From 2f0377c24aaa4ce02f8ea1d15d441f58e2fa92ce Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Thu, 11 Jan 2024 08:04:23 -0300 Subject: [PATCH 01/13] add classification to `develops from` (#724) Co-authored-by: Anita Caron Co-authored-by: Chris Mungall --- src/ontology/ro-edit.owl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 7a086f0e..9c2ce65e 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -2243,6 +2243,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 Date: Thu, 1 Feb 2024 09:56:11 +0000 Subject: [PATCH 02/13] Create new ID range (#781) --- src/ontology/ro-idranges.owl | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/ontology/ro-idranges.owl b/src/ontology/ro-idranges.owl index 836f9614..bd4f0128 100644 --- a/src/ontology/ro-idranges.owl +++ b/src/ontology/ro-idranges.owl @@ -110,4 +110,8 @@ EquivalentTo: xsd:integer[> 20001 , <= 20100] Datatype: idrange:25 Annotations: allocatedto: "Damion Dooley" -EquivalentTo: xsd:integer[> 17500 , <= 18000] \ No newline at end of file +EquivalentTo: xsd:integer[> 17500 , <= 18000] + +Datatype: idrange:26 +Annotations: allocatedto: "Aleix Puig" +EquivalentTo: xsd:integer[> 20100 , <= 20200] \ No newline at end of file From 42c5b306b48ec5163e48e3ae61b0d3cf12dbf858 Mon Sep 17 00:00:00 2001 From: Harshad Date: Mon, 5 Feb 2024 03:43:34 -0600 Subject: [PATCH 03/13] Implementing ontobot-change-agent (#767) Co-authored-by: Anita Caron --- .github/workflows/ontobot.yml | 79 +++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 .github/workflows/ontobot.yml diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml new file mode 100644 index 00000000..4d73f790 --- /dev/null +++ b/.github/workflows/ontobot.yml @@ -0,0 +1,79 @@ +name: Create new pull request + +on: + workflow_dispatch: + issues: + types: [ opened, edited ] + +jobs: + build: + runs-on: ${{ matrix.os }} + container: obolibrary/odkfull:v1.4.3 + strategy: + matrix: + python-version: ["3.9"] + os: [ ubuntu-latest ] + + steps: + - name: Checkout main branch + uses: actions/checkout@v3 + + - name: Return issue number + id: gh-script-issue + uses: actions/github-script@v6 + with: + # github-token: ${{ secrets.GH_TOKEN }} + script: | + const issue_number = context.issue.number + const repo = context.repo.owner+"/"+context.repo.repo + return issue_number + + - name: Return repository name + id: gh-script-repo + uses: actions/github-script@v6 + with: + # github-token: ${{ secrets.GH_TOKEN }} + script: | + const repo = context.repo.owner+"/"+context.repo.repo + return repo + + - name: Set branch name + id: vars + run: | + echo "resource=src/ontology/ro-edit.owl" >> $GITHUB_ENV + echo "branch-name=kgcl_automation_"${{ steps.gh-script-issue.outputs.result }} >> $GITHUB_ENV + + - name: Get jar & enable plugin. + run: | + mkdir -p robot-plugins + wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O robot-plugins/kgcl.jar + echo "ROBOT_PLUGINS_DIRECTORY=$(pwd)/robot-plugins/" >> "$GITHUB_ENV" + + - name: Install dependencies + run: | + pip install ontobot-change-agent + + - name: Run ochange + id: ochange + run: | + ochange process-issue ${{ env.resource }} \ + -r ${{ steps.gh-script-repo.outputs.result }} \ + -n ${{ steps.gh-script-issue.outputs.result }} \ + -g ${{ secrets.GH_TOKEN }} + + - name: Clean-up + run: rm -rf robot-plugins + + - name: Create Pull Request + uses: peter-evans/create-pull-request@v5 + if: ${{ env.PR_TITLE}} + with: + token: ${{ secrets.GH_TOKEN }} + branch-suffix: short-commit-hash + labels: Automated + author: ${{ env.ISSUE_CREATOR }} <${{ env.ISSUE_CREATOR }}@users.noreply.github.com> + committer: ${{ env.ISSUE_CREATOR }} <${{ env.ISSUE_CREATOR }}@users.noreply.github.com> + body: ${{ env.PR_BODY }} + title: ${{ env.PR_TITLE }} + base: ${{ github.head_ref }} + branch: ${{ env.branch-name }} From 6801458e0b91b75d7d3d3cc0e5f36a05ffb92da8 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 6 Feb 2024 15:55:01 +0000 Subject: [PATCH 04/13] Fixes #699 NTR for blood vessels that drain and/or supply (#782) * Add supplies and drains with domain vessel * Change label and add punctuation * Add range and domain * Add examples * Improve definition * Remove 'blood vessel' from ro-edit.owl * Update directly_supplies_drains Updates label to 'directly supplies and drains', the domain is capillary (imported) and is a subproperty of 'supplies' and 'drains' --- src/ontology/imports/uberon_import.owl | 117 +++++++++++++++++++++++-- src/ontology/imports/uberon_terms.txt | 2 + src/ontology/ro-edit.owl | 68 ++++++++++---- 3 files changed, 162 insertions(+), 25 deletions(-) diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl index 6cab6d88..fb38f9e6 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( ) @@ -36,7 +36,7 @@ Annotation( ) Annotation( ) Annotation( ) -Annotation( ) +Annotation( ) Annotation( ) Annotation( ) Annotation( ) @@ -68,7 +68,7 @@ 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 "2023-08-16") +Annotation(owl:versionInfo "2024-02-02") Declaration(Class()) Declaration(Class()) @@ -78,12 +78,20 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +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()) @@ -98,6 +106,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -117,10 +126,30 @@ Declaration(AnnotationProperty()) SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: () SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + ############################ @@ -138,7 +167,6 @@ AnnotationAssertion( "CARO:0000003") AnnotationAssertion( "EHDAA2:0003003") AnnotationAssertion( "EMAPA:0") -AnnotationAssertion( "FBbt:00007001") AnnotationAssertion( "FMA:305751") AnnotationAssertion( "FMA:67135") AnnotationAssertion( "GAID:781") @@ -164,7 +192,6 @@ SubClassOf( "CARO:0001001") Annotation( "FBC:DOS") Annotation( "FBbt:00005099") "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.") AnnotationAssertion( "CARO:0001001") -AnnotationAssertion( "FBbt:00005099") AnnotationAssertion( "NLX:147821") AnnotationAssertion( "funiculus") AnnotationAssertion(Annotation( "FBbt:00005099") "nerve fiber bundle") @@ -183,7 +210,6 @@ AnnotationAssertion( "BILA:0000006") AnnotationAssertion( "CARO:0000006") AnnotationAssertion( "EHDAA2:0003006") -AnnotationAssertion( "FBbt:00007016") AnnotationAssertion( "FMA:67165") AnnotationAssertion( "HAO:0000006") AnnotationAssertion( "TAO:0001836") @@ -207,7 +233,6 @@ AnnotationAssertion( "BILA:0000007") AnnotationAssertion( "CARO:0000007") AnnotationAssertion( "EHDAA2:0003007") -AnnotationAssertion( "FBbt:00007015") AnnotationAssertion( "FMA:67112") AnnotationAssertion( "HAO:0000007") AnnotationAssertion( "TAO:0001835") @@ -228,11 +253,11 @@ AnnotationAssertion( ) AnnotationAssertion( "AAO:0010841") AnnotationAssertion( "AEO:0000000") +AnnotationAssertion( "BFO:0000004") AnnotationAssertion( "BILA:0000000") AnnotationAssertion( "BIRNLEX:6") AnnotationAssertion( "CARO:0000000") AnnotationAssertion( "EHDAA2:0002229") -AnnotationAssertion( "FBbt:10000000") AnnotationAssertion( "FMA:62955") AnnotationAssertion( "HAO:0000000") AnnotationAssertion( "MA:0000001") @@ -249,13 +274,87 @@ AnnotationAssertion( "anatomical entity") SubClassOf( ) +# Class: (blood vessel) + +AnnotationAssertion(Annotation( "BTO:0001102") Annotation( "Wikipedia:Blood_vessel") "A vessel through which blood circulates in the body.") +AnnotationAssertion( "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus") +AnnotationAssertion(Annotation( "EMAPA:35993") "vascular element") +AnnotationAssertion( "AAO:0011004") +AnnotationAssertion( "AEO:0000207") +AnnotationAssertion( "BTO:0001102") +AnnotationAssertion( "CALOHA:TS-0080") +AnnotationAssertion( "EFO:0000817") +AnnotationAssertion( "EHDAA2:0003252") +AnnotationAssertion( "EHDAA:240") +AnnotationAssertion( "EMAPA:32743") +AnnotationAssertion( "EMAPA:35993") +AnnotationAssertion( "FMA:50722") +AnnotationAssertion( "FMA:63183") +AnnotationAssertion( "GAID:169") +AnnotationAssertion( "MA:0000060") +AnnotationAssertion( "MAT:0000393") +AnnotationAssertion( "MESH:D001808") +AnnotationAssertion( "NCIT:C12679") +AnnotationAssertion( "NLXANAT:090901") +AnnotationAssertion( "SCTID:361097006") +AnnotationAssertion( "TAO:0002137") +AnnotationAssertion(Annotation( "ncithesaurus:Blood_Vessel") "UMLS:C0005847") +AnnotationAssertion( "VHOG:0001250") +AnnotationAssertion( "Wikipedia:Blood_vessel") +AnnotationAssertion( "XAO:0001011") +AnnotationAssertion( "ZFA:0005314") +AnnotationAssertion(Annotation( "FMA:50722") "region of vascular tree organ") +AnnotationAssertion(Annotation( "FMA:50722") "vascular tree organ region") +AnnotationAssertion( "UBERON:0001981") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "blood vessel") +SubClassOf( ) +SubClassOf( ) + +# Class: (capillary) + +AnnotationAssertion(Annotation( "ISBN:0073040584") Annotation( "Wikipedia:Capillary") Annotation( "https://github.com/obophenotype/uberon/issues/137") "Any of the smallest blood vessels connecting arterioles with venules.") +AnnotationAssertion( "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element") +AnnotationAssertion( "AAO:0010252") +AnnotationAssertion( "BTO:0002045") +AnnotationAssertion( "CALOHA:TS-2006") +AnnotationAssertion( "EFO:0001906") +AnnotationAssertion( "EMAPA:35198") +AnnotationAssertion( "EV:0100035") +AnnotationAssertion( "FMA:63194") +AnnotationAssertion( "MA:0000065") +AnnotationAssertion( "MESH:D002196") +AnnotationAssertion( "NCIT:C12685") +AnnotationAssertion( "NLXANAT:090902") +AnnotationAssertion( "TAO:0005250") +AnnotationAssertion(Annotation( "ncithesaurus:Capillary") "UMLS:C0935624") +AnnotationAssertion( "VHOG:0001253") +AnnotationAssertion( "Wikipedia:Capillary") +AnnotationAssertion( "XAO:0000116") +AnnotationAssertion( "ZFA:0005250") +AnnotationAssertion( "blood capillary") +AnnotationAssertion( "capillary vessel") +AnnotationAssertion( "UBERON:0001982") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capillary") +AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/issues/2186") +SubClassOf( ) +SubClassOf( ) + # Class: (multicellular anatomical structure) AnnotationAssertion(Annotation( "CARO:0010000") "An anatomical structure that has more than one cell as a part.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "CARO:0010000") -AnnotationAssertion( "FBbt:00100313") AnnotationAssertion(Annotation( "FBbt:00100313") "multicellular structure") AnnotationAssertion( "UBERON:0010000") AnnotationAssertion( ) diff --git a/src/ontology/imports/uberon_terms.txt b/src/ontology/imports/uberon_terms.txt index 5c82d708..773b2303 100644 --- a/src/ontology/imports/uberon_terms.txt +++ b/src/ontology/imports/uberon_terms.txt @@ -4,3 +4,5 @@ UBERON:0000466 UBERON:0000465 UBERON:0010000 UBERON:0000122 +UBERON:0001981 +UBERON:0001982 diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 9c2ce65e..0cfbf9e5 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -599,6 +599,9 @@ Declaration(ObjectProperty(obo:RO_0019000)) Declaration(ObjectProperty(obo:RO_0019001)) Declaration(ObjectProperty(obo:RO_0019002)) Declaration(ObjectProperty(obo:RO_0019501)) +Declaration(ObjectProperty(obo:RO_0020101)) +Declaration(ObjectProperty(obo:RO_0020102)) +Declaration(ObjectProperty(obo:RO_0020103)) Declaration(ObjectProperty(obo:RO_0040035)) Declaration(ObjectProperty(obo:RO_0040036)) Declaration(ObjectProperty(obo:RO_HOM0000000)) @@ -2242,8 +2245,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 ) AnnotationAssertion(rdfs:comment obo:RO_0002202 "This is the transitive form of the develops from relation") AnnotationAssertion(rdfs:label obo:RO_0002202 "develops from"@en) -SubObjectPropertyOf(obo:RO_0002202 obo:RO_0002258) SubObjectPropertyOf(obo:RO_0002202 obo:RO_0002254) +SubObjectPropertyOf(obo:RO_0002202 obo:RO_0002258) InverseObjectProperties(obo:RO_0002202 obo:RO_0002203) TransitiveObjectProperty(obo:RO_0002202) ObjectPropertyDomain(obo:RO_0002202 obo:BFO_0000004) @@ -6564,15 +6567,14 @@ IrreflexiveObjectProperty(obo:RO_0017004) # Object Property: obo:RO_0017005 (contains measured amount) +AnnotationAssertion(obo:IAO_0000112 obo:RO_0017005 "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen.") AnnotationAssertion(obo:IAO_0000115 obo:RO_0017005 "A relation between a container and measurement datum that specifies the actual amount of material in the container.") AnnotationAssertion(terms:contributor obo:RO_0017005 ) AnnotationAssertion(terms:contributor obo:RO_0017005 ) -AnnotationAssertion(obo:IAO_0000112 obo:RO_0017005 "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen.") AnnotationAssertion(rdfs:label obo:RO_0017005 "contains measured amount"@en) ObjectPropertyDomain(obo:RO_0017005 obo:OBI_0000967) ObjectPropertyRange(obo:RO_0017005 obo:COB_0000121) - # Object Property: obo:RO_0018001 (is myristoyltransferase activity) AnnotationAssertion(obo:IAO_0000115 obo:RO_0018001 "Helper relation for OWL definition of RO:0018002 myristoylates") @@ -6789,6 +6791,40 @@ AnnotationAssertion(oboInOwl:created_by obo:RO_0019501 ) +AnnotationAssertion(terms:date obo:RO_0020101 "2024-02-01T10:09:22Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:RO_0020101 "vessel supplies blood to") +SubObjectPropertyOf(obo:RO_0020101 obo:RO_0002178) +ObjectPropertyDomain(obo:RO_0020101 obo:UBERON_0001981) +ObjectPropertyRange(obo:RO_0020101 obo:UBERON_0000061) + +# Object Property: obo:RO_0020102 (vessel drains blood from) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0020102 "cystic vein vessel drains blood from gallbladder") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0020102 "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y.") +AnnotationAssertion(terms:contributor obo:RO_0020102 ) +AnnotationAssertion(terms:date obo:RO_0020102 "2024-02-01T10:09:41Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:RO_0020102 "vessel drains blood from") +SubObjectPropertyOf(obo:RO_0020102 obo:RO_0002179) +ObjectPropertyDomain(obo:RO_0020102 obo:UBERON_0001981) +ObjectPropertyRange(obo:RO_0020102 obo:UBERON_0000061) + +# Object Property: obo:RO_0020103 (directly supplies and drains) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0020103 "alveolar capillary directly supplies and drains some alveolus") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0020103 "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y.") +AnnotationAssertion(terms:contributor obo:RO_0020103 ) +AnnotationAssertion(terms:date obo:RO_0020103 "2024-02-01T10:09:59Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:RO_0020103 "directly supplies and drains") +SubObjectPropertyOf(obo:RO_0020103 obo:RO_0002178) +SubObjectPropertyOf(obo:RO_0020103 obo:RO_0002179) +ObjectPropertyDomain(obo:RO_0020103 obo:UBERON_0001982) +ObjectPropertyRange(obo:RO_0020103 obo:UBERON_0000061) + # Object Property: obo:RO_0040035 (disease relationship) AnnotationAssertion(obo:IAO_0000115 obo:RO_0040035 "This relation groups relations between diseases and any other kind of entity.") @@ -7123,19 +7159,19 @@ DLSafeRule(Annotation(rdfs:seeAlso ) Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002013 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002014 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002015 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002404 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002211 Variable() Variable()) ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012012 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0019002 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0019001 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002264 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002263 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002404 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002211 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012012 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0019002 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0019001 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002264 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002263 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))) AnnotationAssertion(owl:deprecated obo:BFO_0000060 "true"^^xsd:boolean) AnnotationAssertion(obo:IAO_0000115 obo:RO_0000092 "inverse of has disposition") AnnotationAssertion(oboInOwl:inSubset obo:RO_0000092 obo:RO_0002259) From 9e03509232dd8bae541a8de3be31364ca62c2980 Mon Sep 17 00:00:00 2001 From: Jim Balhoff Date: Tue, 6 Feb 2024 12:12:41 -0500 Subject: [PATCH 05/13] Change label of RO:0002297 to reflect anatomical range. (#779) Co-authored-by: Anita Caron --- src/ontology/ro-edit.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 0cfbf9e5..561bd9f7 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -2903,7 +2903,7 @@ AnnotationAssertion(rdfs:label obo:RO_0002296 "results in development of"@en) SubObjectPropertyOf(obo:RO_0002296 obo:RO_0002295) SubObjectPropertyOf(obo:RO_0002296 obo:RO_0040036) -# Object Property: obo:RO_0002297 (results in formation of) +# Object Property: obo:RO_0002297 (results in formation of anatomical entity) AnnotationAssertion(obo:IAO_0000112 obo:RO_0002297 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.") AnnotationAssertion(obo:IAO_0000112 obo:RO_0002297 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"@en) @@ -2913,7 +2913,7 @@ AnnotationAssertion(obo:IAO_0000119 obo:RO_0002297 "GOC:mtg_berkeley_2013") AnnotationAssertion(oboInOwl:inSubset obo:RO_0002297 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002297 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002297 obo:valid_for_gocam) -AnnotationAssertion(rdfs:label obo:RO_0002297 "results in formation of"@en) +AnnotationAssertion(rdfs:label obo:RO_0002297 "results in formation of anatomical entity"@en) SubObjectPropertyOf(obo:RO_0002297 obo:RO_0002234) SubObjectPropertyOf(obo:RO_0002297 obo:RO_0002295) InverseObjectProperties(obo:RO_0002297 obo:RO_0002354) From 3428cae77a0bb96f3c076bfef098ab2ad795d648 Mon Sep 17 00:00:00 2001 From: Bill Duncan Date: Fri, 9 Feb 2024 11:22:44 -0500 Subject: [PATCH 06/13] rename "exposure event or process" to "exposure of organism" (issue 599) (#606) * add exposure event class * change domain of 'related via exposure to' to 'exposure event' * obsolete 'exposure event or process' * add exposure of organism to cob_terms * remove creator "cmartin" (I do not know the ORICID) * change label to exposure of organism * chhange IRI to COB_0001000 * update 'id' annotation to COB:0001000 and removed editor note I thought was confusing * undo `cl_import` change * import `COB:0001000` properly --------- Co-authored-by: Anita Caron Co-authored-by: Anita Caron --- src/ontology/imports/cob_import.owl | 17 +++++++++++++---- src/ontology/imports/cob_terms.txt | 1 + src/ontology/ro-edit.owl | 11 ++++++----- 3 files changed, 20 insertions(+), 9 deletions(-) diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl index 0bf2cc29..7e5506bf 100644 --- a/src/ontology/imports/cob_import.owl +++ b/src/ontology/imports/cob_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-08-23"^^xsd:string) + +Annotation( ) +Annotation(owl:versionInfo "2024-02-09") Declaration(Class()) Declaration(Class()) @@ -21,6 +21,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -38,7 +39,9 @@ Declaration(ObjectProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) ############################ @@ -167,6 +170,12 @@ SubClassOf( "measurement datum") +# Class: (exposure of organism) + +AnnotationAssertion( "A process during which an organism comes into contact with another entity.") +AnnotationAssertion(rdfs:label "exposure of organism"@en) +SubClassOf( ) + # Class: (gene product or complex activity) AnnotationAssertion(rdfs:comment "This is the same as GO molecular function") @@ -188,4 +197,4 @@ SubClassOf( ObjectSomeValuesFrom( )) -) +) \ No newline at end of file diff --git a/src/ontology/imports/cob_terms.txt b/src/ontology/imports/cob_terms.txt index d913c3bb..d7e2168e 100644 --- a/src/ontology/imports/cob_terms.txt +++ b/src/ontology/imports/cob_terms.txt @@ -1 +1,2 @@ COB:0000121 +COB:0001000 diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 561bd9f7..14e12764 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -42,6 +42,7 @@ Annotation(foaf:homepage " https://github.com/oborel/obo-relations/"^^xsd:anyURI Declaration(Class(obo:BFO_0000019)) Declaration(Class(obo:BFO_0000031)) Declaration(Class(obo:CHEBI_50906)) +Declaration(Class(obo:COB_0001000)) Declaration(Class(obo:OGMS_0000031)) Declaration(Class(obo:RO_0002310)) Declaration(Class(obo:RO_0002532)) @@ -2672,7 +2673,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002244 "Any relationship between an AnnotationAssertion(obo:IAO_0000232 obo:RO_0002244 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.") AnnotationAssertion(rdfs:label obo:RO_0002244 "related via exposure to") SubObjectPropertyOf(obo:RO_0002244 obo:RO_0002410) -ObjectPropertyDomain(obo:RO_0002244 obo:RO_0002310) +ObjectPropertyDomain(obo:RO_0002244 obo:COB_0001000) # Object Property: obo:RO_0002245 (over-expressed in) @@ -6904,18 +6905,18 @@ SubClassOf(obo:GO_0016301 ObjectHasSelf(obo:RO_0002481)) SubClassOf(obo:GO_0019107 ObjectHasSelf(obo:RO_0018001)) -# Class: obo:RO_0002310 (exposure event or process) +# Class: obo:RO_0002310 (obsolete exposure event or process) AnnotationAssertion(obo:IAO_0000112 obo:RO_0002310 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human,") AnnotationAssertion(obo:IAO_0000112 obo:RO_0002310 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes."^^xsd:anyURI) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002310 "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002310 "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.") AnnotationAssertion(obo:IAO_0000116 obo:RO_0002310 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions.") AnnotationAssertion(terms:creator obo:RO_0002310 ) AnnotationAssertion(oboInOwl:created_by obo:RO_0002310 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002310 "2017-06-05T17:55:39Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label obo:RO_0002310 "exposure event or process") +AnnotationAssertion(rdfs:label obo:RO_0002310 "obsolete exposure event or process") AnnotationAssertion(rdfs:seeAlso obo:RO_0002310 "https://github.com/oborel/obo-relations/pull/173"^^xsd:anyURI) -SubClassOf(obo:RO_0002310 obo:BFO_0000015) +AnnotationAssertion(owl:deprecated obo:RO_0002310 "true"^^xsd:boolean) # Class: obo:RO_0002532 (sequentially ordered entity) From 1d6435bbaf74151fb91a1001b3327e774413a1d4 Mon Sep 17 00:00:00 2001 From: Nomi Harris Date: Mon, 12 Feb 2024 01:37:04 -0800 Subject: [PATCH 07/13] Correct number of days in 2 years (730, not 630) (#786) I wondered why issue #530 was closed as not having seen any activity in 2 years when it hadn't been 2 years. This is why: this workflow had > days-before-issue-stale: 630 when it should be 730. --- .github/workflows/stale-issues-and-prs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/stale-issues-and-prs.yml b/.github/workflows/stale-issues-and-prs.yml index 72ce6f9a..390c53b7 100644 --- a/.github/workflows/stale-issues-and-prs.yml +++ b/.github/workflows/stale-issues-and-prs.yml @@ -14,7 +14,7 @@ jobs: steps: - uses: actions/stale@v7 with: - days-before-issue-stale: 630 + days-before-issue-stale: 730 days-before-issue-close: 60 close-issue-label: 'autoclosed-unfixed' close-issue-reason: 'not_planned' From a2de6b369a64d3746a37a0077e8497bf85d63c86 Mon Sep 17 00:00:00 2001 From: Jim Balhoff Date: Tue, 13 Feb 2024 05:18:17 -0500 Subject: [PATCH 08/13] Restore parent of 'regulates in another organism' to be 'causally upstream of or within'. (#789) --- src/ontology/ro-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 14e12764..6890634b 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -1492,7 +1492,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002010 Date: Thu, 15 Feb 2024 06:32:24 -0300 Subject: [PATCH 09/13] 2024-02-13 Release (#788) * update orcidio_import * 2024-02-12 release * 2024-02-13 release --------- Co-authored-by: Anita Caron --- core.json | 4 +- core.obo | 8 +- core.owl | 6 +- ro-base.json | 243 ++++- ro-base.obo | 145 ++- ro-base.owl | 445 ++++++--- ro-full.json | 624 ++++++++++++- ro-full.obo | 317 ++++++- ro-full.owl | 875 ++++++++++++++---- ro.json | 624 ++++++++++++- ro.obo | 317 ++++++- ro.owl | 875 ++++++++++++++---- src/ontology/imports/orcidio_import.owl | 40 +- .../subsets/ro-biotic-interaction.json | 49 + .../subsets/ro-biotic-interaction.obo | 20 + .../subsets/ro-biotic-interaction.owl | 37 +- src/ontology/subsets/ro-causal.json | 256 ++++- src/ontology/subsets/ro-causal.obo | 108 ++- src/ontology/subsets/ro-causal.owl | 162 +++- src/ontology/subsets/ro-causal.tsv | 32 +- src/ontology/subsets/ro-chado.json | 277 +++++- src/ontology/subsets/ro-chado.obo | 84 +- src/ontology/subsets/ro-chado.owl | 511 +++++++--- src/ontology/subsets/ro-developmental.json | 256 ++++- src/ontology/subsets/ro-developmental.obo | 108 ++- src/ontology/subsets/ro-developmental.owl | 162 +++- src/ontology/subsets/ro-developmental.tsv | 32 +- src/ontology/subsets/ro-interaction.json | 256 ++++- src/ontology/subsets/ro-interaction.obo | 108 ++- src/ontology/subsets/ro-interaction.owl | 162 +++- src/ontology/subsets/ro-interaction.tsv | 32 +- src/ontology/subsets/ro-mereotopology.json | 256 ++++- src/ontology/subsets/ro-mereotopology.obo | 108 ++- src/ontology/subsets/ro-mereotopology.owl | 162 +++- src/ontology/subsets/ro-mereotopology.tsv | 32 +- src/ontology/subsets/ro-sequence.json | 256 ++++- src/ontology/subsets/ro-sequence.obo | 108 ++- src/ontology/subsets/ro-sequence.owl | 162 +++- src/ontology/subsets/ro-sequence.tsv | 32 +- src/ontology/subsets/ro-time-interval.json | 256 ++++- src/ontology/subsets/ro-time-interval.obo | 108 ++- src/ontology/subsets/ro-time-interval.owl | 162 +++- src/ontology/subsets/ro-time-interval.tsv | 32 +- subsets/ro-biotic-interaction.json | 49 + subsets/ro-biotic-interaction.obo | 20 + subsets/ro-biotic-interaction.owl | 37 +- subsets/ro-causal.json | 256 ++++- subsets/ro-causal.obo | 108 ++- subsets/ro-causal.owl | 162 +++- subsets/ro-causal.tsv | 32 +- subsets/ro-chado.json | 277 +++++- subsets/ro-chado.obo | 84 +- subsets/ro-chado.owl | 511 +++++++--- subsets/ro-developmental.json | 256 ++++- subsets/ro-developmental.obo | 108 ++- subsets/ro-developmental.owl | 162 +++- subsets/ro-developmental.tsv | 32 +- subsets/ro-interaction.json | 256 ++++- subsets/ro-interaction.obo | 108 ++- subsets/ro-interaction.owl | 162 +++- subsets/ro-interaction.tsv | 32 +- subsets/ro-mereotopology.json | 256 ++++- subsets/ro-mereotopology.obo | 108 ++- subsets/ro-mereotopology.owl | 162 +++- subsets/ro-mereotopology.tsv | 32 +- subsets/ro-sequence.json | 256 ++++- subsets/ro-sequence.obo | 108 ++- subsets/ro-sequence.owl | 162 +++- subsets/ro-sequence.tsv | 32 +- subsets/ro-time-interval.json | 256 ++++- subsets/ro-time-interval.obo | 108 ++- subsets/ro-time-interval.owl | 162 +++- subsets/ro-time-interval.tsv | 32 +- 73 files changed, 11595 insertions(+), 1580 deletions(-) diff --git a/core.json b/core.json index cbd70634..a801c5ff 100644 --- a/core.json +++ b/core.json @@ -7,12 +7,12 @@ "val" : "https://creativecommons.org/publicdomain/zero/1.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : "https://github.com/oborel/obo-relations/wiki/ROCore" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/core.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/core.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", diff --git a/core.obo b/core.obo index 5ef0e65d..ef9d44e4 100644 --- a/core.obo +++ b/core.obo @@ -1,9 +1,9 @@ format-version: 1.2 -data-version: ro/releases/2023-08-18/core.owl +data-version: ro/releases/2024-02-13/core.owl ontology: ro/core property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage "https://github.com/oborel/obo-relations/wiki/ROCore" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Term] id: BFO:0000002 @@ -381,8 +381,8 @@ property_value: IAO:0000116 "Location as a relation between instances: The primi property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true [Typedef] diff --git a/core.owl b/core.owl index 5604e8b3..89595aca 100644 --- a/core.owl +++ b/core.owl @@ -13,9 +13,9 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - 2023-08-18 + 2024-02-13 https://github.com/oborel/obo-relations/wiki/ROCore @@ -985,5 +985,5 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + diff --git a/ro-base.json b/ro-base.json index f82d0759..25a78385 100644 --- a/ro-base.json +++ b/ro-base.json @@ -16,12 +16,12 @@ "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro-base.