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Added SDGIO import routines for ecosystem services, natural capital, …
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…and UN sustainable development semantics, etc.
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@pbuttigieg
pbuttigieg committed Mar 21, 2018
1 parent 46688a4 commit a04bb7d
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Showing 4 changed files with 5,337 additions and 11 deletions.
13 changes: 12 additions & 1 deletion src/envo/Makefile
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Expand Up @@ -100,7 +100,7 @@ ENVO_IMPORTS_BASE_URI = $(OBO)/envo

# Ontology dependencies
# We don't include clo, as this is currently not working
IMPORTS = pato uberon chebi ro pco foodon go ncbitaxon
IMPORTS = pato uberon chebi ro pco foodon go ncbitaxon sdgio

# Make this target to regenerate ALL
all_imports: $(patsubst %, imports/%_import.owl,$(IMPORTS)) $(patsubst %, imports/%_import.obo,$(IMPORTS))
Expand Down Expand Up @@ -131,6 +131,13 @@ imports/clo_import.owl: mirror/clo.owl imports/clo_terms.txt
$(ROBOT) extract -i $< -T imports/clo_terms.txt --method BOT -O $(ENVO_IMPORTS_BASE_URI)/$@ -o $@
.PRECIOUS: imports/%_import.owl


# SDGIO: Use ROBOT, driven entirely by terms lists NOT from source ontology
imports/sdgio_import.owl: mirror/sdgio.owl imports/sdgio_terms.txt
$(ROBOT) extract -i $< -T imports/sdgio_terms.txt --method BOT -O $(ENVO_IMPORTS_BASE_URI)/$@ -o $@
.PRECIOUS: imports/%_import.owl


# CHEBI: Use ROBOT, driven entirely by terms lists NOT from source ontology
imports/chebi_import.owl: mirror/chebi.owl imports/chebi_terms.txt
$(ROBOT) extract -i $< -T imports/chebi_terms.txt --method BOT -O $(ENVO_IMPORTS_BASE_URI)/$@ -o $@
Expand Down Expand Up @@ -214,6 +221,10 @@ mirror/agro.owl: envo-edit.owl
owltools $(OBO)/agro.owl --remove-annotation-assertions -l -s -d --remove-axiom-annotations --remove-dangling-annotations --make-subset-by-properties -f $(KEEPRELS) --set-ontology-id $(OBO)/agro.owl -o $@
.PRECIOUS: mirror/%.owl

mirror/sdgio.owl: envo-edit.owl
owltools http://purl.unep.org/sdg/sdgio.owl --remove-annotation-assertions -l -s -d --remove-axiom-annotations --remove-dangling-annotations --make-subset-by-properties -f $(KEEPRELS) --set-ontology-id http://purl.unep.org/sdg/sdgio.owl -o $@
.PRECIOUS: mirror/%.owl

mirror/obi.owl: envo-edit.owl
owltools $(OBO)/obi.owl --remove-annotation-assertions -l -s -d --remove-axiom-annotations --remove-dangling-annotations --make-subset-by-properties -f $(KEEPRELS) --set-ontology-id $(OBO)/obi.owl -o $@
.PRECIOUS: mirror/%.owl
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1 change: 1 addition & 0 deletions src/envo/catalog-v001.xml
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@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/envo/imports/sdgio_import.owl" uri="imports/sdgio_import.owl"/>
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/envo/imports/agro_import.owl" uri="imports/agro_import.owl"/>
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/envo/imports/clo_import.owl" uri="imports/clo_import.owl"/>
<uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/envo/imports/obi_import.owl" uri="imports/obi_import.owl"/>
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23 changes: 13 additions & 10 deletions src/envo/envo-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ Import(<http://purl.obolibrary.org/obo/envo/imports/ncbitaxon_import.owl>)
Import(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>)
Import(<http://purl.obolibrary.org/obo/envo/imports/foodon_import.owl>)
Import(<http://purl.obolibrary.org/obo/envo/imports/po_import.owl>)
Import(<http://purl.obolibrary.org/obo/envo/imports/sdgio_import.owl>)
Import(<http://purl.obolibrary.org/obo/envo/imports/pato_import.owl>)
Import(<http://purl.obolibrary.org/obo/envo/imports/obi_import.owl>)
Import(<http://purl.obolibrary.org/obo/envo/imports/agro_import.owl>)
Expand Down Expand Up @@ -3213,7 +3214,7 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_2100007> "de

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002176> "connects")

# Object Property: <http://purl.obolibrary.org/obo/RO_0002211> (regulates (processual))
# Object Property: <http://purl.obolibrary.org/obo/RO_0002211> (regulates)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002211> "regulates (processual)")

Expand Down Expand Up @@ -9137,11 +9138,12 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://pu
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00000357> "lock"^^xsd:string)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000357> <http://purl.obolibrary.org/obo/ENVO_00000010>)

