From 9e6b6e57cb939c869c143044c72fda28fc12171e Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 12 Jun 2023 07:02:27 -0700 Subject: [PATCH] CARO to Uberon term replacement for #695 (#722) * Add OBI as source for organism Will switch to COB once it has OBI:0100026 * CARO to UBERON term replacement Note a number of object property domain and range get switched. * makefile simplification * Update src/ontology/catalog-v001.xml Co-authored-by: Nico Matentzoglu * Update src/ontology/catalog-v001.xml Co-authored-by: Nico Matentzoglu * Update src/ontology/ro-edit.owl Co-authored-by: Nico Matentzoglu * Update src/ontology/ro-edit.owl Co-authored-by: Nico Matentzoglu * extra slash * drops neuron projection bundle parenting to UBERON_0001062 * Update catalog-v001.xml --------- Co-authored-by: Nico Matentzoglu --- src/ontology/Makefile | 41 +++++---- src/ontology/catalog-v001.xml | 42 ++++------ src/ontology/imports/caro_import.owl | 112 ------------------------- src/ontology/imports/caro_terms.txt | 6 -- src/ontology/imports/obi_import.owl | 60 +++++++++++++ src/ontology/imports/obi_terms.txt | 1 + src/ontology/imports/uberon_import.owl | 6 +- src/ontology/ro-edit.owl | 111 ++++++++++++------------ src/ontology/ro-odk.yaml | 5 +- 9 files changed, 158 insertions(+), 226 deletions(-) delete mode 100644 src/ontology/imports/caro_import.owl delete mode 100644 src/ontology/imports/caro_terms.txt create mode 100644 src/ontology/imports/obi_import.owl create mode 100644 src/ontology/imports/obi_terms.txt diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 2e7b6ad0..e218fca9 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -109,7 +109,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = omo pato cl envo go caro other orcidio uberon +IMPORTS = omo pato cl envo go other orcidio uberon obi IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -354,16 +354,6 @@ $(IMPORTDIR)/go_import.owl: $(MIRRORDIR)/go.owl $(IMPORTDIR)/go_terms_combined.t remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/go_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ $(ANNOTATE_CONVERT_FILE); fi -## Module for ontology: caro - -$(IMPORTDIR)/caro_import.owl: $(MIRRORDIR)/caro.owl $(IMPORTDIR)/caro_terms_combined.txt - if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ - extract -T $(IMPORTDIR)/caro_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ - remove --base-iri $(URIBASE)/CARO --axioms external --preserve-structure false --trim false \ - query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \ - remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/caro_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ - $(ANNOTATE_CONVERT_FILE); fi - ## Module for ontology: other $(IMPORTDIR)/other_import.owl: @@ -388,6 +378,16 @@ $(IMPORTDIR)/uberon_import.owl: $(MIRRORDIR)/uberon.owl $(IMPORTDIR)/uberon_term query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ $(ANNOTATE_CONVERT_FILE); fi +## Module for ontology: obi + +$(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/obi_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ + remove --base-iri $(OBOBASE)/OBI --axioms external --preserve-structure false --trim false \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/obi_terms_combined.txt --select complement \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ + $(ANNOTATE_CONVERT_FILE); fi + .PHONY: refresh-imports refresh-imports: @@ -506,16 +506,6 @@ mirror-go: | $(TMPDIR) mv $@.tmp.owl $(TMPDIR)/$@.owl; fi -## ONTOLOGY: caro -.PHONY: mirror-caro -.PRECIOUS: $(MIRRORDIR)/caro.owl -mirror-caro: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/caro.owl --create-dirs -o $(MIRRORDIR)/caro.