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -1195,12 +1195,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -3975,7 +3980,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -4192,11 +4197,11 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002310", - "lbl" : "exposure event or process", + "lbl" : "obsolete exposure event or process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." + "val" : "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -4219,7 +4224,8 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/173" - } ] + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002312", @@ -8861,6 +8867,43 @@ "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", @@ -10533,6 +10576,54 @@ "val" : "2022-09-26T06:08:01Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11017,6 +11108,25 @@ "val" : "https://orcid.org/0000-0003-1909-9269" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017005", + "lbl" : "contains measured amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a container and measurement datum that specifies the actual amount of material in the container." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2999-0103" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-5714-991X" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -11428,6 +11538,63 @@ "val" : "https://orcid.org/0000-0002-4142-7153" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -13500,10 +13667,6 @@ "sub" : "http://purl.obolibrary.org/obo/CHEBI_50906", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002310", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002532", "pred" : "http://purl.obolibrary.org/obo/RO_0002524", @@ -13908,6 +14071,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -15380,6 +15547,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -15792,6 +15967,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -15968,6 +16151,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -16644,6 +16843,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003000", "pred" : "inverseOf", @@ -16974,7 +17177,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -17286,10 +17489,26 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0017005", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000967" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000121" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/ro-base.obo b/ro-base.obo index 8efea67c..f5733cdf 100644 --- a/ro-base.obo +++ b/ro-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: ro/releases/2023-08-18/ro-base.owl +data-version: ro/releases/2024-02-13/ro-base.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -12,7 +12,7 @@ property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Term] id: BFO:0000002 @@ -128,14 +128,14 @@ id: GO:0019107 [Term] id: RO:0002310 -name: exposure event or process -def: "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] -is_a: BFO:0000015 ! process +name: obsolete exposure event or process +def: "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/pull/173" xsd:anyURI +is_obsolete: true created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:55:39Z @@ -612,8 +612,8 @@ property_value: IAO:0000116 "Most location relations will only hold at certain t property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true transitive_over: BFO:0000050 ! part of @@ -722,8 +722,10 @@ is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 -name: regulates in other organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 ! process range: BFO:0000015 ! process @@ -1270,7 +1272,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -1450,7 +1452,7 @@ def: "a is attached to part of b if a is attached to b, or a is attached to some property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string domain: UBERON:0000061 range: UBERON:0000061 -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002371 BFO:0000050 {RO:0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1516,6 +1518,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true +is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -1702,7 +1705,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -1742,7 +1745,7 @@ def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1980,7 +1983,7 @@ id: RO:0002244 name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 ! exposure event or process +domain: COB:0001000 is_a: RO:0002410 ! causally related to [Typedef] @@ -2219,7 +2222,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002297 -name: results in formation of +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -2367,7 +2370,7 @@ property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -2484,7 +2487,7 @@ name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -2768,7 +2771,7 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -3191,7 +3194,7 @@ property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd: property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -3625,7 +3628,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002480 @@ -3859,7 +3862,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 ! system range: BFO:0000040 ! material entity -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -4110,7 +4113,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of is_asymmetric: true @@ -4370,7 +4373,7 @@ is_a: RO:0002233 ! has input [Typedef] id: RO:0002587 name: results in synthesis of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity [Typedef] id: RO:0002588 @@ -4378,7 +4381,7 @@ name: results in assembly of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity is_a: RO:0002592 ! results in organization of [Typedef] @@ -4679,6 +4682,26 @@ property_value: IAO:0000119 Communal:roosting is_symmetric: true is_a: RO:0008506 ! ecologically co-occurs with +[Typedef] +id: RO:0002802 +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: RO:0002454 ! has host + [Typedef] id: RO:0003000 name: produces @@ -5613,6 +5636,28 @@ is_a: RO:0012011 ! indirectly causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z +[Typedef] +id: RO:0012013 +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + +[Typedef] +id: RO:0012014 +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: RO:0013001 name: has synaptic IO in region @@ -5869,6 +5914,16 @@ property_value: IAO:0000118 "inversely correlated with" xsd:string is_symmetric: true is_a: RO:0002610 ! correlated with +[Typedef] +id: RO:0017005 +name: contains measured amount +def: "A relation between a container and measurement datum that specifies the actual amount of material in the container." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2999-0103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-5714-991X +property_value: IAO:0000112 "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." xsd:string +domain: OBI:0000967 +range: COB:0000121 + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -5988,7 +6043,7 @@ synonym: "is desmotrope of" EXACT [] xref: obo:chebi#is_tautomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38707", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38709"} +property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {seeAlso="CHEBI:38707", seeAlso="CHEBI:38709"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6000,7 +6055,7 @@ def: "Group A is a substituent group from Chemical B if A represents the functio xref: obo:chebi#is_substituent_group_from property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:30795", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:58957"} +property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {seeAlso="CHEBI:30795", seeAlso="CHEBI:58957"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6011,7 +6066,7 @@ def: "Chemical A has functional parent Chemical B if there is chemical transform xref: obo:chebi#has_functional_parent property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50851", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50854"} +property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {seeAlso="CHEBI:50851", seeAlso="CHEBI:50854"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6023,7 +6078,7 @@ synonym: "is optical isomer of" EXACT [] xref: obo:chebi#is_enantiomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:31472"} +property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", seeAlso="CHEBI:31472"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6035,7 +6090,7 @@ def: "Chemical A has parent hydride Chemical B if there exists a molecular graph xref: obo:chebi#has_parent_hydride property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:39106", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:52083"} +property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {seeAlso="CHEBI:39106", seeAlso="CHEBI:52083"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6073,6 +6128,40 @@ def: "Relates a gene to condition, such that a variation in this gene predispose is_a: RO:0003304 ! contributes to condition created_by: https://orcid.org/0000-0002-4142-7153 +[Typedef] +id: RO:0020101 +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: RO:0002178 ! supplies + +[Typedef] +id: RO:0020102 +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: RO:0002179 ! drains + +[Typedef] +id: RO:0020103 +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: RO:0002178 ! supplies +is_a: RO:0002179 ! drains + [Typedef] id: RO:0040035 name: disease relationship diff --git a/ro-base.owl b/ro-base.owl index f6602b63..b64dfefc 100644 --- a/ro-base.owl +++ b/ro-base.owl @@ -18,12 +18,12 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2023-08-18 + 2024-02-13 https://github.com/oborel/obo-relations/ @@ -1994,7 +1994,9 @@ AND t has_input y x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - regulates in other organism + regulates in other organism + + regulates in another organism @@ -3329,6 +3331,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + @@ -4079,7 +4082,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure to @@ -4446,7 +4449,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results in formation of + results in formation of anatomical entity @@ -8339,6 +8342,34 @@ the a supports either the existence of b, or the truth value of b. + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -9805,6 +9836,36 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + positively regulates in other organism + + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + negatively regulates in other organism + + negatively regulates in another organism + + + + @@ -10246,6 +10307,20 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. + A relation between a container and measurement datum that specifies the actual amount of material in the container. + + + contains measured amount + + + + @@ -10616,6 +10691,52 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + directly supplies and drains + + + + @@ -12563,6 +12684,18 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + + + + + + @@ -12632,6 +12765,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + @@ -12671,16 +12810,16 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. - A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. + OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. 2017-06-05T17:55:39Z - exposure event or process + obsolete exposure event or process https://github.com/oborel/obo-relations/pull/173 + true @@ -12768,6 +12907,18 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + + + + + + @@ -12909,10 +13060,10 @@ binary, and takes no temporal argument. /////////////////////////////////////////////////////////////////////////////////////// --> - + - + @@ -12930,66 +13081,54 @@ binary, and takes no temporal argument. - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - @@ -13002,8 +13141,8 @@ binary, and takes no temporal argument. - - + + @@ -13013,7 +13152,7 @@ binary, and takes no temporal argument. - + @@ -13023,7 +13162,7 @@ binary, and takes no temporal argument. - + @@ -13040,8 +13179,8 @@ binary, and takes no temporal argument. - - + + @@ -13303,7 +13442,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13313,8 +13452,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13324,8 +13463,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13342,8 +13481,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13362,7 +13501,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13372,8 +13511,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13383,8 +13522,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13401,8 +13540,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13419,8 +13558,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13430,7 +13569,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13440,8 +13579,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13451,8 +13590,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13471,8 +13610,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13490,8 +13629,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13501,8 +13640,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13512,8 +13651,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13530,8 +13669,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13548,8 +13687,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13559,8 +13698,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13570,8 +13709,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13588,8 +13727,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13606,8 +13745,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13617,8 +13756,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13628,8 +13767,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13646,8 +13785,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13664,8 +13803,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13675,8 +13814,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13691,8 +13830,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13709,8 +13848,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13720,8 +13859,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13736,8 +13875,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13754,8 +13893,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13765,8 +13904,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13781,8 +13920,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13799,8 +13938,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13810,8 +13949,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13826,8 +13965,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13844,8 +13983,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13855,8 +13994,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13871,8 +14010,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13889,8 +14028,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13900,8 +14039,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13916,7 +14055,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13926,7 +14065,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13945,8 +14084,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13956,8 +14095,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -13972,7 +14111,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -13982,7 +14121,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14044,8 +14183,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -14055,8 +14194,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -14071,8 +14210,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -14088,8 +14227,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -14098,9 +14237,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -14114,9 +14253,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -14132,8 +14271,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -14142,9 +14281,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -14158,7 +14297,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -14259,5 +14398,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/ro-full.json b/ro-full.json index ecabec35..3d4c0d6e 100644 --- a/ro-full.json +++ b/ro-full.json @@ -13,12 +13,12 @@ "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro-full.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -153,7 +153,14 @@ "definition" : { "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" }, - "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ] + "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/OBOFoundry/COB/issues/65" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", @@ -459,10 +466,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", - "xrefs" : [ "CARO:mah" ] + "val" : "A material entity that has a plasma membrane and results from cellular division." }, - "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], + "comments" : [ "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.", "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).", "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism." ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -536,6 +542,19 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/COB_0000121", + "lbl" : "measurement datum", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/COB_0001000", + "lbl" : "exposure of organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process during which an organism comes into contact with another entity." + } + } }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", "lbl" : "environmental system", @@ -596,7 +615,7 @@ "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", "xrefs" : [ "GOC:pdt" ] }, - "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], + "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "This is the same as GO molecular function" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecular function" @@ -924,10 +943,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", - "xrefs" : [ "GOC:pdt" ] + "val" : "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." }, - "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "comments" : [ "A biological process is an evolved process", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "biological process" @@ -2273,6 +2291,84 @@ "val" : "EL++ ontology module" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000047", + "lbl" : "processed material", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Is a material entity that is created or changed during material processing." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "processed material" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000967", + "lbl" : "container", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A device that can be used to restrict the location of material entities over time" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "container" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000123" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000968", + "lbl" : "device", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "device" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A voltmeter is a measurement device which is intended to perform some measure function." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Helen Parkinson" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "instrument" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI development call 2012-12-17." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0100026", "lbl" : "organism", @@ -2625,6 +2721,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -3359,12 +3458,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -6139,7 +6243,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -6356,11 +6460,11 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002310", - "lbl" : "exposure event or process", + "lbl" : "obsolete exposure event or process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." + "val" : "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -6383,7 +6487,8 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/173" - } ] + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002312", @@ -11025,6 +11130,43 @@ "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", @@ -12697,6 +12839,54 @@ "val" : "2022-09-26T06:08:01Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -13181,6 +13371,25 @@ "val" : "https://orcid.org/0000-0003-1909-9269" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017005", + "lbl" : "contains measured amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a container and measurement datum that specifies the actual amount of material in the container." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2999-0103" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-5714-991X" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -13592,6 +13801,63 @@ "val" : "https://orcid.org/0000-0002-4142-7153" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -15527,8 +15793,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -15586,8 +15850,6 @@ } ], "xrefs" : [ { "val" : "CARO:0001001" - }, { - "val" : "FBbt:00005099" }, { "val" : "NLX:147821" } ] @@ -15612,8 +15874,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -15658,8 +15918,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -15693,6 +15951,8 @@ "val" : "AAO:0010841" }, { "val" : "AEO:0000000" + }, { + "val" : "BFO:0000004" }, { "val" : "BILA:0000000" }, { @@ -15701,8 +15961,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -15732,6 +15990,143 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "lbl" : "blood vessel", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A vessel through which blood circulates in the body.", + "xrefs" : [ "BTO:0001102", "Wikipedia:Blood_vessel" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "vascular element", + "xrefs" : [ "EMAPA:35993" ] + }, { + "pred" : "hasExactSynonym", + "val" : "region of vascular tree organ", + "xrefs" : [ "FMA:50722" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vascular tree organ region", + "xrefs" : [ "FMA:50722" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011004" + }, { + "val" : "AEO:0000207" + }, { + "val" : "BTO:0001102" + }, { + "val" : "CALOHA:TS-0080" + }, { + "val" : "EFO:0000817" + }, { + "val" : "EHDAA2:0003252" + }, { + "val" : "EHDAA:240" + }, { + "val" : "EMAPA:32743" + }, { + "val" : "EMAPA:35993" + }, { + "val" : "FMA:50722" + }, { + "val" : "FMA:63183" + }, { + "val" : "GAID:169" + }, { + "val" : "MA:0000060" + }, { + "val" : "MAT:0000393" + }, { + "val" : "MESH:D001808" + }, { + "val" : "NCIT:C12679" + }, { + "val" : "NLXANAT:090901" + }, { + "val" : "SCTID:361097006" + }, { + "val" : "TAO:0002137" + }, { + "val" : "UMLS:C0005847" + }, { + "val" : "VHOG:0001250" + }, { + "val" : "Wikipedia:Blood_vessel" + }, { + "val" : "XAO:0001011" + }, { + "val" : "ZFA:0005314" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001982", + "lbl" : "capillary", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any of the smallest blood vessels connecting arterioles with venules.", + "xrefs" : [ "ISBN:0073040584", "Wikipedia:Capillary", "https://github.com/obophenotype/uberon/issues/137" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blood capillary" + }, { + "pred" : "hasExactSynonym", + "val" : "capillary vessel" + } ], + "xrefs" : [ { + "val" : "AAO:0010252" + }, { + "val" : "BTO:0002045" + }, { + "val" : "CALOHA:TS-2006" + }, { + "val" : "EFO:0001906" + }, { + "val" : "EMAPA:35198" + }, { + "val" : "EV:0100035" + }, { + "val" : "FMA:63194" + }, { + "val" : "MA:0000065" + }, { + "val" : "MESH:D002196" + }, { + "val" : "NCIT:C12685" + }, { + "val" : "NLXANAT:090902" + }, { + "val" : "TAO:0005250" + }, { + "val" : "UMLS:C0935624" + }, { + "val" : "VHOG:0001253" + }, { + "val" : "Wikipedia:Capillary" + }, { + "val" : "XAO:0000116" + }, { + "val" : "ZFA:0005250" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2186" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", "lbl" : "multicellular anatomical structure", @@ -15749,8 +16144,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -15938,6 +16331,16 @@ "val" : "is defined by" } ] } + }, { + "id" : "https://orcid.org/0000-0001-6677-8489", + "lbl" : "Aleix Puig-Barbé", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0001-6677-8489" + } ] + } }, { "id" : "https://orcid.org/0000-0001-6996-0040", "lbl" : "Austin Meier", @@ -15978,6 +16381,16 @@ "val" : "data scientist" } ] } + }, { + "id" : "https://orcid.org/0000-0002-2999-0103", + "lbl" : "Jie Zheng", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-2999-0103)" + } ] + } }, { "id" : "https://orcid.org/0000-0002-4366-3088", "lbl" : "Pier Luigi Buttigieg", @@ -15988,6 +16401,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-5714-991X", + "lbl" : "Christian J Stoeckert", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-6601-2165", "lbl" : "Christopher J. Mungall", @@ -16048,6 +16471,26 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1813-6857", + "lbl" : "Pascale Gaudet", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Canadian biocurator" + } ] + } + }, { + "id" : "https://orcid.org/0000-0003-1909-9269", + "lbl" : "S. Clint Dowland", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-1909-9269" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1940-6740", "lbl" : "Anna Maria Masci", @@ -16058,6 +16501,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-3138-4118", + "lbl" : "Jorrit Poelen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "software/data engineer" + } ] + } }, { "id" : "https://orcid.org/0000-0003-4423-4370", "lbl" : "Charles Tapley Hoyt", @@ -16133,6 +16586,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000540", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/COB_0001000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/ENVO_01000254", "pred" : "is_a", @@ -16141,10 +16598,26 @@ "sub" : "http://purl.obolibrary.org/obo/ENVO_01000739", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0003674", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0004842", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0003674" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0005634", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0008150", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0008150", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0003674" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0016301", "pred" : "is_a", @@ -16157,6 +16630,18 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000030", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000047", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000967", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000968" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000968", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000047" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0100026", "pred" : "is_a", @@ -16181,10 +16666,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002124", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002310", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002532", "pred" : "http://purl.obolibrary.org/obo/RO_0002524", @@ -16229,6 +16710,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010000" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001982", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010000", "pred" : "is_a", @@ -16633,6 +17122,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -18105,6 +18598,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -18517,6 +19018,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -18693,6 +19202,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -19369,6 +19894,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003000", "pred" : "inverseOf", @@ -19468,6 +19997,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -19507,6 +20040,13 @@ "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -19525,7 +20065,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", @@ -19533,7 +20073,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", @@ -19699,7 +20239,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -20011,10 +20551,26 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0017005", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000967" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000121" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/ro-full.obo b/ro-full.obo index 6879f323..5d3d9956 100644 --- a/ro-full.obo +++ b/ro-full.obo @@ -1,19 +1,24 @@ format-version: 1.2 -data-version: ro/releases/2023-08-18/ro-full.owl +data-version: ro/releases/2024-02-13/ro-full.owl subsetdef: common_anatomy "" +subsetdef: efo_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: human_reference_atlas "" +subsetdef: pheno_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" +subsetdef: uberon_slim "" subsetdef: upper_level "" +subsetdef: vertebrate_core "" ontology: ro/ro-full property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Term] id: BFO:0000002 @@ -37,7 +42,7 @@ name: independent continuant def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000020 ! characteristic disjoint_from: BFO:0000031 ! generically dependent continuant relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant @@ -52,6 +57,7 @@ name: process def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000015 {all_only="true"} ! part of process relationship: RO:0002214 BFO:0000015 {all_only="true"} ! has prototype process [Term] @@ -62,26 +68,31 @@ disjoint_from: BFO:0000023 ! role [Term] id: BFO:0000017 +name: realizable name: realizable entity def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic disjoint_from: BFO:0000019 ! quality relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity [Term] id: BFO:0000019 name: quality -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 +name: characteristic name: specifically dependent continuant def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of characteristic +relationship: BFO:0000051 BFO:0000020 {all_only="true"} ! has part characteristic +property_value: seeAlso "https://github.com/OBOFoundry/COB/issues/65" xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string [Term] id: BFO:0000023 @@ -122,7 +133,10 @@ is_a: PATO:0000001 ! quality id: CL:0000000 name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] +def: "A material entity that has a plasma membrane and results from cellular division." [] +comment: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). +comment: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. xref: CALOHA:TS-2035 xref: FBbt:00007002 xref: FMA:68646 @@ -160,6 +174,16 @@ xref: WBbt:0003679 is_a: CL:0000000 ! cell property_value: RO:0002175 NCBITaxon:9606 +[Term] +id: COB:0000121 +name: measurement datum + +[Term] +id: COB:0001000 +name: exposure of organism +def: "A process during which an organism comes into contact with another entity." [] +is_a: BFO:0000015 ! process + [Term] id: ENVO:01000254 name: environmental system @@ -183,10 +207,14 @@ is_a: ENVO:01000254 ! environmental system [Term] id: GO:0003674 +name: gene product or complex activity name: molecular_function def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +comment: This is the same as GO molecular function synonym: "molecular function" EXACT [] +is_a: BFO:0000015 ! process +disjoint_from: GO:0008150 ! biological_process [Term] id: GO:0004842 @@ -333,23 +361,30 @@ is_a: GO:0003674 ! molecular_function [Term] id: GO:0005634 +name: cell nucleus name: nucleus def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] synonym: "cell nucleus" EXACT [] synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757] xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus +is_a: BFO:0000040 ! material entity [Term] id: GO:0008150 +name: biological process name: biological_process def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." [] +comment: A biological process is an evolved process comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process +is_a: BFO:0000015 ! process +relationship: BFO:0000051 GO:0003674 ! has part molecular_function created_by: jl creation_date: 2012-09-19T15:05:24Z @@ -388,6 +423,40 @@ property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 "GROUP:OBI:" xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string +[Term] +id: OBI:0000047 +name: processed material +def: "Is a material entity that is created or changed during material processing." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000111 "processed material" xsd:string +property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string + +[Term] +id: OBI:0000967 +name: container +def: "A device that can be used to restrict the location of material entities over time" [] +is_a: OBI:0000968 ! device +property_value: IAO:0000111 "container" xsd:string +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string + +[Term] +id: OBI:0000968 +name: device +def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." [] +is_a: OBI:0000047 ! processed material +property_value: IAO:0000111 "device" xsd:string +property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string +property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." xsd:string +property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string +property_value: IAO:0000118 "instrument" xsd:string +property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string + [Term] id: OBI:0100026 name: organism @@ -414,7 +483,7 @@ is_a: BFO:0000016 ! disposition id: PATO:0000001 name: quality def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic [Term] id: PATO:0000402 @@ -441,14 +510,14 @@ creation_date: 2009-10-06T04:37:14Z [Term] id: RO:0002310 -name: exposure event or process -def: "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] -is_a: BFO:0000015 ! process +name: obsolete exposure event or process +def: "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/pull/173" xsd:anyURI +is_obsolete: true created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:55:39Z @@ -498,7 +567,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -524,7 +592,6 @@ synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 -xref: FBbt:00005099 xref: NLX:147821 is_a: UBERON:0000061 ! anatomical structure @@ -539,7 +606,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -563,7 +629,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -582,11 +647,11 @@ subset: common_anatomy subset: upper_level xref: AAO:0010841 xref: AEO:0000000 +xref: BFO:0000004 xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -601,6 +666,77 @@ is_a: BFO:0000004 ! independent continuant property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:4751 +[Term] +id: UBERON:0001981 +name: blood vessel +def: "A vessel through which blood circulates in the body." [BTO:0001102, Wikipedia:Blood_vessel] +subset: efo_slim +subset: human_reference_atlas +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "region of vascular tree organ" EXACT [FMA:50722] +synonym: "vascular element" BROAD [EMAPA:35993] +synonym: "vascular tree organ region" EXACT [FMA:50722] +xref: AAO:0011004 +xref: AEO:0000207 +xref: BTO:0001102 +xref: CALOHA:TS-0080 +xref: EFO:0000817 +xref: EHDAA2:0003252 +xref: EHDAA:240 +xref: EMAPA:32743 +xref: EMAPA:35993 +xref: FMA:50722 +xref: FMA:63183 +xref: GAID:169 +xref: MA:0000060 +xref: MAT:0000393 +xref: MESH:D001808 +xref: NCIT:C12679 +xref: NLXANAT:090901 +xref: SCTID:361097006 +xref: TAO:0002137 +xref: UMLS:C0005847 {source="ncithesaurus:Blood_Vessel"} +xref: VHOG:0001250 +xref: Wikipedia:Blood_vessel +xref: XAO:0001011 +xref: ZFA:0005314 +is_a: UBERON:0010000 ! multicellular anatomical structure +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string + +[Term] +id: UBERON:0001982 +name: capillary +def: "Any of the smallest blood vessels connecting arterioles with venules." [https://github.com/obophenotype/uberon/issues/137, ISBN:0073040584, Wikipedia:Capillary] +subset: efo_slim +subset: human_reference_atlas +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "blood capillary" EXACT [] +synonym: "capillary vessel" EXACT [] +xref: AAO:0010252 +xref: BTO:0002045 +xref: CALOHA:TS-2006 +xref: EFO:0001906 +xref: EMAPA:35198 +xref: EV:0100035 +xref: FMA:63194 +xref: MA:0000065 +xref: MESH:D002196 +xref: NCIT:C12685 +xref: NLXANAT:090902 +xref: TAO:0005250 +xref: UMLS:C0935624 {source="ncithesaurus:Capillary"} +xref: VHOG:0001253 +xref: Wikipedia:Capillary +xref: XAO:0000116 +xref: ZFA:0005250 +is_a: UBERON:0001981 ! blood vessel +property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string + [Term] id: UBERON:0010000 name: multicellular anatomical structure @@ -609,7 +745,6 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 is_a: UBERON:0000061 ! anatomical structure property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:4751 @@ -753,6 +888,7 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process @@ -796,7 +932,8 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string +range: BFO:0000020 ! characteristic is_inverse_functional: true [Typedef] @@ -824,6 +961,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000002 ! continuant holds_over_chain: BFO:0000051 RO:0000057 @@ -834,7 +972,7 @@ def: "A relationship between a generically dependent continuant and a specifical property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000031 ! generically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! characteristic inverse_of: RO:0000059 ! concretizes [Typedef] @@ -843,7 +981,7 @@ name: concretizes def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string -domain: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic range: BFO:0000031 ! generically dependent continuant [Typedef] @@ -1065,8 +1203,8 @@ property_value: IAO:0000116 "Most location relations will only hold at certain t property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true transitive_over: BFO:0000050 ! part of @@ -1175,8 +1313,10 @@ is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 -name: regulates in other organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 ! process range: BFO:0000015 ! process @@ -1723,7 +1863,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -1903,7 +2043,7 @@ def: "a is attached to part of b if a is attached to b, or a is attached to some property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002371 BFO:0000050 {RO:0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1969,6 +2109,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true +is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -2155,7 +2296,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -2195,7 +2336,7 @@ def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -2433,7 +2574,7 @@ id: RO:0002244 name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 ! exposure event or process +domain: COB:0001000 ! exposure of organism is_a: RO:0002410 ! causally related to [Typedef] @@ -2672,7 +2813,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002297 -name: results in formation of +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -2820,7 +2961,7 @@ property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -2937,7 +3078,7 @@ name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -3221,7 +3362,7 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -3581,7 +3722,7 @@ is_a: RO:0002424 ! differs in id: RO:0002426 name: differs in attribute property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! characteristic is_a: RO:0002424 ! differs in [Typedef] @@ -3644,7 +3785,7 @@ property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd: property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -4078,7 +4219,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002480 @@ -4312,7 +4453,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 ! system range: BFO:0000040 ! material entity -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -4563,7 +4704,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000465 {http://purl.obolibrary.org/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."} ! material anatomical entity +range: UBERON:0000465 {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."} ! material anatomical entity is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of is_asymmetric: true @@ -4754,8 +4895,8 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string -domain: BFO:0000020 ! specifically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic +range: BFO:0000020 ! characteristic [Typedef] id: RO:0002574 @@ -4823,7 +4964,7 @@ is_a: RO:0002233 ! has input [Typedef] id: RO:0002587 name: results in synthesis of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity [Typedef] id: RO:0002588 @@ -4831,7 +4972,7 @@ name: results in assembly of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity is_a: RO:0002592 ! results in organization of [Typedef] @@ -5132,6 +5273,26 @@ property_value: IAO:0000119 Communal:roosting is_symmetric: true is_a: RO:0008506 ! ecologically co-occurs with +[Typedef] +id: RO:0002802 +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: RO:0002454 ! has host + [Typedef] id: RO:0003000 name: produces @@ -6066,6 +6227,28 @@ is_a: RO:0012011 ! indirectly causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z +[Typedef] +id: RO:0012013 +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + +[Typedef] +id: RO:0012014 +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: RO:0013001 name: has synaptic IO in region @@ -6322,6 +6505,16 @@ property_value: IAO:0000118 "inversely correlated with" xsd:string is_symmetric: true is_a: RO:0002610 ! correlated with +[Typedef] +id: RO:0017005 +name: contains measured amount +def: "A relation between a container and measurement datum that specifies the actual amount of material in the container." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2999-0103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-5714-991X +property_value: IAO:0000112 "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." xsd:string +domain: OBI:0000967 ! container +range: COB:0000121 ! measurement datum + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -6441,7 +6634,7 @@ synonym: "is desmotrope of" EXACT [] xref: obo:chebi#is_tautomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38707", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38709"} +property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {seeAlso="CHEBI:38707", seeAlso="CHEBI:38709"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6453,7 +6646,7 @@ def: "Group A is a substituent group from Chemical B if A represents the functio xref: obo:chebi#is_substituent_group_from property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:30795", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:58957"} +property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {seeAlso="CHEBI:30795", seeAlso="CHEBI:58957"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6464,7 +6657,7 @@ def: "Chemical A has functional parent Chemical B if there is chemical transform xref: obo:chebi#has_functional_parent property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50851", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50854"} +property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {seeAlso="CHEBI:50851", seeAlso="CHEBI:50854"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6476,7 +6669,7 @@ synonym: "is optical isomer of" EXACT [] xref: obo:chebi#is_enantiomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:31472"} +property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", seeAlso="CHEBI:31472"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6488,7 +6681,7 @@ def: "Chemical A has parent hydride Chemical B if there exists a molecular graph xref: obo:chebi#has_parent_hydride property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:39106", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:52083"} +property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {seeAlso="CHEBI:39106", seeAlso="CHEBI:52083"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6526,6 +6719,40 @@ def: "Relates a gene to condition, such that a variation in this gene predispose is_a: RO:0003304 ! contributes to condition created_by: https://orcid.org/0000-0002-4142-7153 +[Typedef] +id: RO:0020101 +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 ! blood vessel +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002178 ! supplies + +[Typedef] +id: RO:0020102 +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 ! blood vessel +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002179 ! drains + +[Typedef] +id: RO:0020103 +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 ! capillary +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002178 ! supplies +is_a: RO:0002179 ! drains + [Typedef] id: RO:0040035 name: disease relationship diff --git a/ro-full.owl b/ro-full.owl index 6795b17f..8f426451 100644 --- a/ro-full.owl +++ b/ro-full.owl @@ -17,15 +17,14 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2023-08-18 + 2024-02-13 https://github.com/oborel/obo-relations/ @@ -42,12 +41,6 @@ - - - - - - @@ -1126,59 +1119,81 @@ Where we have an annotation assertion - + - + - + - + + + - + - + + + - + - + + + - + - + + + - + - + + + - + - + - + - + + + + + + + + + + + + + - + - + @@ -1476,23 +1491,6 @@ Where we have an annotation assertion - - - - - - - - - - - + @@ -4454,7 +4463,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure to @@ -4821,7 +4830,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results in formation of + results in formation of anatomical entity @@ -5278,6 +5287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -8714,6 +8724,34 @@ the a supports either the existence of b, or the truth value of b. + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -10180,6 +10218,36 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + positively regulates in other organism + + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + negatively regulates in other organism + + negatively regulates in another organism + + + + @@ -10621,6 +10689,20 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. + A relation between a container and measurement datum that specifies the actual amount of material in the container. + + + contains measured amount + + + + @@ -10991,6 +11073,52 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + directly supplies and drains + + + + @@ -12777,6 +12905,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + @@ -12812,6 +12946,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable realizable entity @@ -12842,10 +12977,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + characteristic specifically dependent continuant + https://github.com/OBOFoundry/COB/issues/65 + https://github.com/oborel/obo-relations/pull/284 @@ -12931,6 +13075,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + A material entity that has a plasma membrane and results from cellular division. CALOHA:TS-2035 FBbt:00007002 FMA:68646 @@ -12940,8 +13085,11 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu VHOG:0001533 WBbt:0004017 XAO:0003012 + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell + cell @@ -12999,6 +13147,24 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + measurement datum + + + + + + + + + A process during which an organism comes into contact with another entity. + exposure of organism + + + + @@ -13043,10 +13209,14 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -13997,12 +14167,14 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus GO:0005634 + cell nucleus nucleus @@ -14026,7 +14198,15 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process @@ -14035,7 +14215,9 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu single organism process single-organism process GO:0008150 + A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. + biological process biological_process @@ -14163,6 +14345,62 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + Is a material entity that is created or changed during material processing. + PERSON: Alan Ruttenberg + processed material + + + + + + + + + container + + A device that can be used to restrict the location of material entities over time + 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) + PERSON: Bjoern Peters + container + + + + + + + + + device + A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + +2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: + +(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. + +(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. + +(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. + +In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + PERSON: Helen Parkinson + instrument + OBI development call 2012-12-17. + device + + + + @@ -14271,16 +14509,16 @@ This issue is outside the scope of OBI. - An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. - A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. + OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. 2017-06-05T17:55:39Z - exposure event or process + obsolete exposure event or process https://github.com/oborel/obo-relations/pull/173 + true @@ -14351,7 +14589,6 @@ This issue is outside the scope of OBI. CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -14393,7 +14630,6 @@ This issue is outside the scope of OBI. A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 - FBbt:00005099 NLX:147821 funiculus nerve fiber bundle @@ -14432,7 +14668,6 @@ This issue is outside the scope of OBI. BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -14465,7 +14700,6 @@ This issue is outside the scope of OBI. BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -14501,11 +14735,11 @@ This issue is outside the scope of OBI. AAO:0010841 AEO:0000000 + BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -14537,6 +14771,132 @@ This issue is outside the scope of OBI. + + + + + A vessel through which blood circulates in the body. + consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus + vascular element + AAO:0011004 + AEO:0000207 + BTO:0001102 + CALOHA:TS-0080 + EFO:0000817 + EHDAA2:0003252 + EHDAA:240 + EMAPA:32743 + EMAPA:35993 + FMA:50722 + FMA:63183 + GAID:169 + MA:0000060 + MAT:0000393 + MESH:D001808 + NCIT:C12679 + NLXANAT:090901 + SCTID:361097006 + TAO:0002137 + UMLS:C0005847 + VHOG:0001250 + Wikipedia:Blood_vessel + XAO:0001011 + ZFA:0005314 + region of vascular tree organ + vascular tree organ region + UBERON:0001981 + + + + + + blood vessel + + + + + A vessel through which blood circulates in the body. + BTO:0001102 + Wikipedia:Blood_vessel + + + + + vascular element + EMAPA:35993 + + + + + UMLS:C0005847 + ncithesaurus:Blood_Vessel + + + + + region of vascular tree organ + FMA:50722 + + + + + vascular tree organ region + FMA:50722 + + + + + + + + + Any of the smallest blood vessels connecting arterioles with venules. + not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element + AAO:0010252 + BTO:0002045 + CALOHA:TS-2006 + EFO:0001906 + EMAPA:35198 + EV:0100035 + FMA:63194 + MA:0000065 + MESH:D002196 + NCIT:C12685 + NLXANAT:090902 + TAO:0005250 + UMLS:C0935624 + VHOG:0001253 + Wikipedia:Capillary + XAO:0000116 + ZFA:0005250 + blood capillary + capillary vessel + UBERON:0001982 + + + + + + capillary + https://github.com/obophenotype/uberon/issues/2186 + + + + + Any of the smallest blood vessels connecting arterioles with venules. + ISBN:0073040584 + Wikipedia:Capillary + https://github.com/obophenotype/uberon/issues/137 + + + + + UMLS:C0935624 + ncithesaurus:Capillary + + + + @@ -14545,7 +14905,6 @@ This issue is outside the scope of OBI. CARO:0010000 - FBbt:00100313 multicellular structure UBERON:0010000 @@ -14751,6 +15110,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0001-6677-8489 + Aleix Puig-Barbé + + + + + Researcher ORCID=0000-0001-6677-8489 + + + + + + Aleix Puig-Barbé + + + + + @@ -14835,6 +15215,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-2999-0103) + Jie Zheng + + + + + researcher (ORCID 0000-0002-2999-0103) + + + + + + Jie Zheng + + + + + @@ -14856,6 +15257,27 @@ binary, and takes no temporal argument. + + + + researcher + Christian J Stoeckert + + + + + researcher + + + + + + Christian J Stoeckert + + + + + @@ -14982,6 +15404,48 @@ binary, and takes no temporal argument. + + + + Canadian biocurator + Pascale Gaudet + + + + + Canadian biocurator + + + + + + Pascale Gaudet + + + + + + + + + Researcher ORCID=0000-0003-1909-9269 + S. Clint Dowland + + + + + Researcher ORCID=0000-0003-1909-9269 + + + + + + S. Clint Dowland + + + + + @@ -15003,6 +15467,27 @@ binary, and takes no temporal argument. + + + + software/data engineer + Jorrit Poelen + + + + + software/data engineer + + + + + + Jorrit Poelen + + + + + @@ -15511,10 +15996,10 @@ No imports /////////////////////////////////////////////////////////////////////////////////////// --> - + - + @@ -15532,66 +16017,54 @@ No imports - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - @@ -15604,8 +16077,8 @@ No imports - - + + @@ -15615,7 +16088,7 @@ No imports - + @@ -15625,7 +16098,7 @@ No imports - + @@ -15642,8 +16115,8 @@ No imports - - + + @@ -15905,7 +16378,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -15915,8 +16388,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15926,8 +16399,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15944,8 +16417,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15964,7 +16437,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -15974,8 +16447,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15985,8 +16458,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16003,8 +16476,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16021,8 +16494,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16032,7 +16505,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16042,8 +16515,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16053,8 +16526,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16073,8 +16546,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16092,8 +16565,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16103,8 +16576,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16114,8 +16587,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16132,8 +16605,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16150,8 +16623,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16161,8 +16634,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16172,8 +16645,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16190,8 +16663,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16208,8 +16681,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16219,8 +16692,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16230,8 +16703,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16248,8 +16721,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16266,8 +16739,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16277,8 +16750,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16293,8 +16766,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16311,8 +16784,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16322,8 +16795,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16338,8 +16811,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16356,8 +16829,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16367,8 +16840,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16383,8 +16856,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16401,8 +16874,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16412,8 +16885,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16428,8 +16901,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16446,8 +16919,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16457,8 +16930,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16473,8 +16946,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16491,8 +16964,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16502,8 +16975,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16518,7 +16991,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16528,7 +17001,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16547,8 +17020,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16558,8 +17031,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16574,7 +17047,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16584,7 +17057,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16646,8 +17119,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16657,8 +17130,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16673,8 +17146,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16690,8 +17163,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16700,9 +17173,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16716,9 +17189,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16734,8 +17207,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16744,9 +17217,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16760,7 +17233,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16861,5 +17334,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/ro.json b/ro.json index e0aadc9d..447a2acb 100644 --- a/ro.json +++ b/ro.json @@ -13,12 +13,12 @@ "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -153,7 +153,14 @@ "definition" : { "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" }, - "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ] + "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/OBOFoundry/COB/issues/65" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", @@ -459,10 +466,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", - "xrefs" : [ "CARO:mah" ] + "val" : "A material entity that has a plasma membrane and results from cellular division." }, - "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], + "comments" : [ "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.", "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).", "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism." ], "xrefs" : [ { "val" : "CALOHA:TS-2035" }, { @@ -536,6 +542,19 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/COB_0000121", + "lbl" : "measurement datum", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/COB_0001000", + "lbl" : "exposure of organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process during which an organism comes into contact with another entity." + } + } }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", "lbl" : "environmental system", @@ -596,7 +615,7 @@ "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", "xrefs" : [ "GOC:pdt" ] }, - "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], + "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", "This is the same as GO molecular function" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecular function" @@ -924,10 +943,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", - "xrefs" : [ "GOC:pdt" ] + "val" : "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." }, - "comments" : [ "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "comments" : [ "A biological process is an evolved process", "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "biological process" @@ -2273,6 +2291,84 @@ "val" : "EL++ ontology module" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000047", + "lbl" : "processed material", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Is a material entity that is created or changed during material processing." