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Merge pull request #962 from EnvironmentOntology/issue-960
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adding exports of subhierarchies
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@pbuttigieg
pbuttigieg authored Jun 5, 2020
2 parents 700b065 + ef57f55 commit 5ecb02c
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Showing 51 changed files with 107,544 additions and 7,105 deletions.
53 changes: 51 additions & 2 deletions src/envo/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -180,7 +180,8 @@ $(ONT)-full.owl: $(SRC) $(OTHER_SRC)
## Note we also include TSV as a format


SUBSETS = envo-basic EnvO-Lite-GSC envoEmpo envoAstro envoPolar envoEmpo envoOmics envoCesab environmental_hazards
SUBSETS = envo-basic EnvO-Lite-GSC envoEmpo envoAstro envoPolar envoEmpo envoOmics envoCesab environmental_hazards \
biome-hierarchy astronomical-body-part-hierarchy material-hierarchy process-hierarchy

SUBSET_ROOTS = $(patsubst %, subsets/%, $(SUBSETS))
SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f)))
Expand All @@ -189,7 +190,7 @@ SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n
all_subsets: $(SUBSET_FILES)

subsets/%.tsv: subsets/%.owl
$(ROBOT) export -i $< -c "ID|label|definition" -e $@
$(ROBOT) export -i $< -c "ID|label|subClassOf [ID]|subClassOf [LABEL]|SYNONYMS|inSubset|definition" -e $@
# $(ROBOT) query -f tsv -i $< -s ./sparql/labels.sparql $@

envo-simple.owl: envo-base.owl
Expand All @@ -210,6 +211,54 @@ subsets/envo-basic.obo: envo-simple.owl
#pato-lite.obo:
# $(OWLTOOLS) $(OBO)/pato.obo --make-subset-by-properties -o -f obo $@

subsets/biome-hierarchy.owl: envo.owl
robot filter --input $< \
--term ENVO:00000428 \
--term IAO:0000115 \
--select "annotations self descendants" \
--signature true \
annotate --ontology-iri $(ONTBASE)/$@ \
--version-iri $(ONTBASE)/releases/$(TODAY)/$@ \
-a owl:versionInfo "$@ $(TODAY)" \
--output $@
.PRECIOUS: subsets/biome-hierarchy.owl

subsets/astronomical-body-part-hierarchy.owl: envo.owl
robot filter --input $< \
--term ENVO:01000813 \
--term IAO:0000115 \
--select "annotations self descendants" \
--signature true \
annotate --ontology-iri $(ONTBASE)/$@ \
--version-iri $(ONTBASE)/releases/$(TODAY)/$@ \
-a owl:versionInfo "$@ $(TODAY)" \
--output $@
.PRECIOUS: subsets/astronomical-body-part-hierarchy.owl

subsets/material-hierarchy.owl: envo.owl
robot filter --input $< \
--term ENVO:00010483 \
--term IAO:0000115 \
--select "annotations self descendants" \
--signature true \
annotate --ontology-iri $(ONTBASE)/$@ \
--version-iri $(ONTBASE)/releases/$(TODAY)/$@ \
-a owl:versionInfo "$@ $(TODAY)" \
--output $@
.PRECIOUS: subsets/material-hierarchy.owl

subsets/process-hierarchy.owl: envo.owl
robot filter --input $< \
--term ENVO:02500000 \
--term IAO:0000115 \
--select "annotations self descendants" \
--signature true \
annotate --ontology-iri $(ONTBASE)/$@ \
--version-iri $(ONTBASE)/releases/$(TODAY)/$@ \
-a owl:versionInfo "$@ $(TODAY)" \
--output $@
.PRECIOUS: subsets/process-hierarchy.owl