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/caro.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CARO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi - - ## ONTOLOGY: other ## You have configured your default mirror type to no_mirror. @@ -537,6 +527,15 @@ mirror-uberon: | $(TMPDIR) mv $@.tmp.owl $(TMPDIR)/$@.owl; fi +## ONTOLOGY: obi +.PHONY: mirror-obi +.PRECIOUS: $(MIRRORDIR)/obi.owl +mirror-obi: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + + $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ cp $(TMPDIR)/mirror-$*.owl $@; fi; fi diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index e140ccc7..81d92baa 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -1,28 +1,20 @@ - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/caro_import.owl b/src/ontology/imports/caro_import.owl deleted file mode 100644 index 2de45160..00000000 --- a/src/ontology/imports/caro_import.owl +++ /dev/null @@ -1,112 +0,0 @@ -Prefix(:=) -Prefix(owl:=) -Prefix(rdf:=) -Prefix(xml:=) -Prefix(xsd:=) -Prefix(rdfs:=) - - -Ontology( - -Annotation( "None") -Annotation( ) -Annotation( "Common Anatomy Reference Ontology") -Annotation( ) -Annotation(rdfs:comment "Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendal.") -Annotation(owl:versionInfo "2022-02-18") -Annotation(owl:versionInfo "2023-02-19") - -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) - - - -############################ -# Classes -############################ - -# Class: (anatomical entity) - -AnnotationAssertion(Annotation( "CAROC:Brownsville2014") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") -AnnotationAssertion( "CARO:0000000") -AnnotationAssertion(rdfs:comment "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.") -AnnotationAssertion(rdfs:label "anatomical entity") -SubClassOf( ) - -# Class: (connected anatomical structure) - -AnnotationAssertion( "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.") -AnnotationAssertion( "CARO:0000003") -AnnotationAssertion(rdfs:comment "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development.") -AnnotationAssertion(rdfs:label "connected anatomical structure") -SubClassOf( ) - -# Class: (material anatomical entity) - -AnnotationAssertion( "An anatomical entity that has mass.") -AnnotationAssertion( "CARO:0000006") -AnnotationAssertion(rdfs:label "material anatomical entity") -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (immaterial anatomical entity) - -AnnotationAssertion( "Anatomical entity that has no mass.") -AnnotationAssertion( "CARO:0000007") -AnnotationAssertion(rdfs:label "immaterial anatomical entity") -SubClassOf( ) -SubClassOf( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (neuron projection bundle) - -AnnotationAssertion( "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.") -AnnotationAssertion( "CARO:0001001") -AnnotationAssertion(rdfs:label "neuron projection bundle") -SubClassOf( ) - -# Class: (organism or virus or viroid) - -AnnotationAssertion( "Material anatomical entity that is a member of an individual species or is a viral or viroid particle.") -AnnotationAssertion( "Melissa Haendel") -AnnotationAssertion(rdfs:label "organism or virus or viroid") -SubClassOf( ) - -# Class: (multicellular anatomical structure) - -AnnotationAssertion( "An anatomical structure that has more than one cell as a part.") -AnnotationAssertion( "djs93") -AnnotationAssertion( "CARO:0010000") -AnnotationAssertion(rdfs:label "multicellular anatomical structure") -SubClassOf( ) -SubClassOf( ) - - -) \ No newline at end of