERROR misused_obsolete_label GENO:0000488 rdfs:label obsolete_is_expression_variant_with@en -ERROR misused_obsolete_label GENO:0000491 rdfs:label obsolete_mutant allele -ERROR misused_obsolete_label GENO:0000680 rdfs:label obsolete_null feature@en ERROR misused_obsolete_label GENO:0000712 rdfs:label ObsoleteDataProperty@en -ERROR misused_obsolete_label GENO:0000724 rdfs:label obsolete_biological sequence or collection@en -ERROR misused_obsolete_label GENO:0000725 rdfs:label obsolete_biological sequence collection@en ERROR misused_obsolete_label GENO:0000741 rdfs:label obsolete_has_regulatory_part@en ERROR misused_obsolete_label GENO:0000742 rdfs:label obsolete_is_alteration_within@en ERROR misused_obsolete_label GENO:0000767 rdfs:label obsolete_has_position_component@en -ERROR misused_obsolete_label GENO:0000768 rdfs:label obsolete_genomic position -ERROR misused_obsolete_label GENO:0000772 rdfs:label obsolete_unspecified@en -ERROR misused_obsolete_label GENO:0000778 rdfs:label obsolete_sequence information entity@en -ERROR misused_obsolete_label GENO:0000848 rdfs:label obsolete_coding sequence alteration@en -ERROR misused_obsolete_label GENO:0000870 rdfs:label obsolete_sequence feature collection@en -ERROR misused_obsolete_label GENO:0000876 rdfs:label obsolete_genetic dosage@en -ERROR misused_obsolete_label GENO:0000883 rdfs:label obsolete_gametic@en -ERROR misused_obsolete_label GENO:0000890 rdfs:label obsolete_canonical allele -ERROR misused_obsolete_label GENO:0000891 rdfs:label obsolete_contextual allele -ERROR misused_obsolete_label GENO:0000901 rdfs:label obsolete_allele cellular context -ERROR misused_obsolete_label GENO:0000915 rdfs:label obsolete_haplotype@en -ERROR misused_obsolete_label GENO:0000916 rdfs:label obsolete_haplotype block@en -ERROR misused_obsolete_label GENO:0000923 rdfs:label obsolete_functional copy number complement -ERROR misused_obsolete_label GENO:0000924 rdfs:label obsolete_intrinsic sequence feature attribute@en -ERROR misused_obsolete_label GENO:0000925 rdfs:label obsolete_extrinsic sequence feature attribute@en -ERROR misused_obsolete_label GENO:0000955 rdfs:label obsolete_variant copy number complement -ERROR misused_obsolete_label GENO:0000956 rdfs:label obsolete_copy number complement@en -ERROR misused_obsolete_label PATO:0000016 rdfs:label obsolete_color brightness@en +ERROR misused_obsolete_label GENO:0000910 rdfs:label obsolete reporter role@en +ERROR misused_obsolete_label GENO:0000911 rdfs:label obsolete selectable marker role@en ERROR misused_obsolete_label RO:0002354 rdfs:label obsolete_formed as result of@en -ERROR misused_obsolete_label SO:0000143 rdfs:label obsolete_assembly_component@en -ERROR misused_obsolete_label SO:0000149 rdfs:label obsolete_contig@en -ERROR misused_obsolete_label SO:0000637 rdfs:label obsolete_engineered_plasmid@en -ERROR misused_obsolete_label SO:0001410 rdfs:label obsolete_experimental_feature@en ERROR duplicate_label http://biohackathon.org/resource/faldo#reference rdfs:label reference ERROR duplicate_label GENO:0000152 rdfs:label reference ERROR multiple_definitions BFO:0000020 IAO:0000115 b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])@en @@ -84,13 +48,12 @@ ERROR multiple_labels BFO:0000031 rdfs:label generically dependent continuant ERROR multiple_labels BFO:0000031 rdfs:label