release-diffs:
cd diffs && make

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417 changes: 310 additions & 107 deletions src/envo/envo-simple.owl
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495 changes: 377 additions & 118 deletions src/envo/envo.owl
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108 changes: 7 additions & 101 deletions src/envo/subsets/EnvO-Lite-GSC.json
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Original file line number Diff line number Diff line change
Expand Up @@ -605,24 +605,6 @@
},
"type" : "CLASS",
"lbl" : "anthropogenic environmental material"
}, {
"id" : "http://purl.obolibrary.org/obo/ENVO_01001110",
"meta" : {
"definition" : {
"val" : "An environmental system which includes both living and non-living components.",
"xrefs" : [ "https://en.wikipedia.org/wiki/Ecosystem" ]
},
"comments" : [ "This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here." ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
"val" : "ENVO"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
"val" : "LTER:173"
} ]
},
"type" : "CLASS",
"lbl" : "ecosystem"
}, {
"id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym",
"type" : "PROPERTY",
Expand Down Expand Up @@ -1811,26 +1793,6 @@
},
"type" : "PROPERTY",
"lbl" : "has_condition"
}, {
"id" : "http://purl.obolibrary.org/obo/ENVO_00000000",
"meta" : {
"comments" : [ "This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass." ],
"subsets" : [ "http://purl.obolibrary.org/obo/subsets/envo-basic.obo#envoPolar" ],
"xrefs" : [ {
"val" : "https://en.wikipedia.org/wiki/Geographic_feature"
} ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "macroscopic spatial feature",
"xrefs" : [ ]
} ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
"val" : "ENVO"
} ]
},
"type" : "CLASS",
"lbl" : "geographic feature"
}, {
"id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym",
"type" : "PROPERTY",
Expand Down Expand Up @@ -2275,32 +2237,6 @@
} ]
},
"type" : "PROPERTY"
}, {
"id" : "http://purl.obolibrary.org/obo/ENVO_01000254",
"meta" : {
"definition" : {
"val" : "A system which has the disposition to environ one or more material entities.",
"xrefs" : [ "DOI:10.1186/2041-1480-4-43" ]
},
"comments" : [ "In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class \"system\". The relation \"environed_by\" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised." ],
"xrefs" : [ {
"val" : "EcoLexicon:environment"
} ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "environment",
"xrefs" : [ ]
} ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
"val" : "2013-09-23T16:04:08Z"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
"val" : "ENVO"
} ]
},
"type" : "CLASS",
"lbl" : "environmental system"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002507",
"meta" : {
Expand All @@ -2316,21 +2252,6 @@
} ]
},
"type" : "PROPERTY"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002508",
"meta" : {
"xrefs" : [ {
"val" : "RO:0002508"
} ],
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
"val" : "ENVO"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
"val" : "determines"
} ]
},
"type" : "PROPERTY"
}, {
"id" : "http://purl.obolibrary.org/obo/RO_0002509",
"meta" : {
Expand Down Expand Up @@ -2599,10 +2520,6 @@
"sub" : "http://purl.obolibrary.org/obo/ENVO_01000549",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ENVO_01001691"
}, {
"sub" : "http://purl.obolibrary.org/obo/ENVO_02500000",
"pred" : "http://purl.obolibrary.org/obo/RO_0002218",
"obj" : "http://purl.obolibrary.org/obo/ENVO_01001110"
}, {
"sub" : "http://purl.obolibrary.org/obo/ENVO_01001684",
"pred" : "is_a",
Expand Down Expand Up @@ -2635,10 +2552,6 @@
"sub" : "http://purl.obolibrary.org/obo/ENVO_01000008",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ENVO_01000549"
}, {
"sub" : "http://purl.obolibrary.org/obo/ENVO_00000000",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ENVO_01000813"
}, {
"sub" : "http://purl.obolibrary.org/obo/ENVO_01000800",
"pred" : "is_a",
Expand Down Expand Up @@ -2691,10 +2604,6 @@
"sub" : "http://purl.obolibrary.org/obo/ENVO_01000820",
"pred" : "http://purl.obolibrary.org/obo/RO_0002131",
"obj" : "http://purl.obolibrary.org/obo/ENVO_01000646"
}, {
"sub" : "http://purl.obolibrary.org/obo/ENVO_01001110",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ENVO_01000254"
}, {
"sub" : "http://purl.obolibrary.org/obo/ENVO_01000637",
"pred" : "is_a",
Expand Down Expand Up @@ -2739,10 +2648,6 @@
"sub" : "http://purl.obolibrary.org/obo/ENVO_01000639",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ENVO_01000281"
}, {
"sub" : "http://purl.obolibrary.org/obo/ENVO_00000027",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ENVO_00000000"
}, {
"sub" : "http://purl.obolibrary.org/obo/ENVO_01000820",
"pred" : "http://purl.obolibrary.org/obo/RO_0002473",
Expand Down Expand Up @@ -2879,16 +2784,20 @@
"sub" : "http://purl.obolibrary.org/obo/ENVO_01000638",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ENVO_01000639"
}, {
"sub" : "http://purl.obolibrary.org/obo/ENVO_00000027",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ENVO_01000813"
} ],
"id" : "http://purl.obolibrary.org/obo/envo/subsets/EnvO-Lite-GSC.owl",
"meta" : {
"subsets" : [ ],
"xrefs" : [ ],
"basicPropertyValues" : [ {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2020-05-14"
"val" : "2020-06-02"
} ],
"version" : "http://purl.obolibrary.org/obo/envo/releases/2020-05-14/subsets/EnvO-Lite-GSC.owl"
"version" : "http://purl.obolibrary.org/obo/envo/releases/2020-06-02/subsets/EnvO-Lite-GSC.owl"
},
"equivalentNodesSets" : [ ],
"logicalDefinitionAxioms" : [ {
Expand All @@ -2907,9 +2816,6 @@
} ]
} ],
"domainRangeAxioms" : [ ],
"propertyChainAxioms" : [ {
"predicateId" : "http://purl.obolibrary.org/obo/RO_0002509",
"chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002507", "http://purl.obolibrary.org/obo/BFO_0000050" ]
} ]
"propertyChainAxioms" : [ ]
} ]
}
42 changes: 3 additions & 39 deletions src/envo/subsets/EnvO-Lite-GSC.obo
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
format-version: 1.2
data-version: envo/releases/2020-05-14/subsets/EnvO-Lite-GSC.owl
data-version: envo/releases/2020-06-02/subsets/EnvO-Lite-GSC.owl
subsetdef: disposition_slim "Disposition slim"
subsetdef: environmental_hazards "environmental_hazards"
subsetdef: EnvO-Lite-GSC "EnvO-Lite-GSC"
Expand All @@ -23,17 +23,7 @@ subsetdef: value_slim "Value slim"
subsetdef: wwfBiome "wwfBiome"
synonymtypedef: PLURAL "plurals"
ontology: envo/subsets/EnvO-Lite-GSC
property_value: owl:versionInfo "2020-05-14" xsd:string