file diff --git a/src/ontology/imports/caro_terms.txt b/src/ontology/imports/caro_terms.txt deleted file mode 100644 index 2861c295..00000000 --- a/src/ontology/imports/caro_terms.txt +++ /dev/null @@ -1,6 +0,0 @@ -CARO:0000003 -CARO:0001001 -CARO:0000006 -CARO:0000000 -CARO:0001010 -CARO:0000007 diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl new file mode 100644 index 00000000..534edad7 --- /dev/null +++ b/src/ontology/imports/obi_import.owl @@ -0,0 +1,60 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2023-05-27") + +Declaration(Class()) +Declaration(Class()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(Datatype(xsd:date)) + + +############################ +# Classes +############################ + +# Class: (organism) + +AnnotationAssertion( "organism"@en) +AnnotationAssertion( "animal"@en) +AnnotationAssertion( "fungus"@en) +AnnotationAssertion( "plant"@en) +AnnotationAssertion( "virus"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) +AnnotationAssertion( "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')") +AnnotationAssertion( "13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI.") +AnnotationAssertion( "GROUP: OBI Biomaterial Branch") +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Organism"@en) +AnnotationAssertion(rdfs:label "organism"@en) +SubClassOf( ) + + +) \ No newline at end of file diff --git a/src/ontology/imports/obi_terms.txt b/src/ontology/imports/obi_terms.txt new file mode 100644 index 00000000..9ded87ec --- /dev/null +++ b/src/ontology/imports/obi_terms.txt @@ -0,0 +1 @@ +OBI:0100026 \ No newline at end of file diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl index 854aee89..05a49e66 100644 --- a/src/ontology/imports/uberon_import.owl +++ b/src/ontology/imports/uberon_import.owl @@ -7,7 +7,7 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( ) Annotation( ) @@ -68,12 +68,11 @@ Annotation( "PMID:16417468 Forgotten and Annotation( "aggregates AAO from 13:04:2012") Annotation( "aggregates TAO from 09:08:2012") Annotation( "aggregates VSAO from 16:07:2012") -Annotation(owl:versionInfo "2023-05-24") +Annotation(owl:versionInfo "2023-06-01") Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -172,7 +171,6 @@ AnnotationAssertion(Annotation( "neural fiber bundle") AnnotationAssertion( "UBERON:0000122") AnnotationAssertion(rdfs:label "neuron projection bundle") -SubClassOf( ) SubClassOf( ) # Class: (material anatomical entity) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index ee0660a8..56e93dbb 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -22,7 +22,6 @@ Import() Import() Import() Import() -Import() Import() Import() Import() @@ -30,9 +29,11 @@ Import() Import() Import() Import() +Import() +Import() Annotation(dc:description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies."@en) -Annotation(dc:title "OBO Relations Ontology"@en) Annotation(dc:license ) +Annotation(dc:title "OBO Relations Ontology"@en) Annotation(foaf:homepage " https://github.com/oborel/obo-relations/"^^xsd:anyURI) Declaration(Class(obo:BFO_0000019)) @@ -668,10 +669,10 @@ Declaration(AnnotationProperty(obo:valid_for_go_gp2term)) Declaration(AnnotationProperty(obo:valid_for_go_ontology)) Declaration(AnnotationProperty(obo:valid_for_gocam)) Declaration(AnnotationProperty(subsets:ro-eco)) -Declaration(AnnotationProperty(dc:date)) Declaration(AnnotationProperty(dc:conformsTo)) Declaration(AnnotationProperty(dc:contributor)) Declaration(AnnotationProperty(dc:creator)) +Declaration(AnnotationProperty(dc:date)) Declaration(AnnotationProperty(dc:description)) Declaration(AnnotationProperty(dc:license)) Declaration(AnnotationProperty(dc:source)) @@ -1414,8 +1415,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002004 "The relationship that holds AnnotationAssertion(obo:IAO_0000117 obo:RO_0002004 ) AnnotationAssertion(rdfs:label obo:RO_0002004 "tracheates"@en) SubObjectPropertyOf(obo:RO_0002004 obo:RO_0001018) -ObjectPropertyDomain(obo:RO_0002004 obo:CARO_0000003) -ObjectPropertyRange(obo:RO_0002004 obo:CARO_0000003) +ObjectPropertyDomain(obo:RO_0002004 obo:UBERON_0000061) +ObjectPropertyRange(obo:RO_0002004 obo:UBERON_0000061) # Object Property: obo:RO_0002005 (innervated_by) @@ -1423,8 +1424,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002005 ) AnnotationAssertion(rdfs:label obo:RO_0002132 "has fasciculating neuron projection"@en) SubObjectPropertyOf(obo:RO_0002132 obo:RO_0002131) -ObjectPropertyDomain(obo:RO_0002132 obo:CARO_0001001) +ObjectPropertyDomain(obo:RO_0002132 obo:UBERON_0000122) ObjectPropertyRange(obo:RO_0002132 ObjectUnionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:BFO_0000050 obo:CL_0000540))) # Object Property: obo:RO_0002134 (innervates) @@ -2024,7 +2025,7 @@ AnnotationAssertion(obo:IAO_0000424 obo:RO_0002134 ") AnnotationAssertion(rdfs:label obo:RO_0002134 "innervates"@en) -ObjectPropertyDomain(obo:RO_0002134 obo:CARO_0001001) +ObjectPropertyDomain(obo:RO_0002134 obo:UBERON_0000122) # Object Property: obo:RO_0002150 (continuous with) @@ -2126,7 +2127,7 @@ AnnotationAssertion(rdfs:comment obo:RO_0002162 "Connects a biological entity to AnnotationAssertion(rdfs:label obo:RO_0002162 "in taxon") AnnotationAssertion(rdfs:seeAlso obo:RO_0002162 ) SubObjectPropertyOf(obo:RO_0002162 obo:RO_0002320) -ObjectPropertyRange(obo:RO_0002162 obo:CARO_0001010) +ObjectPropertyRange(obo:RO_0002162 obo:OBI_0100026) # Object Property: obo:RO_0002163 (spatially disjoint from) @@ -2175,8 +2176,8 @@ AnnotationAssertion(obo:IAO_0000589 obo:RO_0002177 "attached to part of (anatomi AnnotationAssertion(rdfs:label obo:RO_0002177 "attached to part of"@en) SubObjectPropertyOf(obo:RO_0002177 obo:RO_0002323) SubObjectPropertyOf(obo:RO_0002177 obo:RO_0002567) -ObjectPropertyDomain(obo:RO_0002177 obo:CARO_0000003) -ObjectPropertyRange(obo:RO_0002177 obo:CARO_0000003) +ObjectPropertyDomain(obo:RO_0002177 obo:UBERON_0000061) +ObjectPropertyRange(obo:RO_0002177 obo:UBERON_0000061) # Object Property: obo:RO_0002178 (supplies) @@ -2215,7 +2216,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002200 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002200 "has phenotype"@en) SubObjectPropertyOf(obo:RO_0002200 obo:RO_0016001) InverseObjectProperties(obo:RO_0002200 obo:RO_0002201) -ObjectPropertyDomain(obo:RO_0002200 ObjectUnionOf(obo:BFO_0000031 obo:CARO_0000006 obo:OGMS_0000031)) +ObjectPropertyDomain(obo:RO_0002200 ObjectUnionOf(obo:BFO_0000031 obo:OGMS_0000031 obo:UBERON_0000465)) ObjectPropertyRange(obo:RO_0002200 obo:UPHENO_0001001) # Object Property: obo:RO_0002201 (phenotype of) @@ -2295,7 +2296,7 @@ SubObjectPropertyOf(obo:RO_0002206 obo:RO_0002330) InverseObjectProperties(obo:RO_0002206 obo:RO_0002292) ObjectPropertyDomain(obo:RO_0002206 obo:BFO_0000002) ObjectPropertyDomain(obo:RO_0002206 ObjectUnionOf(obo:BFO_0000031 obo:BFO_0000040)) -ObjectPropertyRange(obo:RO_0002206 obo:CARO_0000006) +ObjectPropertyRange(obo:RO_0002206 obo:UBERON_0000465) # Object Property: obo:RO_0002207 (directly develops from) @@ -2310,8 +2311,8 @@ AnnotationAssertion(rdfs:comment obo:RO_0002207 "TODO - add child relations from AnnotationAssertion(rdfs:label obo:RO_0002207 "directly develops from"@en) SubObjectPropertyOf(obo:RO_0002207 