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "processed material" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000967", + "lbl" : "container", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A device that can be used to restrict the location of material entities over time" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "container" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000123" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000968", + "lbl" : "device", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "device" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A voltmeter is a measurement device which is intended to perform some measure function." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Helen Parkinson" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "instrument" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI development call 2012-12-17." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0100026", "lbl" : "organism", @@ -2625,6 +2721,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -3359,12 +3458,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -6139,7 +6243,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -6356,11 +6460,11 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002310", - "lbl" : "exposure event or process", + "lbl" : "obsolete exposure event or process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." + "val" : "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -6383,7 +6487,8 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/173" - } ] + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002312", @@ -11025,6 +11130,43 @@ "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", @@ -12697,6 +12839,54 @@ "val" : "2022-09-26T06:08:01Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -13181,6 +13371,25 @@ "val" : "https://orcid.org/0000-0003-1909-9269" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017005", + "lbl" : "contains measured amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a container and measurement datum that specifies the actual amount of material in the container." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2999-0103" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-5714-991X" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -13592,6 +13801,63 @@ "val" : "https://orcid.org/0000-0002-4142-7153" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -15527,8 +15793,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -15586,8 +15850,6 @@ } ], "xrefs" : [ { "val" : "CARO:0001001" - }, { - "val" : "FBbt:00005099" }, { "val" : "NLX:147821" } ] @@ -15612,8 +15874,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -15658,8 +15918,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -15693,6 +15951,8 @@ "val" : "AAO:0010841" }, { "val" : "AEO:0000000" + }, { + "val" : "BFO:0000004" }, { "val" : "BILA:0000000" }, { @@ -15701,8 +15961,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -15732,6 +15990,143 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "lbl" : "blood vessel", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A vessel through which blood circulates in the body.", + "xrefs" : [ "BTO:0001102", "Wikipedia:Blood_vessel" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "vascular element", + "xrefs" : [ "EMAPA:35993" ] + }, { + "pred" : "hasExactSynonym", + "val" : "region of vascular tree organ", + "xrefs" : [ "FMA:50722" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vascular tree organ region", + "xrefs" : [ "FMA:50722" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011004" + }, { + "val" : "AEO:0000207" + }, { + "val" : "BTO:0001102" + }, { + "val" : "CALOHA:TS-0080" + }, { + "val" : "EFO:0000817" + }, { + "val" : "EHDAA2:0003252" + }, { + "val" : "EHDAA:240" + }, { + "val" : "EMAPA:32743" + }, { + "val" : "EMAPA:35993" + }, { + "val" : "FMA:50722" + }, { + "val" : "FMA:63183" + }, { + "val" : "GAID:169" + }, { + "val" : "MA:0000060" + }, { + "val" : "MAT:0000393" + }, { + "val" : "MESH:D001808" + }, { + "val" : "NCIT:C12679" + }, { + "val" : "NLXANAT:090901" + }, { + "val" : "SCTID:361097006" + }, { + "val" : "TAO:0002137" + }, { + "val" : "UMLS:C0005847" + }, { + "val" : "VHOG:0001250" + }, { + "val" : "Wikipedia:Blood_vessel" + }, { + "val" : "XAO:0001011" + }, { + "val" : "ZFA:0005314" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001982", + "lbl" : "capillary", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any of the smallest blood vessels connecting arterioles with venules.", + "xrefs" : [ "ISBN:0073040584", "Wikipedia:Capillary", "https://github.com/obophenotype/uberon/issues/137" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blood capillary" + }, { + "pred" : "hasExactSynonym", + "val" : "capillary vessel" + } ], + "xrefs" : [ { + "val" : "AAO:0010252" + }, { + "val" : "BTO:0002045" + }, { + "val" : "CALOHA:TS-2006" + }, { + "val" : "EFO:0001906" + }, { + "val" : "EMAPA:35198" + }, { + "val" : "EV:0100035" + }, { + "val" : "FMA:63194" + }, { + "val" : "MA:0000065" + }, { + "val" : "MESH:D002196" + }, { + "val" : "NCIT:C12685" + }, { + "val" : "NLXANAT:090902" + }, { + "val" : "TAO:0005250" + }, { + "val" : "UMLS:C0935624" + }, { + "val" : "VHOG:0001253" + }, { + "val" : "Wikipedia:Capillary" + }, { + "val" : "XAO:0000116" + }, { + "val" : "ZFA:0005250" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2186" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", "lbl" : "multicellular anatomical structure", @@ -15749,8 +16144,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -15938,6 +16331,16 @@ "val" : "is defined by" } ] } + }, { + "id" : "https://orcid.org/0000-0001-6677-8489", + "lbl" : "Aleix Puig-Barbé", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0001-6677-8489" + } ] + } }, { "id" : "https://orcid.org/0000-0001-6996-0040", "lbl" : "Austin Meier", @@ -15978,6 +16381,16 @@ "val" : "data scientist" } ] } + }, { + "id" : "https://orcid.org/0000-0002-2999-0103", + "lbl" : "Jie Zheng", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-2999-0103)" + } ] + } }, { "id" : "https://orcid.org/0000-0002-4366-3088", "lbl" : "Pier Luigi Buttigieg", @@ -15988,6 +16401,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-5714-991X", + "lbl" : "Christian J Stoeckert", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-6601-2165", "lbl" : "Christopher J. Mungall", @@ -16048,6 +16471,26 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1813-6857", + "lbl" : "Pascale Gaudet", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Canadian biocurator" + } ] + } + }, { + "id" : "https://orcid.org/0000-0003-1909-9269", + "lbl" : "S. Clint Dowland", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-1909-9269" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1940-6740", "lbl" : "Anna Maria Masci", @@ -16058,6 +16501,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-3138-4118", + "lbl" : "Jorrit Poelen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "software/data engineer" + } ] + } }, { "id" : "https://orcid.org/0000-0003-4423-4370", "lbl" : "Charles Tapley Hoyt", @@ -16133,6 +16586,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000540", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/COB_0001000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/ENVO_01000254", "pred" : "is_a", @@ -16141,10 +16598,26 @@ "sub" : "http://purl.obolibrary.org/obo/ENVO_01000739", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/ENVO_01000254" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0003674", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0004842", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0003674" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0005634", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0008150", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0008150", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0003674" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0016301", "pred" : "is_a", @@ -16157,6 +16630,18 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000030", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000047", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000967", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000968" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000968", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000047" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0100026", "pred" : "is_a", @@ -16181,10 +16666,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002124", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002310", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002532", "pred" : "http://purl.obolibrary.org/obo/RO_0002524", @@ -16229,6 +16710,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010000" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001982", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010000", "pred" : "is_a", @@ -16633,6 +17122,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -18105,6 +18598,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -18517,6 +19018,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -18693,6 +19202,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -19369,6 +19894,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003000", "pred" : "inverseOf", @@ -19468,6 +19997,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -19507,6 +20040,13 @@ "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], @@ -19525,7 +20065,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", @@ -19533,7 +20073,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", @@ -19699,7 +20239,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -20011,10 +20551,26 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0017005", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000967" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000121" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/ro.obo b/ro.obo index 9cd84f7c..29ad9099 100644 --- a/ro.obo +++ b/ro.obo @@ -1,19 +1,24 @@ format-version: 1.2 -data-version: releases/2023-08-18 +data-version: releases/2024-02-13 subsetdef: common_anatomy "" +subsetdef: efo_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: human_reference_atlas "" +subsetdef: pheno_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" +subsetdef: uberon_slim "" subsetdef: upper_level "" +subsetdef: vertebrate_core "" ontology: ro property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Term] id: BFO:0000002 @@ -37,7 +42,7 @@ name: independent continuant def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000020 ! characteristic disjoint_from: BFO:0000031 ! generically dependent continuant relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant @@ -52,6 +57,7 @@ name: process def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000015 {all_only="true"} ! part of process relationship: RO:0002214 BFO:0000015 {all_only="true"} ! has prototype process [Term] @@ -62,26 +68,31 @@ disjoint_from: BFO:0000023 ! role [Term] id: BFO:0000017 +name: realizable name: realizable entity def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic disjoint_from: BFO:0000019 ! quality relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity [Term] id: BFO:0000019 name: quality -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 +name: characteristic name: specifically dependent continuant def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of characteristic +relationship: BFO:0000051 BFO:0000020 {all_only="true"} ! has part characteristic +property_value: seeAlso "https://github.com/OBOFoundry/COB/issues/65" xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string [Term] id: BFO:0000023 @@ -122,7 +133,10 @@ is_a: PATO:0000001 ! quality id: CL:0000000 name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] +def: "A material entity that has a plasma membrane and results from cellular division." [] +comment: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). +comment: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. xref: CALOHA:TS-2035 xref: FBbt:00007002 xref: FMA:68646 @@ -160,6 +174,16 @@ xref: WBbt:0003679 is_a: CL:0000000 ! cell property_value: RO:0002175 NCBITaxon:9606 +[Term] +id: COB:0000121 +name: measurement datum + +[Term] +id: COB:0001000 +name: exposure of organism +def: "A process during which an organism comes into contact with another entity." [] +is_a: BFO:0000015 ! process + [Term] id: ENVO:01000254 name: environmental system @@ -183,10 +207,14 @@ is_a: ENVO:01000254 ! environmental system [Term] id: GO:0003674 +name: gene product or complex activity name: molecular_function def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +comment: This is the same as GO molecular function synonym: "molecular function" EXACT [] +is_a: BFO:0000015 ! process +disjoint_from: GO:0008150 ! biological_process [Term] id: GO:0004842 @@ -333,23 +361,30 @@ is_a: GO:0003674 ! molecular_function [Term] id: GO:0005634 +name: cell nucleus name: nucleus def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] synonym: "cell nucleus" EXACT [] synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757] xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus +is_a: BFO:0000040 ! material entity [Term] id: GO:0008150 +name: biological process name: biological_process def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +def: "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective." [] +comment: A biological process is an evolved process comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process +is_a: BFO:0000015 ! process +relationship: BFO:0000051 GO:0003674 ! has part molecular_function created_by: jl creation_date: 2012-09-19T15:05:24Z @@ -388,6 +423,40 @@ property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 "GROUP:OBI:" xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string +[Term] +id: OBI:0000047 +name: processed material +def: "Is a material entity that is created or changed during material processing." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000111 "processed material" xsd:string +property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string + +[Term] +id: OBI:0000967 +name: container +def: "A device that can be used to restrict the location of material entities over time" [] +is_a: OBI:0000968 ! device +property_value: IAO:0000111 "container" xsd:string +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string + +[Term] +id: OBI:0000968 +name: device +def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." [] +is_a: OBI:0000047 ! processed material +property_value: IAO:0000111 "device" xsd:string +property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string +property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay." xsd:string +property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string +property_value: IAO:0000118 "instrument" xsd:string +property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string + [Term] id: OBI:0100026 name: organism @@ -414,7 +483,7 @@ is_a: BFO:0000016 ! disposition id: PATO:0000001 name: quality def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -is_a: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000020 ! characteristic [Term] id: PATO:0000402 @@ -441,14 +510,14 @@ creation_date: 2009-10-06T04:37:14Z [Term] id: RO:0002310 -name: exposure event or process -def: "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] -is_a: BFO:0000015 ! process +name: obsolete exposure event or process +def: "OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string property_value: seeAlso "https://github.com/oborel/obo-relations/pull/173" xsd:anyURI +is_obsolete: true created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:55:39Z @@ -498,7 +567,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -524,7 +592,6 @@ synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 -xref: FBbt:00005099 xref: NLX:147821 is_a: UBERON:0000061 ! anatomical structure @@ -539,7 +606,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -563,7 +629,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -582,11 +647,11 @@ subset: common_anatomy subset: upper_level xref: AAO:0010841 xref: AEO:0000000 +xref: BFO:0000004 xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -601,6 +666,77 @@ is_a: BFO:0000004 ! independent continuant property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:4751 +[Term] +id: UBERON:0001981 +name: blood vessel +def: "A vessel through which blood circulates in the body." [BTO:0001102, Wikipedia:Blood_vessel] +subset: efo_slim +subset: human_reference_atlas +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "region of vascular tree organ" EXACT [FMA:50722] +synonym: "vascular element" BROAD [EMAPA:35993] +synonym: "vascular tree organ region" EXACT [FMA:50722] +xref: AAO:0011004 +xref: AEO:0000207 +xref: BTO:0001102 +xref: CALOHA:TS-0080 +xref: EFO:0000817 +xref: EHDAA2:0003252 +xref: EHDAA:240 +xref: EMAPA:32743 +xref: EMAPA:35993 +xref: FMA:50722 +xref: FMA:63183 +xref: GAID:169 +xref: MA:0000060 +xref: MAT:0000393 +xref: MESH:D001808 +xref: NCIT:C12679 +xref: NLXANAT:090901 +xref: SCTID:361097006 +xref: TAO:0002137 +xref: UMLS:C0005847 {source="ncithesaurus:Blood_Vessel"} +xref: VHOG:0001250 +xref: Wikipedia:Blood_vessel +xref: XAO:0001011 +xref: ZFA:0005314 +is_a: UBERON:0010000 ! multicellular anatomical structure +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string + +[Term] +id: UBERON:0001982 +name: capillary +def: "Any of the smallest blood vessels connecting arterioles with venules." [https://github.com/obophenotype/uberon/issues/137, ISBN:0073040584, Wikipedia:Capillary] +subset: efo_slim +subset: human_reference_atlas +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "blood capillary" EXACT [] +synonym: "capillary vessel" EXACT [] +xref: AAO:0010252 +xref: BTO:0002045 +xref: CALOHA:TS-2006 +xref: EFO:0001906 +xref: EMAPA:35198 +xref: EV:0100035 +xref: FMA:63194 +xref: MA:0000065 +xref: MESH:D002196 +xref: NCIT:C12685 +xref: NLXANAT:090902 +xref: TAO:0005250 +xref: UMLS:C0935624 {source="ncithesaurus:Capillary"} +xref: VHOG:0001253 +xref: Wikipedia:Capillary +xref: XAO:0000116 +xref: ZFA:0005250 +is_a: UBERON:0001981 ! blood vessel +property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string + [Term] id: UBERON:0010000 name: multicellular anatomical structure @@ -609,7 +745,6 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 is_a: UBERON:0000061 ! anatomical structure property_value: RO:0002175 NCBITaxon:33090 property_value: RO:0002175 NCBITaxon:4751 @@ -753,6 +888,7 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process @@ -796,7 +932,8 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string +range: BFO:0000020 ! characteristic is_inverse_functional: true [Typedef] @@ -824,6 +961,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 ! occurrent +domain: BFO:0000015 ! process range: BFO:0000002 ! continuant holds_over_chain: BFO:0000051 RO:0000057 @@ -834,7 +972,7 @@ def: "A relationship between a generically dependent continuant and a specifical property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000031 ! generically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! characteristic inverse_of: RO:0000059 ! concretizes [Typedef] @@ -843,7 +981,7 @@ name: concretizes def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string -domain: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic range: BFO:0000031 ! generically dependent continuant [Typedef] @@ -1065,8 +1203,8 @@ property_value: IAO:0000116 "Most location relations will only hold at certain t property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true transitive_over: BFO:0000050 ! part of @@ -1175,8 +1313,10 @@ is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 -name: regulates in other organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 ! process range: BFO:0000015 ! process @@ -1723,7 +1863,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -1903,7 +2043,7 @@ def: "a is attached to part of b if a is attached to b, or a is attached to some property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002371 BFO:0000050 {RO:0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1969,6 +2109,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_transitive: true +is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -2155,7 +2296,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -2195,7 +2336,7 @@ def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -2433,7 +2574,7 @@ id: RO:0002244 name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 ! exposure event or process +domain: COB:0001000 ! exposure of organism is_a: RO:0002410 ! causally related to [Typedef] @@ -2672,7 +2813,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002297 -name: results in formation of +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -2820,7 +2961,7 @@ property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -2937,7 +3078,7 @@ name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -3221,7 +3362,7 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -3581,7 +3722,7 @@ is_a: RO:0002424 ! differs in id: RO:0002426 name: differs in attribute property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! characteristic is_a: RO:0002424 ! differs in [Typedef] @@ -3644,7 +3785,7 @@ property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd: property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -4078,7 +4219,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002480 @@ -4312,7 +4453,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 ! system range: BFO:0000040 ! material entity -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -4563,7 +4704,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000465 {http://purl.obolibrary.org/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."} ! material anatomical entity +range: UBERON:0000465 {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."} ! material anatomical entity is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of is_asymmetric: true @@ -4754,8 +4895,8 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string -domain: BFO:0000020 ! specifically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000020 ! characteristic +range: BFO:0000020 ! characteristic [Typedef] id: RO:0002574 @@ -4823,7 +4964,7 @@ is_a: RO:0002233 ! has input [Typedef] id: RO:0002587 name: results in synthesis of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity [Typedef] id: RO:0002588 @@ -4831,7 +4972,7 @@ name: results in assembly of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity is_a: RO:0002592 ! results in organization of [Typedef] @@ -5132,6 +5273,26 @@ property_value: IAO:0000119 Communal:roosting is_symmetric: true is_a: RO:0008506 ! ecologically co-occurs with +[Typedef] +id: RO:0002802 +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: RO:0002454 ! has host + [Typedef] id: RO:0003000 name: produces @@ -6066,6 +6227,28 @@ is_a: RO:0012011 ! indirectly causally upstream of created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z +[Typedef] +id: RO:0012013 +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + +[Typedef] +id: RO:0012014 +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: RO:0002010 ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: RO:0013001 name: has synaptic IO in region @@ -6322,6 +6505,16 @@ property_value: IAO:0000118 "inversely correlated with" xsd:string is_symmetric: true is_a: RO:0002610 ! correlated with +[Typedef] +id: RO:0017005 +name: contains measured amount +def: "A relation between a container and measurement datum that specifies the actual amount of material in the container." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2999-0103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-5714-991X +property_value: IAO:0000112 "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." xsd:string +domain: OBI:0000967 ! container +range: COB:0000121 ! measurement datum + [Typedef] id: RO:0018001 name: is myristoyltransferase activity @@ -6441,7 +6634,7 @@ synonym: "is desmotrope of" EXACT [] xref: obo:chebi#is_tautomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38707", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:38709"} +property_value: IAO:0000112 "3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol." xsd:string {seeAlso="CHEBI:38707", seeAlso="CHEBI:38709"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6453,7 +6646,7 @@ def: "Group A is a substituent group from Chemical B if A represents the functio xref: obo:chebi#is_substituent_group_from property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:30795", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:58957"} +property_value: IAO:0000112 "carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)" xsd:string {seeAlso="CHEBI:30795", seeAlso="CHEBI:58957"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6464,7 +6657,7 @@ def: "Chemical A has functional parent Chemical B if there is chemical transform xref: obo:chebi#has_functional_parent property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50851", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:50854"} +property_value: IAO:0000112 "hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)" xsd:string {seeAlso="CHEBI:50851", seeAlso="CHEBI:50854"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6476,7 +6669,7 @@ synonym: "is optical isomer of" EXACT [] xref: obo:chebi#is_enantiomer_of property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:31472"} +property_value: IAO:0000112 "dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped." xsd:string {comment="CHEBI:48557", seeAlso="CHEBI:31472"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_symmetric: true is_a: RO:0018030 ! chemical relationship @@ -6488,7 +6681,7 @@ def: "Chemical A has parent hydride Chemical B if there exists a molecular graph xref: obo:chebi#has_parent_hydride property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0003-4423-4370 property_value: http://purl.org/dc/terms/date "2023-03-18T23:49:31Z" xsd:dateTime -property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:39106", http://www.w3.org/2000/01/rdf-schema#seeAlso="CHEBI:52083"} +property_value: IAO:0000112 "pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates." xsd:string {seeAlso="CHEBI:39106", seeAlso="CHEBI:52083"} property_value: seeAlso https://github.com/oborel/obo-relations/issues/697 is_a: RO:0018030 ! chemical relationship @@ -6526,6 +6719,40 @@ def: "Relates a gene to condition, such that a variation in this gene predispose is_a: RO:0003304 ! contributes to condition created_by: https://orcid.org/0000-0002-4142-7153 +[Typedef] +id: RO:0020101 +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 ! blood vessel +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002178 ! supplies + +[Typedef] +id: RO:0020102 +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 ! blood vessel +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002179 ! drains + +[Typedef] +id: RO:0020103 +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 ! capillary +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002178 ! supplies +is_a: RO:0002179 ! drains + [Typedef] id: RO:0040035 name: disease relationship diff --git a/ro.owl b/ro.owl index c50e7d26..8f5e4eb0 100644 --- a/ro.owl +++ b/ro.owl @@ -17,15 +17,14 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2023-08-18 + 2024-02-13 https://github.com/oborel/obo-relations/ @@ -42,12 +41,6 @@ - - - - - - @@ -1126,59 +1119,81 @@ Where we have an annotation assertion - + - + - + - + + + - + - + + + - + - + + + - + - + + + - + - + + + - + - + - + - + + + + + + + + + + + + + - + - + @@ -1476,23 +1491,6 @@ Where we have an annotation assertion - - - - - - - - - - - + @@ -4454,7 +4463,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. related via exposure to @@ -4821,7 +4830,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results in formation of + results in formation of anatomical entity @@ -5278,6 +5287,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -8714,6 +8724,34 @@ the a supports either the existence of b, or the truth value of b. + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -10180,6 +10218,36 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + positively regulates in other organism + + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + negatively regulates in other organism + + negatively regulates in another organism + + + + @@ -10621,6 +10689,20 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. + A relation between a container and measurement datum that specifies the actual amount of material in the container. + + + contains measured amount + + + + @@ -10991,6 +11073,52 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + directly supplies and drains + + + + @@ -12777,6 +12905,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + @@ -12812,6 +12946,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable realizable entity @@ -12842,10 +12977,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + characteristic specifically dependent continuant + https://github.com/OBOFoundry/COB/issues/65 + https://github.com/oborel/obo-relations/pull/284 @@ -12931,6 +13075,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + A material entity that has a plasma membrane and results from cellular division. CALOHA:TS-2035 FBbt:00007002 FMA:68646 @@ -12940,8 +13085,11 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu VHOG:0001533 WBbt:0004017 XAO:0003012 + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell + cell @@ -12999,6 +13147,24 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + measurement datum + + + + + + + + + A process during which an organism comes into contact with another entity. + exposure of organism + + + + @@ -13043,10 +13209,14 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -13997,12 +14167,14 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus GO:0005634 + cell nucleus nucleus @@ -14026,7 +14198,15 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + + + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process @@ -14035,7 +14215,9 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu single organism process single-organism process GO:0008150 + A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. + biological process biological_process @@ -14163,6 +14345,62 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + Is a material entity that is created or changed during material processing. + PERSON: Alan Ruttenberg + processed material + + + + + + + + + container + + A device that can be used to restrict the location of material entities over time + 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) + PERSON: Bjoern Peters + container + + + + + + + + + device + A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + +2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: + +(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. + +(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. + +(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. + +In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + PERSON: Helen Parkinson + instrument + OBI development call 2012-12-17. + device + + + + @@ -14271,16 +14509,16 @@ This issue is outside the scope of OBI. - An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. - A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. + OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. 2017-06-05T17:55:39Z - exposure event or process + obsolete exposure event or process https://github.com/oborel/obo-relations/pull/173 + true @@ -14351,7 +14589,6 @@ This issue is outside the scope of OBI. CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -14393,7 +14630,6 @@ This issue is outside the scope of OBI. A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 - FBbt:00005099 NLX:147821 funiculus nerve fiber bundle @@ -14432,7 +14668,6 @@ This issue is outside the scope of OBI. BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -14465,7 +14700,6 @@ This issue is outside the scope of OBI. BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -14501,11 +14735,11 @@ This issue is outside the scope of OBI. AAO:0010841 AEO:0000000 + BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -14537,6 +14771,132 @@ This issue is outside the scope of OBI. + + + + + A vessel through which blood circulates in the body. + consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus + vascular element + AAO:0011004 + AEO:0000207 + BTO:0001102 + CALOHA:TS-0080 + EFO:0000817 + EHDAA2:0003252 + EHDAA:240 + EMAPA:32743 + EMAPA:35993 + FMA:50722 + FMA:63183 + GAID:169 + MA:0000060 + MAT:0000393 + MESH:D001808 + NCIT:C12679 + NLXANAT:090901 + SCTID:361097006 + TAO:0002137 + UMLS:C0005847 + VHOG:0001250 + Wikipedia:Blood_vessel + XAO:0001011 + ZFA:0005314 + region of vascular tree organ + vascular tree organ region + UBERON:0001981 + + + + + + blood vessel + + + + + A vessel through which blood circulates in the body. + BTO:0001102 + Wikipedia:Blood_vessel + + + + + vascular element + EMAPA:35993 + + + + + UMLS:C0005847 + ncithesaurus:Blood_Vessel + + + + + region of vascular tree organ + FMA:50722 + + + + + vascular tree organ region + FMA:50722 + + + + + + + + + Any of the smallest blood vessels connecting arterioles with venules. + not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element + AAO:0010252 + BTO:0002045 + CALOHA:TS-2006 + EFO:0001906 + EMAPA:35198 + EV:0100035 + FMA:63194 + MA:0000065 + MESH:D002196 + NCIT:C12685 + NLXANAT:090902 + TAO:0005250 + UMLS:C0935624 + VHOG:0001253 + Wikipedia:Capillary + XAO:0000116 + ZFA:0005250 + blood capillary + capillary vessel + UBERON:0001982 + + + + + + capillary + https://github.com/obophenotype/uberon/issues/2186 + + + + + Any of the smallest blood vessels connecting arterioles with venules. + ISBN:0073040584 + Wikipedia:Capillary + https://github.com/obophenotype/uberon/issues/137 + + + + + UMLS:C0935624 + ncithesaurus:Capillary + + + + @@ -14545,7 +14905,6 @@ This issue is outside the scope of OBI. CARO:0010000 - FBbt:00100313 multicellular structure UBERON:0010000 @@ -14751,6 +15110,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0001-6677-8489 + Aleix Puig-Barbé + + + + + Researcher ORCID=0000-0001-6677-8489 + + + + + + Aleix Puig-Barbé + + + + + @@ -14835,6 +15215,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-2999-0103) + Jie Zheng + + + + + researcher (ORCID 0000-0002-2999-0103) + + + + + + Jie Zheng + + + + + @@ -14856,6 +15257,27 @@ binary, and takes no temporal argument. + + + + researcher + Christian J Stoeckert + + + + + researcher + + + + + + Christian J Stoeckert + + + + + @@ -14982,6 +15404,48 @@ binary, and takes no temporal argument. + + + + Canadian biocurator + Pascale Gaudet + + + + + Canadian biocurator + + + + + + Pascale Gaudet + + + + + + + + + Researcher ORCID=0000-0003-1909-9269 + S. Clint Dowland + + + + + Researcher ORCID=0000-0003-1909-9269 + + + + + + S. Clint Dowland + + + + + @@ -15003,6 +15467,27 @@ binary, and takes no temporal argument. + + + + software/data engineer + Jorrit Poelen + + + + + software/data engineer + + + + + + Jorrit Poelen + + + + + @@ -15514,10 +15999,10 @@ No imports /////////////////////////////////////////////////////////////////////////////////////// --> - + - + @@ -15535,66 +16020,54 @@ No imports - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - @@ -15607,8 +16080,8 @@ No imports - - + + @@ -15618,7 +16091,7 @@ No imports - + @@ -15628,7 +16101,7 @@ No imports - + @@ -15645,8 +16118,8 @@ No imports - - + + @@ -15908,7 +16381,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -15918,8 +16391,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15929,8 +16402,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15947,8 +16420,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15967,7 +16440,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -15977,8 +16450,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -15988,8 +16461,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16006,8 +16479,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16023,8 +16496,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16034,7 +16507,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16044,8 +16517,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16055,8 +16528,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16075,8 +16548,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16094,8 +16567,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16105,8 +16578,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16116,8 +16589,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16134,8 +16607,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16152,8 +16625,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16163,8 +16636,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16174,8 +16647,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16192,8 +16665,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16210,8 +16683,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16221,8 +16694,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16232,8 +16705,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16250,8 +16723,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16268,8 +16741,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16279,8 +16752,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16295,8 +16768,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16313,8 +16786,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16324,8 +16797,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16340,8 +16813,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16358,8 +16831,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16369,8 +16842,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16385,8 +16858,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16403,8 +16876,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16414,8 +16887,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16430,8 +16903,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16448,8 +16921,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16459,8 +16932,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16475,8 +16948,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16493,8 +16966,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16504,8 +16977,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16520,7 +16993,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16530,7 +17003,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16549,8 +17022,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16560,8 +17033,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16576,7 +17049,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16586,7 +17059,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16648,8 +17121,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16659,8 +17132,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16675,8 +17148,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16692,8 +17165,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16702,9 +17175,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16718,9 +17191,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16736,8 +17209,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -16746,9 +17219,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -16762,7 +17235,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -16863,5 +17336,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/src/ontology/imports/orcidio_import.owl b/src/ontology/imports/orcidio_import.owl index 46124dcd..1044bba3 100644 --- a/src/ontology/imports/orcidio_import.owl +++ b/src/ontology/imports/orcidio_import.owl @@ -7,21 +7,27 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-08-16") + +Annotation(owl:versionInfo "2024-02-12") +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -34,6 +40,11 @@ Declaration(AnnotationProperty()) # Named Individuals ############################ +# Individual: (Aleix Puig-Barbé) + +AnnotationAssertion(Annotation( ) "Researcher ORCID=0000-0001-6677-8489") +AnnotationAssertion(Annotation( ) rdfs:label "Aleix Puig-Barbé") + # Individual: (Austin Meier) AnnotationAssertion(Annotation( ) "Researcher") @@ -54,11 +65,21 @@ AnnotationAssertion(Annotation( ) "data scientist") AnnotationAssertion(Annotation( ) rdfs:label "Anne Thessen") +# Individual: (Jie Zheng) + +AnnotationAssertion(Annotation( ) "researcher (ORCID 0000-0002-2999-0103)") +AnnotationAssertion(Annotation( ) rdfs:label "Jie Zheng") + # Individual: (Pier Luigi Buttigieg) AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Pier Luigi Buttigieg") +# Individual: (Christian J Stoeckert) + +AnnotationAssertion(Annotation( ) "researcher") +AnnotationAssertion(Annotation( ) rdfs:label "Christian J Stoeckert") + # Individual: (Christopher J. Mungall) AnnotationAssertion(Annotation( ) "bioinformatics researcher") @@ -89,11 +110,26 @@ AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Lindsay G Cowell") +# Individual: (Pascale Gaudet) + +AnnotationAssertion(Annotation( ) "Canadian biocurator") +AnnotationAssertion(Annotation( ) rdfs:label "Pascale Gaudet") + +# Individual: (S. Clint Dowland) + +AnnotationAssertion(Annotation( ) "Researcher ORCID=0000-0003-1909-9269") +AnnotationAssertion(Annotation( ) rdfs:label "S. Clint Dowland") + # Individual: (Anna Maria Masci) AnnotationAssertion(Annotation( ) "researcher") AnnotationAssertion(Annotation( ) rdfs:label "Anna Maria Masci") +# Individual: (Jorrit Poelen) + +AnnotationAssertion(Annotation( ) "software/data engineer") +AnnotationAssertion(Annotation( ) rdfs:label "Jorrit Poelen") + # Individual: (Charles Tapley Hoyt) AnnotationAssertion(Annotation( ) "American chemist") diff --git a/src/ontology/subsets/ro-biotic-interaction.json b/src/ontology/subsets/ro-biotic-interaction.json index 8309ba7d..9fd62d8e 100644 --- a/src/ontology/subsets/ro-biotic-interaction.json +++ b/src/ontology/subsets/ro-biotic-interaction.json @@ -736,6 +736,43 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008501", "lbl" : "epiphyte of", @@ -1021,6 +1058,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002641", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002635" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008501", "pred" : "subPropertyOf", @@ -1113,6 +1158,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008501", "pred" : "inverseOf", diff --git a/src/ontology/subsets/ro-biotic-interaction.obo b/src/ontology/subsets/ro-biotic-interaction.obo index 1f33ac3f..82eed56a 100644 --- a/src/ontology/subsets/ro-biotic-interaction.obo +++ b/src/ontology/subsets/ro-biotic-interaction.obo @@ -441,6 +441,26 @@ def: "inverse of intracellular endoparasite of" [] subset: RO:0002259 is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002802 +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: RO:0002454 ! has host + [Typedef] id: RO:0008501 name: epiphyte of diff --git a/src/ontology/subsets/ro-biotic-interaction.owl b/src/ontology/subsets/ro-biotic-interaction.owl index 9017b92f..2373adf8 100644 --- a/src/ontology/subsets/ro-biotic-interaction.owl +++ b/src/ontology/subsets/ro-biotic-interaction.owl @@ -7,6 +7,7 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> @@ -65,6 +66,12 @@ + + + + + + @@ -754,6 +761,34 @@ + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -822,5 +857,5 @@ - + diff --git a/src/ontology/subsets/ro-causal.json b/src/ontology/subsets/ro-causal.json index 22c6414d..995c9dab 100644 --- a/src/ontology/subsets/ro-causal.json +++ b/src/ontology/subsets/ro-causal.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index aae8993f..b2bf3775 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index 40bb5909..5284eca2 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-causal.tsv b/src/ontology/subsets/ro-causal.tsv index f63b8b06..958994a5 100644 --- a/src/ontology/subsets/ro-causal.tsv +++ b/src/ontology/subsets/ro-causal.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid1 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid18 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid22 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid26 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid33 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid37 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid40 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid5 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid52 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid58 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid61 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid64 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid67 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid1 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid18 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid22 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid26 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid33 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid37 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid40 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid5 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid52 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid58 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid61 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid64 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid67 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid9 @@ -29,6 +29,7 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 + @@ -39,7 +40,6 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 - @@ -47,6 +47,8 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 + + diff --git a/src/ontology/subsets/ro-chado.json b/src/ontology/subsets/ro-chado.json index a473678c..492b6f02 100644 --- a/src/ontology/subsets/ro-chado.json +++ b/src/ontology/subsets/ro-chado.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/subsets/ro-chado.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/subsets/ro-chado.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -1838,6 +1838,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -2572,12 +2575,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -5352,7 +5360,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -10143,6 +10151,43 @@ "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", @@ -11815,6 +11860,54 @@ "val" : "2022-09-26T06:08:01Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -12299,6 +12392,25 @@ "val" : "https://orcid.org/0000-0003-1909-9269" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017005", + "lbl" : "contains measured amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a container and measurement datum that specifies the actual amount of material in the container." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2999-0103" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-5714-991X" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -12710,6 +12822,63 @@ "val" : "https://orcid.org/0000-0002-4142-7153" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -14789,6 +14958,16 @@ "val" : "is defined by" } ] } + }, { + "id" : "https://orcid.org/0000-0001-6677-8489", + "lbl" : "Aleix Puig-Barbé", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0001-6677-8489" + } ] + } }, { "id" : "https://orcid.org/0000-0001-6996-0040", "lbl" : "Austin Meier", @@ -14829,6 +15008,16 @@ "val" : "data scientist" } ] } + }, { + "id" : "https://orcid.org/0000-0002-2999-0103", + "lbl" : "Jie Zheng", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-2999-0103)" + } ] + } }, { "id" : "https://orcid.org/0000-0002-4366-3088", "lbl" : "Pier Luigi Buttigieg", @@ -14839,6 +15028,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-5714-991X", + "lbl" : "Christian J Stoeckert", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-6601-2165", "lbl" : "Christopher J. Mungall", @@ -14899,6 +15098,26 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1813-6857", + "lbl" : "Pascale Gaudet", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Canadian biocurator" + } ] + } + }, { + "id" : "https://orcid.org/0000-0003-1909-9269", + "lbl" : "S. Clint Dowland", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-1909-9269" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1940-6740", "lbl" : "Anna Maria Masci", @@ -14909,6 +15128,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-3138-4118", + "lbl" : "Jorrit Poelen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "software/data engineer" + } ] + } }, { "id" : "https://orcid.org/0000-0003-4423-4370", "lbl" : "Charles Tapley Hoyt", @@ -15308,6 +15537,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -16780,6 +17013,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -17192,6 +17433,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -17360,6 +17609,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -18036,6 +18301,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003000", "pred" : "inverseOf", diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo index fe43ab79..dd45dd89 100644 --- a/src/ontology/subsets/ro-chado.obo +++ b/src/ontology/subsets/ro-chado.obo @@ -1,19 +1,24 @@ format-version: 1.2 subsetdef: common_anatomy "" +subsetdef: efo_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: human_reference_atlas "" +subsetdef: pheno_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" +subsetdef: uberon_slim "" subsetdef: upper_level "" +subsetdef: vertebrate_core "" default-namespace: relationship ontology: ro/subsets/ro-chado.obo property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Typedef] id: BFO:0000050 @@ -312,8 +317,9 @@ is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 -name: regulates_in_other_organism +name: regulates_in_another_organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "regulates in other organism" EXACT [] is_a: RO:0002418 ! causally upstream of or within [Typedef] @@ -630,7 +636,7 @@ id: RO:0002131 name: overlaps def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -735,7 +741,7 @@ is_a: RO:0002323 ! mereotopologically related to id: RO:0002177 name: attached_to_part_of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002371 BFO:0000050 {RO:0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -775,6 +781,7 @@ id: RO:0002202 name: develops_from def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] is_transitive: true +is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -883,7 +890,7 @@ is_a: RO:0002216 ! capable of part of id: RO:0002216 name: capable_of_part_of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -1229,7 +1236,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002297 -name: results_in_formation_of +name: results_in_formation_of_anatomical_entity is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -1307,7 +1314,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002314 name: characteristic_of_part_of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -1373,7 +1380,7 @@ def: "A grouping relationship for any relationship directly involving a function id: RO:0002329 name: part_of_structure_that_is_capable_of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -1843,7 +1850,7 @@ id: RO:0002432 name: is_active_in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -2114,7 +2121,7 @@ is_a: RO:0002476 ! child nucleus of id: RO:0002479 name: has_part_that_occurs_in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002480 @@ -2280,7 +2287,7 @@ is_a: RO:0002566 ! causally influences id: RO:0002509 name: determined_by_part_of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -2618,12 +2625,12 @@ is_a: RO:0002233 ! has input [Typedef] id: RO:0002587 name: results_in_synthesis_of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity [Typedef] id: RO:0002588 name: results_in_assembly_of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity is_a: RO:0002592 ! results in organization of [Typedef] @@ -2871,6 +2878,19 @@ def: "Two or more individuals sharing the same roost site (cave, mine, tree or t is_symmetric: true is_a: RO:0008506 ! ecologically co-occurs with +[Typedef] +id: RO:0002802 +name: reservoir_host_of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has_reservoir_host +def: "inverse of reservoir host of" [] +is_a: RO:0002454 ! has host + [Typedef] id: RO:0003000 name: produces @@ -3498,6 +3518,20 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of +[Typedef] +id: RO:0012013 +name: positively_regulates_in_another_organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "positively regulates in other organism" EXACT [] +is_a: RO:0002010 ! regulates in another organism + +[Typedef] +id: RO:0012014 +name: negatively_regulates_in_another_organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "negatively regulates in other organism" EXACT [] +is_a: RO:0002010 ! regulates in another organism + [Typedef] id: RO:0013001 name: has_synaptic_IO_in_region @@ -3681,6 +3715,11 @@ def: "A relation between entities in which one increases as the other decreases. is_symmetric: true is_a: RO:0002610 ! correlated with +[Typedef] +id: RO:0017005 +name: contains_measured_amount +def: "A relation between a container and measurement datum that specifies the actual amount of material in the container." [] + [Typedef] id: RO:0018001 name: is_myristoyltransferase_activity @@ -3820,6 +3859,25 @@ name: confers_susceptibility_to_condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] is_a: RO:0003304 ! contributes to condition +[Typedef] +id: RO:0020101 +name: vessel_supplies_blood_to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +is_a: RO:0002178 ! supplies + +[Typedef] +id: RO:0020102 +name: vessel_drains_blood_from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +is_a: RO:0002179 ! drains + +[Typedef] +id: RO:0020103 +name: directly_supplies_and_drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +is_a: RO:0002178 ! supplies +is_a: RO:0002179 ! drains + [Typedef] id: RO:0040035 name: disease_relationship diff --git a/src/ontology/subsets/ro-chado.owl b/src/ontology/subsets/ro-chado.owl index 389234a4..76b4fd58 100644 --- a/src/ontology/subsets/ro-chado.owl +++ b/src/ontology/subsets/ro-chado.owl @@ -17,12 +17,11 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2023-08-18 + + 2024-02-13 @@ -38,12 +37,6 @@ - - - - - - @@ -1122,59 +1115,81 @@ Where we have an annotation assertion - + - + - + - + + + - + - + + + - + - + + + - + - + + + - + - + + + - + - + - + - + + + + + + + + + + + + + - + - + @@ -1472,23 +1487,6 @@ Where we have an annotation assertion - - - - - - - - - - - + @@ -4538,7 +4545,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results in formation of + results in formation of anatomical entity @@ -4985,6 +4992,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -8278,6 +8286,34 @@ the a supports either the existence of b, or the truth value of b. + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -9636,6 +9672,36 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + positively regulates in other organism + + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + negatively regulates in other organism + + negatively regulates in another organism + + + + @@ -10065,6 +10131,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. + A relation between a container and measurement datum that specifies the actual amount of material in the container. + + + contains measured amount + + + + @@ -10433,6 +10511,46 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + vessel supplies blood to + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + vessel drains blood from + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + directly supplies and drains + + + + @@ -12276,6 +12394,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0001-6677-8489 + Aleix Puig-Barbé + + + + + Researcher ORCID=0000-0001-6677-8489 + + + + + + Aleix Puig-Barbé + + + + + @@ -12360,6 +12499,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-2999-0103) + Jie Zheng + + + + + researcher (ORCID 0000-0002-2999-0103) + + + + + + Jie Zheng + + + + + @@ -12381,6 +12541,27 @@ binary, and takes no temporal argument. + + + + researcher + Christian J Stoeckert + + + + + researcher + + + + + + Christian J Stoeckert + + + + + @@ -12507,6 +12688,48 @@ binary, and takes no temporal argument. + + + + Canadian biocurator + Pascale Gaudet + + + + + Canadian biocurator + + + + + + Pascale Gaudet + + + + + + + + + Researcher ORCID=0000-0003-1909-9269 + S. Clint Dowland + + + + + Researcher ORCID=0000-0003-1909-9269 + + + + + + S. Clint Dowland + + + + + @@ -12528,6 +12751,27 @@ binary, and takes no temporal argument. + + + + software/data engineer + Jorrit Poelen + + + + + software/data engineer + + + + + + Jorrit Poelen + + + + + @@ -13003,28 +13247,28 @@ No imports /////////////////////////////////////////////////////////////////////////////////////// --> - + - + - + - + - + - + - + - + @@ -13033,15 +13277,6 @@ No imports - - - - - - - - - @@ -13065,8 +13300,8 @@ No imports - - + + @@ -13076,8 +13311,8 @@ No imports - - + + @@ -13087,8 +13322,8 @@ No imports - - + + @@ -13105,8 +13340,8 @@ No imports - - + + @@ -13123,8 +13358,8 @@ No imports - - + + @@ -13134,8 +13369,8 @@ No imports - - + + @@ -13145,8 +13380,8 @@ No imports - - + + @@ -13163,8 +13398,8 @@ No imports - - + + @@ -13181,8 +13416,8 @@ No imports - - + + @@ -13192,8 +13427,8 @@ No imports - - + + @@ -13203,8 +13438,8 @@ No imports - - + + @@ -13221,8 +13456,8 @@ No imports - - + + @@ -13239,8 +13474,8 @@ No imports - - + + @@ -13250,8 +13485,8 @@ No imports - - + + @@ -13266,8 +13501,8 @@ No imports - - + + @@ -13284,8 +13519,8 @@ No imports - - + + @@ -13295,8 +13530,8 @@ No imports - - + + @@ -13311,8 +13546,8 @@ No imports - - + + @@ -13329,8 +13564,8 @@ No imports - - + + @@ -13340,8 +13575,8 @@ No imports - - + + @@ -13356,8 +13591,8 @@ No imports - - + + @@ -13374,8 +13609,8 @@ No imports - - + + @@ -13385,8 +13620,8 @@ No imports - - + + @@ -13401,8 +13636,8 @@ No imports - - + + @@ -13419,8 +13654,8 @@ No imports - - + + @@ -13430,8 +13665,8 @@ No imports - - + + @@ -13446,8 +13681,8 @@ No imports - - + + @@ -13507,8 +13742,8 @@ No imports - - + + @@ -13518,8 +13753,8 @@ No imports - - + + @@ -13534,8 +13769,8 @@ No imports - - + + @@ -13551,8 +13786,8 @@ No imports - - + + @@ -13561,9 +13796,9 @@ No imports - - - + + + @@ -13577,9 +13812,9 @@ No imports - - - + + + @@ -13595,8 +13830,8 @@ No imports - - + + @@ -13605,9 +13840,9 @@ No imports - - - + + + @@ -13621,7 +13856,7 @@ No imports - + @@ -13722,5 +13957,5 @@ No imports - + diff --git a/src/ontology/subsets/ro-developmental.json b/src/ontology/subsets/ro-developmental.json index f4109945..d6d32493 100644 --- a/src/ontology/subsets/ro-developmental.json +++ b/src/ontology/subsets/ro-developmental.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index 1b9a7611..6518ba78 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index d5a7ed64..5f2ee16a 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-developmental.tsv b/src/ontology/subsets/ro-developmental.tsv index 2409aaef..3095b994 100644 --- a/src/ontology/subsets/ro-developmental.tsv +++ b/src/ontology/subsets/ro-developmental.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid1 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid18 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid22 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid26 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid33 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid37 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid40 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid5 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid52 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid58 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid61 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid64 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid67 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid1 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid18 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid22 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid26 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid33 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid37 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid40 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid5 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid52 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid58 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid61 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid64 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid67 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid9 @@ -29,6 +29,7 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 + @@ -39,7 +40,6 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 - @@ -47,6 +47,8 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 + + diff --git a/src/ontology/subsets/ro-interaction.json b/src/ontology/subsets/ro-interaction.json index f20717da..63fc49ba 100644 --- a/src/ontology/subsets/ro-interaction.json +++ b/src/ontology/subsets/ro-interaction.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo index 4ef159e2..122c9d98 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index cd814966..6c96e01f 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-interaction.tsv b/src/ontology/subsets/ro-interaction.tsv index 9b1bc3ad..8318d6a8 100644 --- a/src/ontology/subsets/ro-interaction.tsv +++ b/src/ontology/subsets/ro-interaction.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid1 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid18 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid22 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid26 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid33 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid37 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid40 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid5 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid52 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid58 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid61 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid64 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid67 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid1 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid18 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid22 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid26 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid33 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid37 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid40 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid5 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid52 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid58 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid61 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid64 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid67 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid9 @@ -29,6 +29,7 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 + @@ -39,7 +40,6 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 - @@ -47,6 +47,8 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 + + diff --git a/src/ontology/subsets/ro-mereotopology.json b/src/ontology/subsets/ro-mereotopology.json index b4fa7b87..d0fdda09 100644 --- a/src/ontology/subsets/ro-mereotopology.json +++ b/src/ontology/subsets/ro-mereotopology.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index b3bbb2c2..31d0bd7e 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index 0fd2522d..b0654e52 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-mereotopology.tsv b/src/ontology/subsets/ro-mereotopology.tsv index 58250b17..87955ff5 100644 --- a/src/ontology/subsets/ro-mereotopology.tsv +++ b/src/ontology/subsets/ro-mereotopology.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid1 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid18 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid22 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid26 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid33 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid37 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid40 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid5 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid52 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid58 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid61 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid64 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid67 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid1 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid18 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid22 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid26 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid33 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid37 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid40 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid5 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid52 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid58 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid61 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid64 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid67 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid9 @@ -29,6 +29,7 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 + @@ -39,7 +40,6 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 - @@ -47,6 +47,8 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 + + diff --git a/src/ontology/subsets/ro-sequence.json b/src/ontology/subsets/ro-sequence.json index 10e06877..2cfc531b 100644 --- a/src/ontology/subsets/ro-sequence.json +++ b/src/ontology/subsets/ro-sequence.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index 37ac9123..bbbc3979 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index 985fe0d8..359bce8a 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-sequence.tsv b/src/ontology/subsets/ro-sequence.tsv index 80c67530..aabcd030 100644 --- a/src/ontology/subsets/ro-sequence.tsv +++ b/src/ontology/subsets/ro-sequence.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid1 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid18 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid22 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid26 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid33 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid37 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid40 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid5 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid52 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid58 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid61 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid64 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid67 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid1 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid18 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid22 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid26 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid33 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid37 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid40 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid5 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid52 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid58 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid61 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid64 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid67 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid9 @@ -29,6 +29,7 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 + @@ -39,7 +40,6 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 - @@ -47,6 +47,8 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 + + diff --git a/src/ontology/subsets/ro-time-interval.json b/src/ontology/subsets/ro-time-interval.json index ca09a23e..4acf12c3 100644 --- a/src/ontology/subsets/ro-time-interval.json +++ b/src/ontology/subsets/ro-time-interval.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index 394d300d..54ead77f 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index 1d0ac69e..a8cde506 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-time-interval.tsv b/src/ontology/subsets/ro-time-interval.tsv index 58e569a4..dadfed7a 100644 --- a/src/ontology/subsets/ro-time-interval.tsv +++ b/src/ontology/subsets/ro-time-interval.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid1 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid18 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid22 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid26 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid33 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid37 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid40 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid5 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid52 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid58 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid61 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid64 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid67 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid1 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid18 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid22 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid26 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid33 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid37 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid40 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid5 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid52 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid58 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid61 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid64 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid67 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid9 @@ -29,6 +29,7 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 + @@ -39,7 +40,6 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 - @@ -47,6 +47,8 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 + + diff --git a/subsets/ro-biotic-interaction.json b/subsets/ro-biotic-interaction.json index 8309ba7d..9fd62d8e 100644 --- a/subsets/ro-biotic-interaction.json +++ b/subsets/ro-biotic-interaction.json @@ -736,6 +736,43 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0008501", "lbl" : "epiphyte of", @@ -1021,6 +1058,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002641", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002635" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008501", "pred" : "subPropertyOf", @@ -1113,6 +1158,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008501", "pred" : "inverseOf", diff --git a/subsets/ro-biotic-interaction.obo b/subsets/ro-biotic-interaction.obo index 1f33ac3f..82eed56a 100644 --- a/subsets/ro-biotic-interaction.obo +++ b/subsets/ro-biotic-interaction.obo @@ -441,6 +441,26 @@ def: "inverse of intracellular endoparasite of" [] subset: RO:0002259 is_a: RO:0002635 ! has endoparasite +[Typedef] +id: RO:0002802 +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: RO:0002454 ! has host + [Typedef] id: RO:0008501 name: epiphyte of diff --git a/subsets/ro-biotic-interaction.owl b/subsets/ro-biotic-interaction.owl index 9017b92f..2373adf8 100644 --- a/subsets/ro-biotic-interaction.owl +++ b/subsets/ro-biotic-interaction.owl @@ -7,6 +7,7 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> @@ -65,6 +66,12 @@ + + + + + + @@ -754,6 +761,34 @@ + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -822,5 +857,5 @@ - + diff --git a/subsets/ro-causal.json b/subsets/ro-causal.json index 22c6414d..995c9dab 100644 --- a/subsets/ro-causal.json +++ b/subsets/ro-causal.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index aae8993f..b2bf3775 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index 40bb5909..5284eca2 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-causal.tsv b/subsets/ro-causal.tsv index f63b8b06..958994a5 100644 --- a/subsets/ro-causal.tsv +++ b/subsets/ro-causal.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid1 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid18 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid22 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid26 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid33 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid37 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid40 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid5 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid52 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid58 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid61 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid64 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid67 -_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid1 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid18 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid22 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid26 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid33 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid37 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid40 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid5 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid52 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid58 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid61 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid64 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid67 +_:B56e66877X2De04dX2D49a7X2Dab5dX2D23605b891bb6genid9 @@ -29,6 +29,7 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 + @@ -39,7 +40,6 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 - @@ -47,6 +47,8 @@ _:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 + + diff --git a/subsets/ro-chado.json b/subsets/ro-chado.json index a473678c..492b6f02 100644 --- a/subsets/ro-chado.json +++ b/subsets/ro-chado.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-18" + "val" : "2024-02-13" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/subsets/ro-chado.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/subsets/ro-chado.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -1838,6 +1838,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -2572,12 +2575,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" @@ -5352,7 +5360,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -10143,6 +10151,43 @@ "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", @@ -11815,6 +11860,54 @@ "val" : "2022-09-26T06:08:01Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -12299,6 +12392,25 @@ "val" : "https://orcid.org/0000-0003-1909-9269" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017005", + "lbl" : "contains measured amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a container and measurement datum that specifies the actual amount of material in the container." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "anticoagulant-containing test tube contains measured amount 5 ml of blood specimen." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2999-0103" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-5714-991X" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0018001", "lbl" : "is myristoyltransferase activity", @@ -12710,6 +12822,63 @@ "val" : "https://orcid.org/0000-0002-4142-7153" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -14789,6 +14958,16 @@ "val" : "is defined by" } ] } + }, { + "id" : "https://orcid.org/0000-0001-6677-8489", + "lbl" : "Aleix Puig-Barbé", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0001-6677-8489" + } ] + } }, { "id" : "https://orcid.org/0000-0001-6996-0040", "lbl" : "Austin Meier", @@ -14829,6 +15008,16 @@ "val" : "data scientist" } ] } + }, { + "id" : "https://orcid.org/0000-0002-2999-0103", + "lbl" : "Jie Zheng", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher (ORCID 0000-0002-2999-0103)" + } ] + } }, { "id" : "https://orcid.org/0000-0002-4366-3088", "lbl" : "Pier Luigi Buttigieg", @@ -14839,6 +15028,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0002-5714-991X", + "lbl" : "Christian J Stoeckert", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "researcher" + } ] + } }, { "id" : "https://orcid.org/0000-0002-6601-2165", "lbl" : "Christopher J. Mungall", @@ -14899,6 +15098,26 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-1813-6857", + "lbl" : "Pascale Gaudet", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Canadian biocurator" + } ] + } + }, { + "id" : "https://orcid.org/0000-0003-1909-9269", + "lbl" : "S. Clint Dowland", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "Researcher ORCID=0000-0003-1909-9269" + } ] + } }, { "id" : "https://orcid.org/0000-0003-1940-6740", "lbl" : "Anna Maria Masci", @@ -14909,6 +15128,16 @@ "val" : "researcher" } ] } + }, { + "id" : "https://orcid.org/0000-0003-3138-4118", + "lbl" : "Jorrit Poelen", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "software/data engineer" + } ] + } }, { "id" : "https://orcid.org/0000-0003-4423-4370", "lbl" : "Charles Tapley Hoyt", @@ -15308,6 +15537,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -16780,6 +17013,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -17192,6 +17433,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -17360,6 +17609,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -18036,6 +18301,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003000", "pred" : "inverseOf", diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index fe43ab79..dd45dd89 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -1,19 +1,24 @@ format-version: 1.2 subsetdef: common_anatomy "" +subsetdef: efo_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: human_reference_atlas "" +subsetdef: pheno_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" +subsetdef: uberon_slim "" subsetdef: upper_level "" +subsetdef: vertebrate_core "" default-namespace: relationship ontology: ro/subsets/ro-chado.obo property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-08-18" xsd:string +property_value: owl:versionInfo "2024-02-13" xsd:string [Typedef] id: BFO:0000050 @@ -312,8 +317,9 @@ is_a: RO:0002292 ! expresses [Typedef] id: RO:0002010 -name: regulates_in_other_organism +name: regulates_in_another_organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "regulates in other organism" EXACT [] is_a: RO:0002418 ! causally upstream of or within [Typedef] @@ -630,7 +636,7 @@ id: RO:0002131 name: overlaps def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -735,7 +741,7 @@ is_a: RO:0002323 ! mereotopologically related to id: RO:0002177 name: attached_to_part_of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002371 BFO:0000050 {RO:0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -775,6 +781,7 @@ id: RO:0002202 name: develops_from def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] is_transitive: true +is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -883,7 +890,7 @@ is_a: RO:0002216 ! capable of part of id: RO:0002216 name: capable_of_part_of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -1229,7 +1236,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure [Typedef] id: RO:0002297 -name: results_in_formation_of +name: results_in_formation_of_anatomical_entity is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -1307,7 +1314,7 @@ is_a: RO:0040036 ! results in changes to anatomical or cellular structure id: RO:0002314 name: characteristic_of_part_of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -1373,7 +1380,7 @@ def: "A grouping relationship for any relationship directly involving a function id: RO:0002329 name: part_of_structure_that_is_capable_of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -1843,7 +1850,7 @@ id: RO:0002432 name: is_active_in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -2114,7 +2121,7 @@ is_a: RO:0002476 ! child nucleus of id: RO:0002479 name: has_part_that_occurs_in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000051 BFO:0000066 {RO:0002581="true"} [Typedef] id: RO:0002480 @@ -2280,7 +2287,7 @@ is_a: RO:0002566 ! causally influences id: RO:0002509 name: determined_by_part_of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002507 BFO:0000050 {RO:0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -2618,12 +2625,12 @@ is_a: RO:0002233 ! has input [Typedef] id: RO:0002587 name: results_in_synthesis_of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity [Typedef] id: RO:0002588 name: results_in_assembly_of -is_a: RO:0002297 ! results in formation of +is_a: RO:0002297 ! results in formation of anatomical entity is_a: RO:0002592 ! results in organization of [Typedef] @@ -2871,6 +2878,19 @@ def: "Two or more individuals sharing the same roost site (cave, mine, tree or t is_symmetric: true is_a: RO:0008506 ! ecologically co-occurs with +[Typedef] +id: RO:0002802 +name: reservoir_host_of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +is_a: RO:0002453 ! host of +inverse_of: RO:0002803 ! has reservoir host + +[Typedef] +id: RO:0002803 +name: has_reservoir_host +def: "inverse of reservoir host of" [] +is_a: RO:0002454 ! has host + [Typedef] id: RO:0003000 name: produces @@ -3498,6 +3518,20 @@ def: "p indirectly regulates q iff p is indirectly causally upstream of q and p is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of +[Typedef] +id: RO:0012013 +name: positively_regulates_in_another_organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "positively regulates in other organism" EXACT [] +is_a: RO:0002010 ! regulates in another organism + +[Typedef] +id: RO:0012014 +name: negatively_regulates_in_another_organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +synonym: "negatively regulates in other organism" EXACT [] +is_a: RO:0002010 ! regulates in another organism + [Typedef] id: RO:0013001 name: has_synaptic_IO_in_region @@ -3681,6 +3715,11 @@ def: "A relation between entities in which one increases as the other decreases. is_symmetric: true is_a: RO:0002610 ! correlated with +[Typedef] +id: RO:0017005 +name: contains_measured_amount +def: "A relation between a container and measurement datum that specifies the actual amount of material in the container." [] + [Typedef] id: RO:0018001 name: is_myristoyltransferase_activity @@ -3820,6 +3859,25 @@ name: confers_susceptibility_to_condition def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] is_a: RO:0003304 ! contributes to condition +[Typedef] +id: RO:0020101 +name: vessel_supplies_blood_to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +is_a: RO:0002178 ! supplies + +[Typedef] +id: RO:0020102 +name: vessel_drains_blood_from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +is_a: RO:0002179 ! drains + +[Typedef] +id: RO:0020103 +name: directly_supplies_and_drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +is_a: RO:0002178 ! supplies +is_a: RO:0002179 ! drains + [Typedef] id: RO:0040035 name: disease_relationship diff --git a/subsets/ro-chado.owl b/subsets/ro-chado.owl index 389234a4..76b4fd58 100644 --- a/subsets/ro-chado.owl +++ b/subsets/ro-chado.owl @@ -17,12 +17,11 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2023-08-18 + + 2024-02-13 @@ -38,12 +37,6 @@ - - - - - - @@ -1122,59 +1115,81 @@ Where we have an annotation assertion - + - + - + - + + + - + - + + + - + - + + + - + - + + + - + - + + + - + - + - + - + + + + + + + + + + + + + - + - + @@ -1472,23 +1487,6 @@ Where we have an annotation assertion - - - - - - - - - - - + @@ -4538,7 +4545,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results in formation of + results in formation of anatomical entity @@ -4985,6 +4992,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of enables + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -8278,6 +8286,34 @@ the a supports either the existence of b, or the truth value of b. + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + + has reservoir host + + + + @@ -9636,6 +9672,36 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + positively regulates in other organism + + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + negatively regulates in other organism + + negatively regulates in another organism + + + + @@ -10065,6 +10131,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. + A relation between a container and measurement datum that specifies the actual amount of material in the container. + + + contains measured amount + + + + @@ -10433,6 +10511,46 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + vessel supplies blood to + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + vessel drains blood from + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + directly supplies and drains + + + + @@ -12276,6 +12394,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0001-6677-8489 + Aleix Puig-Barbé + + + + + Researcher ORCID=0000-0001-6677-8489 + + + + + + Aleix Puig-Barbé + + + + + @@ -12360,6 +12499,27 @@ binary, and takes no temporal argument. + + + + researcher (ORCID 0000-0002-2999-0103) + Jie Zheng + + + + + researcher (ORCID 0000-0002-2999-0103) + + + + + + Jie Zheng + + + + + @@ -12381,6 +12541,27 @@ binary, and takes no temporal argument. + + + + researcher + Christian J Stoeckert + + + + + researcher + + + + + + Christian J Stoeckert + + + + + @@ -12507,6 +12688,48 @@ binary, and takes no temporal argument. + + + + Canadian biocurator + Pascale Gaudet + + + + + Canadian biocurator + + + + + + Pascale Gaudet + + + + + + + + + Researcher ORCID=0000-0003-1909-9269 + S. Clint Dowland + + + + + Researcher ORCID=0000-0003-1909-9269 + + + + + + S. Clint Dowland + + + + + @@ -12528,6 +12751,27 @@ binary, and takes no temporal argument. + + + + software/data engineer + Jorrit Poelen + + + + + software/data engineer + + + + + + Jorrit Poelen + + + + + @@ -13003,28 +13247,28 @@ No imports /////////////////////////////////////////////////////////////////////////////////////// --> - + - + - + - + - + - + - + - + @@ -13033,15 +13277,6 @@ No imports - - - - - - - - - @@ -13065,8 +13300,8 @@ No imports - - + + @@ -13076,8 +13311,8 @@ No imports - - + + @@ -13087,8 +13322,8 @@ No imports - - + + @@ -13105,8 +13340,8 @@ No imports - - + + @@ -13123,8 +13358,8 @@ No imports - - + + @@ -13134,8 +13369,8 @@ No imports - - + + @@ -13145,8 +13380,8 @@ No imports - - + + @@ -13163,8 +13398,8 @@ No imports - - + + @@ -13181,8 +13416,8 @@ No imports - - + + @@ -13192,8 +13427,8 @@ No imports - - + + @@ -13203,8 +13438,8 @@ No imports - - + + @@ -13221,8 +13456,8 @@ No imports - - + + @@ -13239,8 +13474,8 @@ No imports - - + + @@ -13250,8 +13485,8 @@ No imports - - + + @@ -13266,8 +13501,8 @@ No imports - - + + @@ -13284,8 +13519,8 @@ No imports - - + + @@ -13295,8 +13530,8 @@ No imports - - + + @@ -13311,8 +13546,8 @@ No imports - - + + @@ -13329,8 +13564,8 @@ No imports - - + + @@ -13340,8 +13575,8 @@ No imports - - + + @@ -13356,8 +13591,8 @@ No imports - - + + @@ -13374,8 +13609,8 @@ No imports - - + + @@ -13385,8 +13620,8 @@ No imports - - + + @@ -13401,8 +13636,8 @@ No imports - - + + @@ -13419,8 +13654,8 @@ No imports - - + + @@ -13430,8 +13665,8 @@ No imports - - + + @@ -13446,8 +13681,8 @@ No imports - - + + @@ -13507,8 +13742,8 @@ No imports - - + + @@ -13518,8 +13753,8 @@ No imports - - + + @@ -13534,8 +13769,8 @@ No imports - - + + @@ -13551,8 +13786,8 @@ No imports - - + + @@ -13561,9 +13796,9 @@ No imports - - - + + + @@ -13577,9 +13812,9 @@ No imports - - - + + + @@ -13595,8 +13830,8 @@ No imports - - + + @@ -13605,9 +13840,9 @@ No imports - - - + + + @@ -13621,7 +13856,7 @@ No imports - + @@ -13722,5 +13957,5 @@ No imports - + diff --git a/subsets/ro-developmental.json b/subsets/ro-developmental.json index f4109945..d6d32493 100644 --- a/subsets/ro-developmental.json +++ b/subsets/ro-developmental.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index 1b9a7611..6518ba78 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index d5a7ed64..5f2ee16a 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-developmental.tsv b/subsets/ro-developmental.tsv index 2409aaef..3095b994 100644 --- a/subsets/ro-developmental.tsv +++ b/subsets/ro-developmental.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid1 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid18 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid22 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid26 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid33 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid37 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid40 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid5 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid52 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid58 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid61 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid64 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid67 -_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid1 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid18 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid22 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid26 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid33 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid37 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid40 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid5 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid52 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid58 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid61 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid64 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid67 +_:B96aeef78X2D01c6X2D43f1X2D9baaX2D6302c703a7e6genid9 @@ -29,6 +29,7 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 + @@ -39,7 +40,6 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 - @@ -47,6 +47,8 @@ _:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 + + diff --git a/subsets/ro-interaction.json b/subsets/ro-interaction.json index f20717da..63fc49ba 100644 --- a/subsets/ro-interaction.json +++ b/subsets/ro-interaction.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index 4ef159e2..122c9d98 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index cd814966..6c96e01f 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-interaction.tsv b/subsets/ro-interaction.tsv index 9b1bc3ad..8318d6a8 100644 --- a/subsets/ro-interaction.tsv +++ b/subsets/ro-interaction.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid1 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid18 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid22 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid26 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid33 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid37 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid40 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid5 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid52 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid58 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid61 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid64 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid67 -_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid1 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid18 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid22 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid26 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid33 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid37 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid40 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid5 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid52 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid58 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid61 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid64 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid67 +_:B53bc3a22X2D7cc0X2D4c6eX2D8e96X2D41709dfab1a8genid9 @@ -29,6 +29,7 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 + @@ -39,7 +40,6 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 - @@ -47,6 +47,8 @@ _:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 + + diff --git a/subsets/ro-mereotopology.json b/subsets/ro-mereotopology.json index b4fa7b87..d0fdda09 100644 --- a/subsets/ro-mereotopology.json +++ b/subsets/ro-mereotopology.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index b3bbb2c2..31d0bd7e 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 0fd2522d..b0654e52 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-mereotopology.tsv b/subsets/ro-mereotopology.tsv index 58250b17..87955ff5 100644 --- a/subsets/ro-mereotopology.tsv +++ b/subsets/ro-mereotopology.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid1 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid18 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid22 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid26 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid33 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid37 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid40 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid5 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid52 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid58 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid61 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid64 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid67 -_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid1 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid18 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid22 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid26 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid33 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid37 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid40 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid5 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid52 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid58 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid61 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid64 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid67 +_:B4ab6609aX2D05c1X2D44ddX2DafeeX2D85940ae4927egenid9 @@ -29,6 +29,7 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 + @@ -39,7 +40,6 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 - @@ -47,6 +47,8 @@ _:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 + + diff --git a/subsets/ro-sequence.json b/subsets/ro-sequence.json index 10e06877..2cfc531b 100644 --- a/subsets/ro-sequence.json +++ b/subsets/ro-sequence.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index 37ac9123..bbbc3979 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index 985fe0d8..359bce8a 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-sequence.tsv b/subsets/ro-sequence.tsv index 80c67530..aabcd030 100644 --- a/subsets/ro-sequence.tsv +++ b/subsets/ro-sequence.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid1 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid18 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid22 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid26 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid33 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid37 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid40 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid5 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid52 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid58 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid61 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid64 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid67 -_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid1 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid18 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid22 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid26 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid33 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid37 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid40 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid5 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid52 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid58 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid61 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid64 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid67 +_:Bca3b86e9X2D0016X2D42ceX2Db533X2Db70751f6f5bfgenid9 @@ -29,6 +29,7 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 + @@ -39,7 +40,6 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 - @@ -47,6 +47,8 @@ _:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 + + diff --git a/subsets/ro-time-interval.json b/subsets/ro-time-interval.json index ca09a23e..4acf12c3 100644 --- a/subsets/ro-time-interval.json +++ b/subsets/ro-time-interval.json @@ -241,6 +241,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_characteristic" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/284" } ] } }, { @@ -745,12 +748,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002010", - "lbl" : "regulates in other organism", + "lbl" : "regulates in another organism", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "regulates in other organism" + } ], "xrefs" : [ { "val" : "RO:0002010" } ], @@ -759,7 +767,7 @@ "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates_in_other_organism" + "val" : "regulates_in_another_organism" } ] } }, { @@ -3699,7 +3707,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -3723,7 +3731,7 @@ "val" : "GOC:mtg_berkeley_2013" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" + "val" : "results_in_formation_of_anatomical_entity" } ] } }, { @@ -8652,6 +8660,55 @@ "val" : "co-roosts_with" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002802", + "lbl" : "reservoir host of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." + }, + "comments" : [ "A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts." ], + "xrefs" : [ { + "val" : "RO:0002802" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://doi.org/10.3390/v13071356" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-3120-4802" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "reservoir_host_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002803", + "lbl" : "has reservoir host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of reservoir host of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002803" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_reservoir_host" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003002", "lbl" : "represses expression of", @@ -10542,6 +10599,66 @@ "val" : "indirectly_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012013", + "lbl" : "positively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "positively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:28Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates_in_another_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0012014", + "lbl" : "negatively regulates in another organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "negatively regulates in other organism" + } ], + "xrefs" : [ { + "val" : "RO:0012014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1813-6857" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2023-10-12T10:02:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates_in_another_organism" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013001", "lbl" : "has synaptic IO in region", @@ -11118,6 +11235,81 @@ "val" : "confers_susceptibility_to_condition" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020101", + "lbl" : "vessel supplies blood to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brachial artery vessel supplies blood to brachialis muscle" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:22Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_supplies_blood_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020102", + "lbl" : "vessel drains blood from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." + }, + "xrefs" : [ { + "val" : "RO:0020102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "cystic vein vessel drains blood from gallbladder" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:41Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "vessel_drains_blood_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0020103", + "lbl" : "directly supplies and drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." + }, + "xrefs" : [ { + "val" : "RO:0020103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "alveolar capillary directly supplies and drains some alveolus" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-02-01T10:09:59Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_supplies_and_drains" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0040035", "lbl" : "disease relationship", @@ -11522,6 +11714,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0016001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002202", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002254" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002202", "pred" : "subPropertyOf", @@ -12830,6 +13026,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002801", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0008506" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002803", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0003002", "pred" : "subPropertyOf", @@ -13230,6 +13434,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012013", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0012014", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0013001", "pred" : "subPropertyOf", @@ -13338,6 +13550,22 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0019501", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0003304" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020101", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020102", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002178" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0020103", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002179" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", @@ -13650,6 +13878,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002802", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002803" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004000", "pred" : "inverseOf", @@ -13729,7 +13961,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", @@ -13853,7 +14085,7 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0001000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -14110,6 +14342,18 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020101", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020102", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001981" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0020103", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001982" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index 394d300d..54ead77f 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -125,7 +125,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string @@ -1037,6 +1037,7 @@ domain: BFO:0000004 range: BFO:0000004 is_transitive: true is_a: developmentally_preceded_by ! developmentally preceded by +is_a: has_developmental_contribution_from ! has developmental contribution from inverse_of: develops_into ! develops into [Typedef] @@ -1242,6 +1243,19 @@ xref: RO:0011021 property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 is_a: regulates_quantity_of ! regulates quantity of +[Typedef] +id: directly_supplies_and_drains +name: directly supplies and drains +def: "x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y." [] +xref: RO:0020103 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:59Z" xsd:dateTime +property_value: IAO:0000112 "alveolar capillary directly supplies and drains some alveolus" xsd:string +domain: UBERON:0001982 +range: UBERON:0000061 +is_a: drains ! drains +is_a: supplies ! supplies + [Typedef] id: disease_arises_from_alteration_in_structure name: disease arises from alteration in structure @@ -1777,6 +1791,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string range: BFO:0000020 is_inverse_functional: true @@ -2245,7 +2260,7 @@ xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to is_a: biomechanically_related_to ! biomechanically related to @@ -2368,6 +2383,7 @@ property_value: IAO:0000112 "this process has participant this input material (o property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string domain: BFO:0000003 +domain: BFO:0000015 range: BFO:0000002 [Typedef] @@ -2545,6 +2561,15 @@ is_a: regulated_by ! regulated by created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_reservoir_host +name: has reservoir host +def: "inverse of reservoir host of" [] +subset: RO:0002259 +xref: RO:0002803 +property_value: IAO:0000112 "An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s." xsd:string +is_a: has_host ! has host + [Typedef] id: has_role name: has role @@ -2594,7 +2619,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: UBERON:0000061 -range: UBERON:0000465 {http://purl.obolibrary.org/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."} +range: UBERON:0000465 {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."