# Class: <http://purl.obolibrary.org/obo/ENVO_00000358> (protected area)
# Class: <http://purl.obolibrary.org/obo/ENVO_00000358> (area of protected biodiversity)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Protected_area"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000358> "An area of land and/or a body of water especially dedicated to the protection and maintenance of biological diversity, and of natural and associated cultural resources, and managed through legal or other effective means."^^xsd:string)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Protected_area"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000358> "An area of land or of a body of water in which management practices, through legal or other effective means, prioritise the protection and maintenance of biological diversity, and of natural and associated cultural resources."^^xsd:string)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/ENVO_00000358> "protected area"^^xsd:string)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_00000358> "This class needs revision. Protected areas may be designated for multiple uses, and more clarity is needed. Further, biodiversity may not prioritise biodiversity conservation. At a very general level, \"protection\" suggests that some forms of use are, in principle, excluded.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00000358> "protected area"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00000358> "area of protected biodiversity")
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000358> <http://purl.obolibrary.org/obo/ENVO_01000408>)

# Class: <http://purl.obolibrary.org/obo/ENVO_00000359> (natural monument)
Expand Down Expand Up @@ -25155,11 +25157,11 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.ob
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01000777> "nurdle"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000777> <http://purl.obolibrary.org/obo/ENVO_01000776>)

# Class: <http://purl.obolibrary.org/obo/ENVO_01000778> (important site)
# Class: <http://purl.obolibrary.org/obo/ENVO_01000778> (key biodiversity area)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "http://www.iucn.org/about/union/secretariat/offices/iucnmed/iucn_med_programme/species/key_biodiversity_areas/") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Key_Biodiversity_Area") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01000778> "An environmental zone which contains, as determined by an officially mandated selection process, one or more ecosystems which include, as parts, ecological communities of global significance for conservation due to their vulnerability and irreplaceability.")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/ENVO_01000778> "The narrow synonyms will be made into subclasses in their own right.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_01000778> "key biodiversity area")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/ENVO_01000778> "important site")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/ENVO_01000778> "Alliance for Zero Extinction Sites")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/ENVO_01000778> "Ecologically and Biologically Significant Area")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/ENVO_01000778> "IUCN Important Site for Freshwater Biodiversity")
Expand All @@ -25171,7 +25173,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynon
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/ENVO_01000778> "Ramsar Sites")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01000778> "envoPolar")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01000778> "The selection process which determines the whether an area is an important site must follow the best practice specifications and guidelines developed by the International Union for Conservation of Nature (IUCN), using globally standardised criteria and thresholds. Note that the label 'important site' is chosen to align with SDGIO. The definition is that of \"key biodiversity area\".")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01000778> "important site"@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01000778> "key biodiversity area")
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000778> <http://purl.obolibrary.org/obo/ENVO_01000408>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000778> ObjectMinCardinality(1 <http://purl.obolibrary.org/obo/RO_0002131> <http://purl.obolibrary.org/obo/ENVO_01001110>))

Expand Down Expand Up @@ -28734,12 +28736,13 @@ EquivalentClasses(<http://purl.obolibrary.org/obo/ENVO_01001168> ObjectIntersect
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001168> <http://purl.obolibrary.org/obo/ENVO_02500000>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001168> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002418> <http://purl.obolibrary.org/obo/ENVO_01001174>))

# Class: <http://purl.obolibrary.org/obo/ENVO_01001169> (IUCN protected area)
# Class: <http://purl.obolibrary.org/obo/ENVO_01001169> (area protected according to IUCN guidelines)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://www.iucn.org/sites/dev/files/import/downloads/iucn_assignment_1.pdf") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01001169> "A protected area in which management objectives have been declared, by a local governing body or authority, to adhere to the guidelines set forth by the International Union for the Conservation of Nature (IUCN).")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/ENVO_01001169> "Axiomatise with SDGIO classes once available: https://github.com/SDG-InterfaceOntology/sdgio/issues/114")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000118> <http://purl.obolibrary.org/obo/ENVO_01001169> "IUCN protected area"@en)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://www.iucn.org/sites/dev/files/import/downloads/iucn_assignment_1.pdf") rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01001169> "The international recognition of an area as an IUCN protected area generally depends on the assigning government or authority reporting its assignments to the United Nations Environment Programme World Conservation Monitoring Centre.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001169> "IUCN protected area"@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001169> "area protected according to IUCN guidelines")
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001169> <http://purl.obolibrary.org/obo/ENVO_00000358>)

# Class: <http://purl.obolibrary.org/obo/ENVO_01001170> (active ecosystem management process)
Expand Down Expand Up @@ -29279,7 +29282,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001224> <http://purl.obolibrar

# Class: <http://purl.obolibrary.org/obo/ENVO_01001225> (IUCN protected area with sustainable use of natural resources)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://www.iucn.org/theme/protected-areas/about/protected-areas-categories/category-ib-wilderness-area") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01001225> "")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://www.iucn.org/theme/protected-areas/about/protected-areas-categories/category-ib-wilderness-area") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01001225> "An IUCN protected area which")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://www.iucn.org/theme/protected-areas/about/protected-areas-categories/category-ib-wilderness-area") <http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> <http://purl.obolibrary.org/obo/ENVO_01001225> "IUCN-PACS:VI")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://www.iucn.org/theme/protected-areas/about/protected-areas-categories/category-ib-wilderness-area") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_01001225> "")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://www.iucn.org/theme/protected-areas/about/protected-areas-categories/category-ib-wilderness-area") rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01001225> "Note that this ENVO class is not authoritative: see the associated IUCN references for a complete definition of all Protected Areas.")
Expand Down
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