generically dependent continuant@en ERROR multiple_labels BFO:0000040 rdfs:label material entity ERROR multiple_labels BFO:0000040 rdfs:label material entity@en +ERROR multiple_labels GENO:0000910 rdfs:label obsolete reporter role@en +ERROR multiple_labels GENO:0000910 rdfs:label reporter@en +ERROR multiple_labels GENO:0000911 rdfs:label obsolete selectable marker role@en +ERROR multiple_labels GENO:0000911 rdfs:label selectable marker@en ERROR multiple_labels IAO:0000030 rdfs:label information content entity ERROR multiple_labels IAO:0000030 rdfs:label information content entity@en -WARN duplicate_label_synonym GENO:0000017 IAO:0000118 reference sequence -WARN duplicate_label_synonym GENO:0000501 IAO:0000118 wild-type allele -WARN duplicate_label_synonym SO:0000667 IAO:0000118 insertion -WARN duplicate_label_synonym SO:0001744 IAO:0000118 UPD -WARN duplicate_label_synonym SO:1000036 IAO:0000118 inversion WARN missing_definition http://biohackathon.org/resource/faldo#BothStrandsPosition IAO:0000115 WARN missing_definition http://biohackathon.org/resource/faldo#ForwardStrandPosition IAO:0000115 WARN missing_definition http://biohackathon.org/resource/faldo#ReverseStrandPosition IAO:0000115 @@ -105,7 +68,6 @@ WARN missing_definition CHEBI:23367 IAO:0000115 WARN missing_definition CHEBI:33696 IAO:0000115 WARN missing_definition CL:0000000 IAO:0000115 WARN missing_definition ENVO:01000254 IAO:0000115 -WARN missing_definition GENO:0000091 IAO:0000115 WARN missing_definition GENO:0000092 IAO:0000115 WARN missing_definition GENO:0000113 IAO:0000115 WARN missing_definition GENO:0000118 IAO:0000115 @@ -116,7 +78,6 @@ WARN missing_definition GENO:0000136 IAO:0000115 WARN missing_definition GENO:0000137 IAO:0000115 WARN missing_definition GENO:0000139 IAO:0000115 WARN missing_definition GENO:0000140 IAO:0000115 -WARN missing_definition GENO:0000150 IAO:0000115 WARN missing_definition GENO:0000160 IAO:0000115 WARN missing_definition GENO:0000220 IAO:0000115 WARN missing_definition GENO:0000243 IAO:0000115 @@ -160,8 +121,6 @@ WARN missing_definition GENO:0000712 IAO:0000115 WARN missing_definition GENO:0000720 IAO:0000115 WARN missing_definition GENO:0000721 IAO:0000115 WARN missing_definition GENO:0000722 IAO:0000115 -WARN missing_definition GENO:0000724 IAO:0000115 -WARN missing_definition GENO:0000725 IAO:0000115 WARN missing_definition GENO:0000740 IAO:0000115 WARN missing_definition GENO:0000741 IAO:0000115 WARN missing_definition GENO:0000743 IAO:0000115 @@ -184,7 +143,6 @@ WARN missing_definition GENO:0000844 IAO:0000115 WARN missing_definition GENO:0000845 IAO:0000115 WARN missing_definition GENO:0000849 IAO:0000115 WARN missing_definition GENO:0000867 IAO:0000115 -WARN missing_definition GENO:0000876 IAO:0000115 WARN missing_definition GENO:0000887 IAO:0000115 WARN missing_definition GENO:0000905 IAO:0000115 WARN missing_definition GENO:0000906 IAO:0000115 @@ -204,7 +162,6 @@ WARN missing_definition NCBITaxon:8090 IAO:0000115 WARN missing_definition NCBITaxon:9606 IAO:0000115 WARN missing_definition OBI:0000086 IAO:0000115 WARN missing_definition OBI:0100026 IAO:0000115 -WARN missing_definition PATO:0000016 IAO:0000115 WARN missing_definition PATO:0000383 IAO:0000115 WARN missing_definition PATO:0000384 IAO:0000115 WARN missing_definition PATO:0001894 IAO:0000115 @@ -225,7 +182,6 @@ WARN missing_definition SO:0000248 IAO:0000115 WARN missing_definition SO:0000281 IAO:0000115 WARN missing_definition SO:0000337 IAO:0000115 WARN missing_definition SO:0000577 IAO:0000115 -WARN missing_definition SO:0000637 IAO:0000115 WARN missing_definition SO:0000699 IAO:0000115 WARN missing_definition SO:0000804 IAO:0000115 WARN missing_definition SO:0001785 IAO:0000115 diff --git a/src/ontology/reports/geno-edit.owl-obo-report.tsv b/src/ontology/reports/geno-edit.owl-obo-report.tsv index 6312b9e..5ec2453 100644 --- a/src/ontology/reports/geno-edit.owl-obo-report.tsv +++ b/src/ontology/reports/geno-edit.owl-obo-report.tsv @@ -5,59 +5,23 @@ ERROR duplicate_definition GENO:0000846 IAO:0000115 A relation used to describe ERROR duplicate_definition GENO:0000874 IAO:0000115 A relation used to describe a process contextualizing the identity of an entity. ERROR duplicate_definition GENO:0000719 IAO:0000115 A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. ERROR duplicate_definition GENO:0000899 IAO:0000115 A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype. -ERROR misused_obsolete_label GENO:0000019 rdfs:label obsolete_sequence feature collection -ERROR misused_obsolete_label GENO:0000022 rdfs:label obsolete_genomic feature collection -ERROR misused_obsolete_label GENO:0000029 rdfs:label obsolete_reference single locus complement -ERROR misused_obsolete_label GENO:0000037 rdfs:label obsolete_unspecified feature -ERROR misused_obsolete_label GENO:0000042 rdfs:label obsolete_reference junction -ERROR misused_obsolete_label GENO:0000060 rdfs:label obsolete_reference gene allele -ERROR misused_obsolete_label GENO:0000091 rdfs:label obsolete_experimental insertion -ERROR misused_obsolete_label GENO:0000125 rdfs:label obsolete_sequence feature collection attribute -ERROR misused_obsolete_label GENO:0000142 rdfs:label obsolete_dominant inheritance -ERROR misused_obsolete_label GENO:0000150 rdfs:label obsolete_autosomal recessive inheritance ERROR misused_obsolete_label GENO:0000242 rdfs:label obsolete_specifies ERROR misused_obsolete_label GENO:0000243 rdfs:label obsolete_approximates_sequence ERROR misused_obsolete_label GENO:0000244 rdfs:label obsolete_resolves_to_sequence ERROR misused_obsolete_label GENO:0000253 rdfs:label obsolete_is_specified_by -ERROR misused_obsolete_label GENO:0000324 rdfs:label obsolete_chromosome complement ERROR misused_obsolete_label GENO:0000359 rdfs:label obsolete_is_phenotype_of_genotype ERROR misused_obsolete_label GENO:0000368 rdfs:label obsolete_participates_in_inheritance_process ERROR misused_obsolete_label GENO:0000410 rdfs:label obsolete_is_genetic_variant_of ERROR misused_obsolete_label GENO:0000411 rdfs:label obsolete_has_genetic_variant -ERROR misused_obsolete_label GENO:0000415 rdfs:label obsolete_reagent sequence feature ERROR misused_obsolete_label GENO:0000486 rdfs:label obsolete_is_variant_with@en ERROR misused_obsolete_label GENO:0000488 rdfs:label obsolete_is_expression_variant_with@en -ERROR misused_obsolete_label GENO:0000491 rdfs:label obsolete_mutant allele -ERROR misused_obsolete_label GENO:0000680 rdfs:label obsolete_null feature@en ERROR misused_obsolete_label GENO:0000712 rdfs:label ObsoleteDataProperty@en -ERROR misused_obsolete_label GENO:0000724 rdfs:label obsolete_biological