obo:RO_0002202) InverseObjectProperties(obo:RO_0002207 obo:RO_0002210) -ObjectPropertyDomain(obo:RO_0002207 ObjectUnionOf(obo:CARO_0010000 obo:CL_0000000)) -ObjectPropertyRange(obo:RO_0002207 ObjectUnionOf(obo:CARO_0010000 obo:CL_0000000)) +ObjectPropertyDomain(obo:RO_0002207 ObjectUnionOf(obo:CL_0000000 obo:UBERON_0010000)) +ObjectPropertyRange(obo:RO_0002207 ObjectUnionOf(obo:CL_0000000 obo:UBERON_0010000)) # Object Property: obo:RO_0002208 (parasitoid of) @@ -2521,7 +2522,7 @@ AnnotationAssertion(obo:IAO_0000119 obo:RO_0002226 "EHDAA2") AnnotationAssertion(obo:IAO_0000119 obo:RO_0002226 "Jonathan Bard, EHDAA2") AnnotationAssertion(rdfs:label obo:RO_0002226 "develops in"@en) SubObjectPropertyOf(obo:RO_0002226 obo:RO_0002258) -ObjectPropertyDomain(obo:RO_0002226 obo:CARO_0000000) +ObjectPropertyDomain(obo:RO_0002226 obo:UBERON_0001062) # Object Property: obo:RO_0002227 (obligate parasite of) @@ -2725,8 +2726,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002254 ) SubObjectPropertyOf(obo:RO_0002295 obo:RO_0002324) ObjectPropertyDomain(obo:RO_0002295 obo:GO_0008150) -ObjectPropertyRange(obo:RO_0002295 obo:CARO_0000000) +ObjectPropertyRange(obo:RO_0002295 obo:UBERON_0001062) # Object Property: obo:RO_0002296 (results in development of) @@ -2981,7 +2982,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002303 subsets:ro-eco) AnnotationAssertion(rdfs:comment obo:RO_0002303 "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.") AnnotationAssertion(rdfs:label obo:RO_0002303 "has habitat"@en) SubObjectPropertyOf(obo:RO_0002303 obo:RO_0002321) -ObjectPropertyDomain(obo:RO_0002303 obo:CARO_0001010) +ObjectPropertyDomain(obo:RO_0002303 obo:OBI_0100026) ObjectPropertyRange(obo:RO_0002303 obo:ENVO_01000254) # Object Property: obo:RO_0002304 (causally upstream of, positive effect) @@ -3062,7 +3063,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002315 obo:valid_for_gocam) AnnotationAssertion(rdfs:label obo:RO_0002315 "results in acquisition of features of"@en) SubObjectPropertyOf(obo:RO_0002315 obo:RO_0002295) SubObjectPropertyOf(obo:RO_0002315 obo:RO_0040036) -ObjectPropertyRange(obo:RO_0002315 obo:CARO_0000003) +ObjectPropertyRange(obo:RO_0002315 obo:UBERON_0000061) # Object Property: obo:RO_0002320 (evolutionarily related to) @@ -3422,7 +3423,7 @@ AnnotationAssertion(rdfs:label obo:RO_0002372 "has muscle origin"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0002372 ) SubObjectPropertyOf(obo:RO_0002372 obo:RO_0002371) SubObjectPropertyOf(obo:RO_0002372 obo:RO_0002567) -ObjectPropertyDomain(Annotation(rdfs:comment "We need to import uberon muscle to create a stricter domain constraint") obo:RO_0002372 obo:CARO_0000003) +ObjectPropertyDomain(Annotation(rdfs:comment "We need to import uberon muscle to create a stricter domain constraint") obo:RO_0002372 obo:UBERON_0000061) # Object Property: obo:RO_0002373 (has muscle insertion) @@ -3433,7 +3434,7 @@ AnnotationAssertion(rdfs:label obo:RO_0002373 "has muscle insertion"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0002373 ) SubObjectPropertyOf(obo:RO_0002373 obo:RO_0002371) SubObjectPropertyOf(obo:RO_0002373 obo:RO_0002567) -ObjectPropertyDomain(Annotation(obo:IAO_0000116 "We need to import uberon muscle into RO to use as a stricter domain constraint") obo:RO_0002373 obo:CARO_0000003) +ObjectPropertyDomain(Annotation(obo:IAO_0000116 "We need to import uberon muscle into RO to use as a stricter domain constraint") obo:RO_0002373 obo:UBERON_0000061) # Object Property: obo:RO_0002374 (derived from ancestral fusion of) @@ -3570,8 +3571,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002384 "x has developmental potentia AnnotationAssertion(obo:IAO_0000117 obo:RO_0002384 ) AnnotationAssertion(rdfs:label obo:RO_0002384 "has developmental potential involving"@en) SubObjectPropertyOf(obo:RO_0002384 obo:RO_0002324) -ObjectPropertyDomain(obo:RO_0002384 obo:CARO_0000000) -ObjectPropertyRange(obo:RO_0002384 obo:CARO_0000000) +ObjectPropertyDomain(obo:RO_0002384 obo:UBERON_0001062) +ObjectPropertyRange(obo:RO_0002384 obo:UBERON_0001062) # Object Property: obo:RO_0002385 (has potential to developmentally contribute to) @@ -4772,8 +4773,8 @@ SubObjectPropertyOf(obo:RO_0002551 obo:BFO_0000051) InverseObjectProperties(obo:RO_0002551 obo:RO_0002576) AsymmetricObjectProperty(obo:RO_0002551) IrreflexiveObjectProperty(obo:RO_0002551) -ObjectPropertyDomain(obo:RO_0002551 obo:CARO_0000003) -ObjectPropertyRange(Annotation(obo:IAO_0000116 "This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.") obo:RO_0002551 obo:CARO_0000006) +ObjectPropertyDomain(obo:RO_0002551 obo:UBERON_0000061) +ObjectPropertyRange(Annotation(obo:IAO_0000116 "This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.") obo:RO_0002551 obo:UBERON_0000465) # Object Property: obo:RO_0002552 (results in ending of) @@ -4898,8 +4899,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002567 ) SubObjectPropertyOf(obo:RO_0002574 obo:RO_0002437) -ObjectPropertyDomain(obo:RO_0002574 obo:CARO_0001010) -ObjectPropertyRange(obo:RO_0002574 obo:CARO_0001010) +ObjectPropertyDomain(obo:RO_0002574 obo:OBI_0100026) +ObjectPropertyRange(obo:RO_0002574 obo:OBI_0100026) # Object Property: obo:RO_0002576 (skeleton of) @@ -4979,8 +4980,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002576 ) AnnotationAssertion(rdfs:label obo:RO_0009004 "has consumer"@en) ObjectPropertyDomain(obo:RO_0009004 obo:BFO_0000040) -ObjectPropertyRange(obo:RO_0009004 obo:CARO_0001010) +ObjectPropertyRange(obo:RO_0009004 obo:OBI_0100026) # Object Property: obo:RO_0009005 (has primary substance added) @@ -6756,16 +6757,16 @@ DataPropertyRange(obo:RO_0002029 DatatypeRestriction(xsd:short xsd:minInclusive # Classes ############################ -# Class: obo:BFO_0000002 (continuant) +# Class: obo:BFO_0000002 (obo:BFO_0000002) SubClassOf(obo:BFO_0000002 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000002)) SubClassOf(obo:BFO_0000002 ObjectAllValuesFrom(obo:RO_HOM0000000 obo:BFO_0000002)) -# Class: obo:BFO_0000003 (occurrent) +# Class: obo:BFO_0000003 (obo:BFO_0000003) SubClassOf(obo:BFO_0000003 ObjectAllValuesFrom(obo:RO_HOM0000000 obo:BFO_0000003)) -# Class: obo:BFO_0000015 (process) +# Class: obo:BFO_0000015 (obo:BFO_0000015) SubClassOf(obo:BFO_0000015 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000015)) @@ -7067,4 +7068,4 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002086 subsets:ro-eco) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002089 subsets:ro-eco) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002093 subsets:ro-eco) AnnotationAssertion(Annotation(rdfs:comment "This is an experimental annotation") obo:IAO_0000589 rdfs:isDefinedBy "is defined by") -) +) \ No newline at end of file diff --git a/src/ontology/ro-odk.yaml b/src/ontology/ro-odk.yaml index 77e9d803..5b2a24a9 100644 --- a/src/ontology/ro-odk.yaml +++ b/src/ontology/ro-odk.yaml @@ -39,9 +39,6 @@ import_group: - id: go make_base: TRUE module_type: minimal - - id: caro - make_base: TRUE - module_type: minimal - id: other module_type: custom mirror_type: no_mirror @@ -52,6 +49,8 @@ import_group: - https://orcid.org/ - id: uberon module_type: filter + - id: obi + module_type: filter subset_group: products: