Temp: ordo mappings

monarch-initiative · Mar 27, 2024 · d5b088e · d5b088e
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diff --git a/.gitignore b/.gitignore
@@ -1,132 +1,135 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-.idea/
-tmp/
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+.idea/
+tmp/
+
+# Custom
+_archive/
diff --git a/config/icd11.sssom-metadata.yml b/config/icd11.sssom-metadata.yml
@@ -0,0 +1,19 @@
+creator_id: 0000-0002-2906-7319
+curie_map:
+  GTR: http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/GTR/
+  HP: http://purl.obolibrary.org/obo/HP_
+  MESH: http://identifiers.org/mesh/
+  MONDO: http://purl.obolibrary.org/obo/MONDO_
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  OMIM: https://omim.org/entry/
+  Orphanet: http://www.orpha.net/ORDO/Orphanet_
+  SCTID: http://identifiers.org/snomedct/
+  UMLS: http://purl.obolibrary.org/obo/UMLS_
+  oboInOwl: http://www.geneontology.org/formats/oboInOwl#
+  owl: http://www.w3.org/2002/07/owl#
+  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
+  rdfs: http://www.w3.org/2000/01/rdf-schema#
+  semapv: https://w3id.org/semapv/
+  skos: http://www.w3.org/2004/02/skos/core#
+  sssom: https://w3id.org/sssom/
+license: http://w3id.org/sssom/license/unspecified
diff --git a/makefile b/makefile
@@ -1,46 +1,57 @@
-.DEFAULT_GOAL := all
-.PHONY: all release clean
-TODAY ?=$(shell date +%Y-%m-%d)
-VERSION=v$(TODAY)
-SOURCE_URL=https://icd11files.blob.core.windows.net/tmp/whofic-2023-04-08.owl.gz
-
-
-# MAIN COMMANDS / GOALS ------------------------------------------------------------------------------------------------
-all: tmp/output/release/icd11foundation.owl
-
-clean:
-	rm -rf tmp/
-
-tmp/output/release/icd11foundation.owl: tmp/output/intermediate1-unicode-cleaned.owl
-	robot remove --axioms equivalent -i $< -o $@
-
-# Cleans all unicode characters
-tmp/output/intermediate1-unicode-cleaned.owl: tmp/input/source.owl | tmp/output/release/
-	tr -cd '\11\12\15\40-\176' < $< > $@
-
-tmp/output/release/:
-	mkdir -p $@
-
-tmp/input/:
-	mkdir -p $@
-
-tmp/input/source.owl: tmp/input/source.gz
-	gunzip -c $< > $@
-
-tmp/input/source.gz: | tmp/input/
-	wget ${SOURCE_URL} -O $@
-
-# Requires GitHub CLI: https://cli.github.com/
-release: | tmp/output/release/
-	@test $(VERSION)
-	gh release create $(VERSION) --notes "New release." --title "$(VERSION)" tmp/output/release/*
-
-# HELP -----------------------------------------------------------------------------------------------------------------
-help:
-	@echo "-----------------------------------"
-	@echo "	Command reference: GARD OWL Ingest"
-	@echo "-----------------------------------"
-	@echo "all"
-	@echo "Runs ingest and creates all release artefacts.\n"
-	@echo "release"
-	@echo "Uploads release to GitHub.\n"
+.DEFAULT_GOAL := all
+.PHONY: all release clean
+TODAY ?=$(shell date +%Y-%m-%d)
+VERSION=v$(TODAY)
+SOURCE_URL=https://icd11files.blob.core.windows.net/tmp/whofic-2023-04-08.owl.gz
+
+
+# MAIN COMMANDS / GOALS ------------------------------------------------------------------------------------------------
+all: tmp/output/release/icd11foundation.owl
+
+clean:
+	rm -rf tmp/
+
+tmp/output/release/icd11foundation.owl: tmp/output/intermediate1-unicode-cleaned.owl
+	robot remove --axioms equivalent -i $< -o $@
+
+# Cleans all unicode characters
+tmp/output/intermediate1-unicode-cleaned.owl: tmp/input/source.owl | tmp/output/release/
+	tr -cd '\11\12\15\40-\176' < $< > $@
+
+tmp/output/release/:
+	mkdir -p $@
+
+tmp/input/:
+	mkdir -p $@
+
+tmp/input/source.owl: tmp/input/source.gz
+	gunzip -c $< > $@
+	rm $<
+
+tmp/input/source.gz: | tmp/input/
+	wget ${SOURCE_URL} -O $@
+
+# Requires GitHub CLI: https://cli.github.com/
+release: | tmp/output/release/
+	@test $(VERSION)
+	gh release create $(VERSION) --notes "New release." --title "$(VERSION)" tmp/output/release/*
+
+# Mappings
+tmp/input/mappings.json: | tmp/input/
+	wget -qO tmp/input/en_product1.json.tar.gz https://www.orphadata.com/data/json/en_product1.json.tar.gz
+	tar -xvf tmp/input/en_product1.json.tar.gz -C tmp/input/
+	mv tmp/input/en_product1.json $@
+	rm tmp/input/en_product1.json.tar.gz
+
+tmp/output/release/ordo-icd11.sssom.tsv: tmp/input/mappings.json | tmp/output/release/
+	python3 src/make_sssom.py $< > $@
+
+# HELP -----------------------------------------------------------------------------------------------------------------
+help:
+	@echo "-----------------------------------"
+	@echo "	Command reference: GARD OWL Ingest"
+	@echo "-----------------------------------"
+	@echo "all"
+	@echo "Runs ingest and creates all release artefacts.\n"
+	@echo "release"
+	@echo "Uploads release to GitHub.\n"