sequence or collection@en -ERROR misused_obsolete_label GENO:0000725 rdfs:label obsolete_biological sequence collection@en ERROR misused_obsolete_label GENO:0000741 rdfs:label obsolete_has_regulatory_part@en ERROR misused_obsolete_label GENO:0000742 rdfs:label obsolete_is_alteration_within@en ERROR misused_obsolete_label GENO:0000767 rdfs:label obsolete_has_position_component@en -ERROR misused_obsolete_label GENO:0000768 rdfs:label obsolete_genomic position -ERROR misused_obsolete_label GENO:0000772 rdfs:label obsolete_unspecified@en -ERROR misused_obsolete_label GENO:0000778 rdfs:label obsolete_sequence information entity@en -ERROR misused_obsolete_label GENO:0000848 rdfs:label obsolete_coding sequence alteration@en -ERROR misused_obsolete_label GENO:0000870 rdfs:label obsolete_sequence feature collection@en -ERROR misused_obsolete_label GENO:0000876 rdfs:label obsolete_genetic dosage@en -ERROR misused_obsolete_label GENO:0000883 rdfs:label obsolete_gametic@en -ERROR misused_obsolete_label GENO:0000890 rdfs:label obsolete_canonical allele -ERROR misused_obsolete_label GENO:0000891 rdfs:label obsolete_contextual allele -ERROR misused_obsolete_label GENO:0000901 rdfs:label obsolete_allele cellular context -ERROR misused_obsolete_label GENO:0000915 rdfs:label obsolete_haplotype@en -ERROR misused_obsolete_label GENO:0000916 rdfs:label obsolete_haplotype block@en -ERROR misused_obsolete_label GENO:0000923 rdfs:label obsolete_functional copy number complement -ERROR misused_obsolete_label GENO:0000924 rdfs:label obsolete_intrinsic sequence feature attribute@en -ERROR misused_obsolete_label GENO:0000925 rdfs:label obsolete_extrinsic sequence feature attribute@en -ERROR misused_obsolete_label GENO:0000955 rdfs:label obsolete_variant copy number complement -ERROR misused_obsolete_label GENO:0000956 rdfs:label obsolete_copy number complement@en -ERROR misused_obsolete_label PATO:0000016 rdfs:label obsolete_color brightness@en +ERROR misused_obsolete_label GENO:0000910 rdfs:label obsolete reporter role@en +ERROR misused_obsolete_label GENO:0000911 rdfs:label obsolete selectable marker role@en ERROR misused_obsolete_label RO:0002354 rdfs:label obsolete_formed as result of@en -ERROR misused_obsolete_label SO:0000143 rdfs:label obsolete_assembly_component@en -ERROR misused_obsolete_label SO:0000149 rdfs:label obsolete_contig@en -ERROR misused_obsolete_label SO:0000637 rdfs:label obsolete_engineered_plasmid@en -ERROR misused_obsolete_label SO:0001410 rdfs:label obsolete_experimental_feature@en ERROR duplicate_label http://biohackathon.org/resource/faldo#reference rdfs:label reference ERROR duplicate_label GENO:0000152 rdfs:label reference ERROR multiple_definitions BFO:0000020 IAO:0000115 b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])@en @@ -84,13 +48,12 @@ ERROR multiple_labels BFO:0000031 rdfs:label generically dependent continuant ERROR multiple_labels BFO:0000031 rdfs:label generically dependent continuant@en ERROR multiple_labels BFO:0000040 rdfs:label material entity ERROR multiple_labels BFO:0000040 rdfs:label material entity@en +ERROR multiple_labels GENO:0000910 rdfs:label obsolete reporter role@en +ERROR multiple_labels GENO:0000910 rdfs:label reporter@en +ERROR multiple_labels GENO:0000911 rdfs:label obsolete selectable marker role@en +ERROR multiple_labels