[Term]
id: ENVO:00000000
name: geographic feature
namespace: ENVO
comment: This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass.
subset: envoPolar
synonym: "macroscopic spatial feature" EXACT []
xref: https://en.wikipedia.org/wiki/Geographic_feature
is_a: ENVO:01000813 ! astronomical body part
property_value: owl:versionInfo "2020-06-02" xsd:string

[Term]
id: ENVO:00000027
Expand All @@ -49,7 +39,7 @@ xref: FTT:982
xref: Geonames:H.SPNG
xref: SWEETRealm:Spring
xref: TGN:21126
is_a: ENVO:00000000 ! geographic feature
is_a: ENVO:01000813 ! astronomical body part
is_a: ENVO:01001784 ! compound astronomical body part
relationship: part_of ENVO:01001311 ! solid surface layer

Expand Down Expand Up @@ -366,16 +356,6 @@ is_a: ENVO:00010483 ! environmental material
created_by: ORCID:0000-0002-4366-3088
creation_date: 2010-03-20T08:40:04Z

[Term]
id: ENVO:01000254
name: environmental system
namespace: ENVO
def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43]
comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
synonym: "environment" EXACT []
xref: EcoLexicon:environment
creation_date: 2013-09-23T16:04:08Z

[Term]
id: ENVO:01000256
name: mineral material
Expand Down Expand Up @@ -574,15 +554,6 @@ relationship: overlaps ENVO:01000646 ! lithosphere
relationship: overlaps ENVO:01000817 ! biosphere
relationship: overlaps ENVO:01000819 ! hydrosphere

[Term]
id: ENVO:01001110
name: ecosystem
namespace: ENVO
alt_id: LTER:173 {xref="https://vocab.lternet.edu/vocab/vocab/index.php?tema=173&/ecosystems"}
def: "An environmental system which includes both living and non-living components." [https://en.wikipedia.org/wiki/Ecosystem]
comment: This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
is_a: ENVO:01000254 ! environmental system

[Term]
id: ENVO:01001112
name: fossilization of organic material
Expand Down Expand Up @@ -698,7 +669,6 @@ name: environmental system process
namespace: ENVO
def: "A process in which includes the components of an environmental system as participants." []
comment: This is a convenience class for organisation and should not be used for annotation.
relationship: obsolete_has_active_participant ENVO:01001110 ! ecosystem

[Typedef]
id: adjacent_to
Expand Down Expand Up @@ -801,12 +771,6 @@ xref: RO:0002507
id: determined_by_part_of
namespace: ENVO
xref: RO:0002509
holds_over_chain: determined_by part_of

[Typedef]
id: determines
namespace: ENVO
xref: RO:0002508

[Typedef]
id: disconnected_from
Expand Down
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