GENO:0000911 rdfs:label selectable marker@en ERROR multiple_labels IAO:0000030 rdfs:label information content entity ERROR multiple_labels IAO:0000030 rdfs:label information content entity@en -WARN duplicate_label_synonym GENO:0000017 IAO:0000118 reference sequence -WARN duplicate_label_synonym GENO:0000501 IAO:0000118 wild-type allele -WARN duplicate_label_synonym SO:0000667 IAO:0000118 insertion -WARN duplicate_label_synonym SO:0001744 IAO:0000118 UPD -WARN duplicate_label_synonym SO:1000036 IAO:0000118 inversion WARN missing_definition http://biohackathon.org/resource/faldo#BothStrandsPosition IAO:0000115 WARN missing_definition http://biohackathon.org/resource/faldo#ForwardStrandPosition IAO:0000115 WARN missing_definition http://biohackathon.org/resource/faldo#ReverseStrandPosition IAO:0000115 @@ -105,7 +68,6 @@ WARN missing_definition CHEBI:23367 IAO:0000115 WARN missing_definition CHEBI:33696 IAO:0000115 WARN missing_definition CL:0000000 IAO:0000115 WARN missing_definition ENVO:01000254 IAO:0000115 -WARN missing_definition GENO:0000091 IAO:0000115 WARN missing_definition GENO:0000092 IAO:0000115 WARN missing_definition GENO:0000113 IAO:0000115 WARN missing_definition GENO:0000118 IAO:0000115 @@ -116,7 +78,6 @@ WARN missing_definition GENO:0000136 IAO:0000115 WARN missing_definition GENO:0000137 IAO:0000115 WARN missing_definition GENO:0000139 IAO:0000115 WARN missing_definition GENO:0000140 IAO:0000115 -WARN missing_definition GENO:0000150 IAO:0000115 WARN missing_definition GENO:0000160 IAO:0000115 WARN missing_definition GENO:0000220 IAO:0000115 WARN missing_definition GENO:0000243 IAO:0000115 @@ -160,8 +121,6 @@ WARN missing_definition GENO:0000712 IAO:0000115 WARN missing_definition GENO:0000720 IAO:0000115 WARN missing_definition GENO:0000721 IAO:0000115 WARN missing_definition GENO:0000722 IAO:0000115 -WARN missing_definition GENO:0000724 IAO:0000115 -WARN missing_definition GENO:0000725 IAO:0000115 WARN missing_definition GENO:0000740 IAO:0000115 WARN missing_definition GENO:0000741 IAO:0000115 WARN missing_definition GENO:0000743 IAO:0000115 @@ -184,7 +143,6 @@ WARN missing_definition GENO:0000844 IAO:0000115 WARN missing_definition GENO:0000845 IAO:0000115 WARN missing_definition GENO:0000849 IAO:0000115 WARN missing_definition GENO:0000867 IAO:0000115 -WARN missing_definition GENO:0000876 IAO:0000115 WARN missing_definition GENO:0000887 IAO:0000115 WARN missing_definition GENO:0000905 IAO:0000115 WARN missing_definition GENO:0000906 IAO:0000115 @@ -204,7 +162,6 @@ WARN missing_definition NCBITaxon:8090 IAO:0000115 WARN missing_definition NCBITaxon:9606 IAO:0000115 WARN missing_definition OBI:0000086 IAO:0000115 WARN missing_definition OBI:0100026 IAO:0000115 -WARN missing_definition PATO:0000016 IAO:0000115 WARN missing_definition PATO:0000383 IAO:0000115 WARN missing_definition PATO:0000384 IAO:0000115 WARN missing_definition PATO:0001894 IAO:0000115 @@ -225,7 +182,6 @@ WARN missing_definition SO:0000248 IAO:0000115 WARN missing_definition SO:0000281 IAO:0000115 WARN missing_definition SO:0000337 IAO:0000115 WARN missing_definition SO:0000577 IAO:0000115 -WARN missing_definition SO:0000637 IAO:0000115 WARN missing_definition SO:0000699 IAO:0000115 WARN missing_definition SO:0000804 IAO:0000115 WARN missing_definition SO:0001785 IAO:0000115