} is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -3641,6 +3666,18 @@ xref: RO:0019002 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: negatively_regulates_in_another_organism +name: negatively regulates in another organism +def: "x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "negatively regulates in other organism" EXACT [] +xref: RO:0012014 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004050 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:42Z + [Typedef] id: obligate_parasite_of name: obligate parasite of @@ -3934,6 +3971,18 @@ xref: RO:0019001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 is_a: regulates_characteristic ! regulates characteristic +[Typedef] +id: positively_regulates_in_another_organism +name: positively regulates in another organism +def: "x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "positively regulates in other organism" EXACT [] +xref: RO:0012013 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1813-6857 +property_value: RO:0004049 RO:0002010 +is_a: regulates_in_another_organism ! regulates in another organism +creation_date: 2023-10-12T10:02:28Z + [Typedef] id: preceded_by name: preceded by @@ -4190,9 +4239,11 @@ range: PATO:0000001 is_a: causally_related_to ! causally related to [Typedef] -id: regulates_in_other_organism -name: regulates in other organism +id: regulates_in_another_organism +name: regulates in another organism def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +synonym: "regulates in other organism" EXACT [] xref: RO:0002010 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: BFO:0000015 @@ -4228,7 +4279,7 @@ name: related via exposure to def: "Any relationship between an exposure event or process and any other entity." [] xref: RO:0002244 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string -domain: RO:0002310 +domain: COB:0001000 is_a: causally_related_to ! causally related to [Typedef] @@ -4263,6 +4314,19 @@ domain: BFO:0000040 range: BFO:0000040 is_a: directly_negatively_regulates_activity_of ! directly negatively regulates activity of +[Typedef] +id: reservoir_host_of +name: reservoir host of +def: "A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host." [] +comment: A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. +xref: RO:0002802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3120-4802 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000112 "An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s." xsd:string +property_value: IAO:0000119 https://doi.org/10.3390/v13071356 +is_a: host_of ! host of +inverse_of: has_reservoir_host ! has reservoir host + [Typedef] id: results_in_acquisition_of_features_of name: results in acquisition of features of @@ -4294,7 +4358,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002588 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity is_a: results_in_organization_of ! results in organization of [Typedef] @@ -4426,8 +4490,8 @@ is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in change is_a: results_in_developmental_progression_of ! results in developmental progression of [Typedef] -id: results_in_formation_of -name: results in formation of +id: results_in_formation_of_anatomical_entity +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam @@ -4544,7 +4608,7 @@ is_a: results_in_developmental_progression_of ! results in developmental progres id: results_in_synthesis_of name: results in synthesis of xref: RO:0002587 -is_a: results_in_formation_of ! results in formation of +is_a: results_in_formation_of_anatomical_entity ! results in formation of anatomical entity [Typedef] id: results_in_transport_across @@ -5100,6 +5164,30 @@ property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: molecularly_interacts_with ! molecularly interacts with +[Typedef] +id: vessel_drains_blood_from +name: vessel drains blood from +def: "x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y." [] +xref: RO:0020102 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:41Z" xsd:dateTime +property_value: IAO:0000112 "cystic vein vessel drains blood from gallbladder" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: drains ! drains + +[Typedef] +id: vessel_supplies_blood_to +name: vessel supplies blood to +def: "x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y." [] +xref: RO:0020101 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-02-01T10:09:22Z" xsd:dateTime +property_value: IAO:0000112 "brachial artery vessel supplies blood to brachialis muscle" xsd:string +domain: UBERON:0001981 +range: UBERON:0000061 +is_a: supplies ! supplies + [Typedef] id: visited_by name: visited by diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index 1d0ac69e..a8cde506 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -278,6 +278,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of + part of part of @@ -309,6 +310,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part + has part has part @@ -388,7 +390,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. RO:0000053 has_characteristic + has characteristic has characteristic + https://github.com/oborel/obo-relations/pull/284 @@ -416,6 +420,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has participant this blood coagulation has participant this blood clot @@ -427,6 +432,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant has participant @@ -775,8 +781,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 - regulates_in_other_organism - regulates in other organism + regulates in other organism + + regulates_in_another_organism + regulates in another organism @@ -1964,6 +1972,7 @@ N1 SubclassOf ( + @@ -2588,7 +2597,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 @@ -2917,8 +2926,8 @@ If you need an axiom that says 'has_participant min 2 object', you sho - results_in_formation_of - results in formation of + results_in_formation_of_anatomical_entity + results in formation of anatomical entity @@ -3343,6 +3352,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati RO:0002333 enabled_by + enabled by enabled by https://wiki.geneontology.org/Enabled_by @@ -6313,6 +6323,38 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. + A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. + + + + RO:0002802 + reservoir_host_of + A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. + reservoir host of + + + + + + + + + An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. + inverse of reservoir host of + RO:0002803 + + has_reservoir_host + has reservoir host + + + + @@ -7695,6 +7737,40 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:28Z + RO:0012013 + positively regulates in other organism + + positively_regulates_in_another_organism + positively regulates in another organism + + + + + + + + + x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + + 2023-10-12T10:02:42Z + RO:0012014 + negatively regulates in other organism + + negatively_regulates_in_another_organism + negatively regulates in another organism + + + + @@ -8075,6 +8151,58 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + brachial artery vessel supplies blood to brachialis muscle + x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. + + 2024-02-01T10:09:22Z + RO:0020101 + vessel_supplies_blood_to + vessel supplies blood to + + + + + + + + + + + cystic vein vessel drains blood from gallbladder + x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. + + 2024-02-01T10:09:41Z + RO:0020102 + vessel_drains_blood_from + vessel drains blood from + + + + + + + + + + + + alveolar capillary directly supplies and drains some alveolus + x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. + + 2024-02-01T10:09:59Z + RO:0020103 + directly_supplies_and_drains + directly supplies and drains + + + + @@ -8210,6 +8338,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -8270,12 +8404,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -8318,6 +8446,18 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + diff --git a/subsets/ro-time-interval.tsv b/subsets/ro-time-interval.tsv index 58e569a4..dadfed7a 100644 --- a/subsets/ro-time-interval.tsv +++ b/subsets/ro-time-interval.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid1 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid18 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid22 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid26 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid33 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid37 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid40 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid5 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid52 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid58 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid61 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid64 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid67 -_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid1 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid18 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid22 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid26 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid33 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid37 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid40 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid5 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid52 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid58 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid61 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid64 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid67 +_:B1f0ff49aX2D7625X2D498dX2D9b5dX2Dcb5c162aae39genid9 @@ -29,6 +29,7 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 + @@ -39,7 +40,6 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 - @@ -47,6 +47,8 @@ _:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 + + From 797a4e7a0d1bbf76ef828211fd063145a73e11b8 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Tue, 27 Feb 2024 16:35:33 +0000 Subject: [PATCH 10/13] Add properties has_numerator and has_denominator (#792) * Create ID range Create an ID range for Ray Stefancsik. * Add properties has_numerator and has_denominator Fix #774 Fix #775 * Fix annotation properties * Implement improvements Discussed on RO call (2024-02-26): * Add domain: Use PATO:0001470 "proportionality to", aka "ratio" * Add as a subproperty of has-part * Add range: PATO:quality (== COB:characteristic) Resolve #774 Resolve #775 --- src/ontology/imports/pato_import.owl | 19 +++++++++++++++++-- src/ontology/imports/pato_terms.txt | 3 ++- src/ontology/ro-edit.owl | 22 ++++++++++++++++++++++ src/ontology/ro-idranges.owl | 6 +++++- 4 files changed, 46 insertions(+), 4 deletions(-) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 64359663..56a973aa 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -7,7 +7,7 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( "An ontology of phenotypic qualities (properties, attributes or characteristics).") Annotation( ) @@ -16,12 +16,13 @@ Annotation( "quality") Annotation( "1.2") Annotation(owl:versionInfo "2023-05-18") -Annotation(owl:versionInfo "2023-08-16") +Annotation(owl:versionInfo "2024-02-27") Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -38,6 +39,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -70,6 +72,19 @@ AnnotationAssertion( "linear") SubClassOf( ) +# Class: (proportionality to) + +AnnotationAssertion(Annotation( "PATOC:nw") "A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity.") +AnnotationAssertion( "proportion") +AnnotationAssertion( "proportionality") +AnnotationAssertion( "quotient") +AnnotationAssertion( "ratio") +AnnotationAssertion( "rate") +AnnotationAssertion( "PATO:0001470") +AnnotationAssertion(rdfs:comment "Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right.") +AnnotationAssertion(rdfs:label "proportionality to") +SubClassOf( ) + # Class: (laminar) AnnotationAssertion(Annotation( "PATOC:GVG") "A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.") diff --git a/src/ontology/imports/pato_terms.txt b/src/ontology/imports/pato_terms.txt index ce1ec8e4..905465c0 100644 --- a/src/ontology/imports/pato_terms.txt +++ b/src/ontology/imports/pato_terms.txt @@ -1,4 +1,5 @@ PATO:0002124 PATO:0001199 PATO:0000402 -PATO:0000001 \ No newline at end of file +PATO:0000001 +PATO:0001470 diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 6890634b..476ed07b 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -603,6 +603,8 @@ Declaration(ObjectProperty(obo:RO_0019501)) Declaration(ObjectProperty(obo:RO_0020101)) Declaration(ObjectProperty(obo:RO_0020102)) Declaration(ObjectProperty(obo:RO_0020103)) +Declaration(ObjectProperty(obo:RO_0020202)) +Declaration(ObjectProperty(obo:RO_0020203)) Declaration(ObjectProperty(obo:RO_0040035)) Declaration(ObjectProperty(obo:RO_0040036)) Declaration(ObjectProperty(obo:RO_HOM0000000)) @@ -6826,6 +6828,26 @@ SubObjectPropertyOf(obo:RO_0020103 obo:RO_0002179) ObjectPropertyDomain(obo:RO_0020103 obo:UBERON_0001982) ObjectPropertyRange(obo:RO_0020103 obo:UBERON_0000061) +# Object Property: obo:RO_0020202 (has numerator) + +AnnotationAssertion(Annotation(terms:contributor "https://orcid.org/0000-0002-8280-0487") obo:IAO_0000115 obo:RO_0020202 "A relationship between a ratio or proportion and its dividend.") +AnnotationAssertion(oboInOwl:created_by obo:RO_0020202 ) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0020202 "has dividend") +AnnotationAssertion(rdfs:label obo:RO_0020202 "has numerator") +SubObjectPropertyOf(obo:RO_0020202 obo:BFO_0000051) +ObjectPropertyDomain(obo:RO_0020202 obo:PATO_0001470) +ObjectPropertyRange(obo:RO_0020202 obo:PATO_0000001) + +# Object Property: obo:RO_0020203 (has denominator) + +AnnotationAssertion(Annotation(terms:contributor "https://orcid.org/0000-0002-8280-0487") obo:IAO_0000115 obo:RO_0020203 "A relationship between a ratio or proportion and its divisor.") +AnnotationAssertion(oboInOwl:created_by obo:RO_0020203 ) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0020203 "has divisor") +AnnotationAssertion(rdfs:label obo:RO_0020203 "has denominator") +SubObjectPropertyOf(obo:RO_0020203 obo:BFO_0000051) +ObjectPropertyDomain(obo:RO_0020203 obo:PATO_0001470) +ObjectPropertyRange(obo:RO_0020203 obo:PATO_0000001) + # Object Property: obo:RO_0040035 (disease relationship) AnnotationAssertion(obo:IAO_0000115 obo:RO_0040035 "This relation groups relations between diseases and any other kind of entity.") diff --git a/src/ontology/ro-idranges.owl b/src/ontology/ro-idranges.owl index bd4f0128..96ff7352 100644 --- a/src/ontology/ro-idranges.owl +++ b/src/ontology/ro-idranges.owl @@ -114,4 +114,8 @@ EquivalentTo: xsd:integer[> 17500 , <= 18000] Datatype: idrange:26 Annotations: allocatedto: "Aleix Puig" -EquivalentTo: xsd:integer[> 20100 , <= 20200] \ No newline at end of file +EquivalentTo: xsd:integer[> 20100 , <= 20200] + +Datatype: idrange:27 +Annotations: allocatedto: "Ray Stefancsik" +EquivalentTo: xsd:integer[> 20201 , <= 20300] From 132fa7488028d63b45f4d950ed6ea3c59ec878c9 Mon Sep 17 00:00:00 2001 From: diatomsRcool Date: Thu, 29 Feb 2024 05:49:10 -0500 Subject: [PATCH 11/13] adding eco relations definitions (#762) * adding eco relations definitions * responding to comments in PR * updating definitions of eats and aquires nutriets from --------- Co-authored-by: Anita Caron Co-authored-by: Chris Mungall --- src/ontology/ro-edit.owl | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 476ed07b..3514946b 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -3879,8 +3879,8 @@ SubObjectPropertyOf(obo:RO_0002433 obo:RO_0002131) # Object Property: obo:RO_0002434 (interacts with) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002434 "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) +AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002434 ) AnnotationAssertion(obo:IAO_0000232 obo:RO_0002434 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002434 "in pairwise interaction with") @@ -3997,6 +3997,7 @@ SubObjectPropertyOf(obo:RO_0002443 obo:RO_0002440) # Object Property: obo:RO_0002444 (parasite of) AnnotationAssertion(obo:IAO_0000112 obo:RO_0002444 "Pediculus humanus capitis parasite of human") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002444 "A parasite-host relationship where an organism benefits at the expense of another.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002444 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002444 "parasitizes") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002444 "direct parasite of") @@ -4009,6 +4010,7 @@ InverseObjectProperties(obo:RO_0002444 obo:RO_0002445) # Object Property: obo:RO_0002445 (parasitized by) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002445 "Inverse of parasite of") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002445 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002445 "has parasite") AnnotationAssertion(obo:IAO_0000118 obo:RO_0002445 "parasitised by") @@ -4136,11 +4138,12 @@ SubObjectPropertyOf(obo:RO_0002456 obo:RO_0002442) # Object Property: obo:RO_0002457 (acquires nutrients from) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002457 "Inverse of provides nutrients for") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002457 ) AnnotationAssertion(obo:IAO_0000232 obo:RO_0002457 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion.") AnnotationAssertion(oboInOwl:inSubset obo:RO_0002457 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002457 "acquires nutrients from") -SubObjectPropertyOf(obo:RO_0002457 obo:RO_0002438) +SubObjectPropertyOf(obo:RO_0002457 obo:RO_0002437) InverseObjectProperties(obo:RO_0002457 obo:RO_0002469) # Object Property: obo:RO_0002458 (preyed upon by) @@ -4226,27 +4229,30 @@ SubObjectPropertyOf(obo:RO_0002468 obo:RO_0002465) # Object Property: obo:RO_0002469 (provides nutrients for) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002469 "A biotic interaction where a material entity provides nutrition for an organism.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002469 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002469 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002469 "provides nutrients for") -SubObjectPropertyOf(obo:RO_0002469 obo:RO_0002438) +SubObjectPropertyOf(obo:RO_0002469 obo:RO_0002437) # Object Property: obo:RO_0002470 (eats) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002470 "A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002470 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002470 "is subject of eating interaction with") AnnotationAssertion(oboInOwl:inSubset obo:RO_0002470 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002470 "eats") -SubObjectPropertyOf(obo:RO_0002470 obo:RO_0002438) +SubObjectPropertyOf(obo:RO_0002470 obo:RO_0002437) # Object Property: obo:RO_0002471 (is eaten by) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002471 "Inverse of eats") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002471 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002471 "eaten by") AnnotationAssertion(obo:IAO_0000118 obo:RO_0002471 "is target of eating interaction with") AnnotationAssertion(oboInOwl:inSubset obo:RO_0002471 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002471 "is eaten by") -SubObjectPropertyOf(obo:RO_0002471 obo:RO_0002438) +SubObjectPropertyOf(obo:RO_0002471 obo:RO_0002437) # Object Property: obo:RO_0002472 (is evidence for) @@ -4830,6 +4836,7 @@ SubObjectPropertyOf(obo:RO_0002555 obo:RO_0002574) # Object Property: obo:RO_0002556 (pathogen of) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002556 "Inverse of has pathogen") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002556 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002556 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002556 "pathogen of") @@ -4838,6 +4845,7 @@ InverseObjectProperties(obo:RO_0002556 obo:RO_0002557) # Object Property: obo:RO_0002557 (has pathogen) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002557 "A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002557 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002557 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002557 "has pathogen") From bf9a48f19828228eab22e960f981bc4dc9262ebf Mon Sep 17 00:00:00 2001 From: Bill Duncan Date: Mon, 4 Mar 2024 11:57:28 -0500 Subject: [PATCH 12/13] NTR: owns; is owned by (#705) * add individual "Bill Duncan" * add owns/is owned by relations * add 'defined by inverse' annotation to 'is owned by' * add examples of usage * add inverse of axiom for is owned by * fix typo in defintion of owns * add defintion source to "is owned by" * add OBIB:0000735 as source for "owns" * remove complex example of usage * change conflicting IRIs * Fixes contributor annotations for NTR: owns; is owned by (#772) * Update ro-edit.owl Changed dc:contributor to terms:contributor. * Replacing more "dc" with "terms" * For NTR: owns; is owned by; replaces other "dc" with "terms" (#773) * Update ro-edit.owl Changed dc:contributor to terms:contributor. * Replacing more "dc" with "terms" * add Bill Duncan to orcidio_import.owl * remove individual Bill Duncan from ro-edit * remove individual "Bill Duncan" * run update for orcidio * add "William D Duncan" to orcidio_import.owl * add "William D Duncan" as contributor * add "William D Duncan" as contributor * remove dcterms:source from definition of is owned by * remove dcterms:source from definition of owns --------- Co-authored-by: Anita Caron Co-authored-by: Clint Dowland <52045818+CDowland@users.noreply.github.com> Co-authored-by: Anita Caron --- src/ontology/imports/orcidio_import.owl | 13 ++++++ src/ontology/ro-edit.owl | 60 ++++++++++++++++++------- 2 files changed, 56 insertions(+), 17 deletions(-) diff --git a/src/ontology/imports/orcidio_import.owl b/src/ontology/imports/orcidio_import.owl index 1044bba3..507a3345 100644 --- a/src/ontology/imports/orcidio_import.owl +++ b/src/ontology/imports/orcidio_import.owl @@ -14,6 +14,7 @@ Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -25,6 +26,8 @@ Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) + +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -60,6 +63,11 @@ AnnotationAssertion(Annotation( ) "researcher, metadata, diseases, University of Maryland") AnnotationAssertion(Annotation( ) rdfs:label "Lynn Schriml") +# Individual: (William D Duncan) + +AnnotationAssertion(Annotation( ) "researcher") +AnnotationAssertion(Annotation( ) rdfs:label "William D Duncan") + # Individual: (Anne Thessen) AnnotationAssertion(Annotation( ) "data scientist") @@ -115,6 +123,11 @@ AnnotationAssertion(Annotation( ) "Canadian biocurator") AnnotationAssertion(Annotation( ) rdfs:label "Pascale Gaudet") + +# Individual: (Mathias Brochhausen) + +AnnotationAssertion(Annotation( ) "researcher") +AnnotationAssertion(Annotation( ) rdfs:label "Mathias Brochhausen") # Individual: (S. Clint Dowland) AnnotationAssertion(Annotation( ) "Researcher ORCID=0000-0003-1909-9269") diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 3514946b..84fb6809 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -579,6 +579,8 @@ Declaration(ObjectProperty(obo:RO_0017001)) Declaration(ObjectProperty(obo:RO_0017003)) Declaration(ObjectProperty(obo:RO_0017004)) Declaration(ObjectProperty(obo:RO_0017005)) +Declaration(ObjectProperty(obo:RO_0017008)) +Declaration(ObjectProperty(obo:RO_0017009)) Declaration(ObjectProperty(obo:RO_0018001)) Declaration(ObjectProperty(obo:RO_0018002)) Declaration(ObjectProperty(obo:RO_0018003)) @@ -2634,10 +2636,10 @@ SubObjectPropertyOf(obo:RO_0002237 obo:RO_0002444) # Object Property: obo:RO_0002238 (has component participant) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002238 "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys.") -AnnotationAssertion(obo:IAO_0000117 obo:RO_0002238 ) AnnotationAssertion(obo:IAO_0000232 obo:RO_0002238 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'.") +AnnotationAssertion(terms:contributor obo:RO_0002238 ) AnnotationAssertion(rdfs:label obo:RO_0002238 "has component participant"@en) SubObjectPropertyOf(obo:RO_0002238 obo:RO_0000057) @@ -3879,8 +3881,8 @@ SubObjectPropertyOf(obo:RO_0002433 obo:RO_0002131) # Object Property: obo:RO_0002434 (interacts with) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002434 "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") +AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002434 ) AnnotationAssertion(obo:IAO_0000232 obo:RO_0002434 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002434 "in pairwise interaction with") @@ -6549,10 +6551,10 @@ SubObjectPropertyOf(obo:RO_0016004 obo:RO_0002244) AnnotationAssertion(obo:IAO_0000112 obo:RO_0017001 "A diagnostic testing device utilizes a specimen.") AnnotationAssertion(obo:IAO_0000115 obo:RO_0017001 "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion(obo:IAO_0000117 obo:RO_0017001 ) -AnnotationAssertion(obo:IAO_0000117 obo:RO_0017001 ) AnnotationAssertion(obo:IAO_0000232 obo:RO_0017001 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion(obo:IAO_0000232 obo:RO_0017001 "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion(terms:contributor obo:RO_0017001 ) +AnnotationAssertion(terms:contributor obo:RO_0017001 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0017001 "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasBroadSynonym obo:RO_0017001 "utilizes") AnnotationAssertion(rdfs:label obo:RO_0017001 "device utilizes material"@en) @@ -6586,6 +6588,30 @@ AnnotationAssertion(rdfs:label obo:RO_0017005 "contains measured amount"@en) ObjectPropertyDomain(obo:RO_0017005 obo:OBI_0000967) ObjectPropertyRange(obo:RO_0017005 obo:COB_0000121) +# Object Property: obo:RO_0017008 (owns) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0017008 "biobank organization owns a specimen") +AnnotationAssertion(obo:IAO_0000112 obo:RO_0017008 "hospital owns a laboratory facility") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0017008 "A primitive relation that holds between entities x and y in which y is at x’s full disposal.") +AnnotationAssertion(terms:contributor obo:RO_0017008 ) +AnnotationAssertion(terms:contributor obo:RO_0017008 ) +AnnotationAssertion(terms:contributor obo:RO_0017008 ) +AnnotationAssertion(terms:description obo:RO_0017008 "This primitive relation is the foundation of the owner’s right to have the owned entity at his/her full disposal.") +AnnotationAssertion(oboInOwl:creation_date obo:RO_0017008 "2023-03-29T16:57:03Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:RO_0017008 "owns"@en) +InverseObjectProperties(obo:RO_0017008 obo:RO_0017009) + +# Object Property: obo:RO_0017009 (is owned by) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0017009 "freezer is owned by a biobank organization") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0017009 "Inverse of the owns relation.") +AnnotationAssertion(terms:contributor obo:RO_0017009 ) +AnnotationAssertion(terms:contributor obo:RO_0017009 ) +AnnotationAssertion(terms:contributor obo:RO_0017009 ) +AnnotationAssertion(oboInOwl:creation_date obo:RO_0017009 "2023-03-29T17:06:06Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:inSubset obo:RO_0017009 obo:RO_0002259) +AnnotationAssertion(rdfs:label obo:RO_0017009 "is owned by"@en) + # Object Property: obo:RO_0018001 (is myristoyltransferase activity) AnnotationAssertion(obo:IAO_0000115 obo:RO_0018001 "Helper relation for OWL definition of RO:0018002 myristoylates") @@ -7190,19 +7216,19 @@ DLSafeRule(Annotation(rdfs:seeAlso ) Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002013 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002014 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002015 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002404 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002211 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012012 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0019002 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0019001 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002264 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002263 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002404 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002211 Variable() Variable()) ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012012 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0019002 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0019001 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002264 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002263 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))) AnnotationAssertion(owl:deprecated obo:BFO_0000060 "true"^^xsd:boolean) AnnotationAssertion(obo:IAO_0000115 obo:RO_0000092 "inverse of has disposition") AnnotationAssertion(oboInOwl:inSubset obo:RO_0000092 obo:RO_0002259) From a389e118be644291a1b3a195ca435de2bdfe26bd Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 5 Mar 2024 17:39:56 +0200 Subject: [PATCH 13/13] Migrate to ODK 1.5 (#793) * Remove injected labels from COB * Update ODK 1.5 files * Remove annotations from COB import to avoid multiple label bug * Fix main branch ref * Add a few more BFO rels to list of base namespaces * Add fix towards for the base file in RO * Update ro.Makefile --- .github/workflows/qc.yml | 4 +- src/ontology/Makefile | 191 ++++++++++++------ src/ontology/imports/cob_import.owl | 34 +--- src/ontology/ro-odk.yaml | 7 + src/ontology/ro.Makefile | 25 +++ src/ontology/run.sh | 38 +++- src/scripts/run-command.sh | 4 + src/scripts/update_repo.sh | 5 +- src/sparql/iri-range-violation.sparql | 2 +- src/sparql/label-with-iri-violation.sparql | 2 +- .../owldef-self-reference-violation.sparql | 2 +- src/sparql/ro_terms.sparql | 2 +- 12 files changed, 213 insertions(+), 103 deletions(-) create mode 100755 src/scripts/run-command.sh diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 07909b27..b4732692 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,12 +19,12 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.4 + container: obolibrary/odkfull:v1.5 # Steps represent a sequence of tasks that will be executed as part of the job steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Run ontology QC checks env: diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 78c658e4..7b34e452 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for ro # Generated using ontology-development-kit -# ODK Version: v1.4.1 +# ODK Version: v1.5 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use ro.Makefile instead @@ -9,6 +9,9 @@ # ---------------------------------------- # More information: https://github.com/INCATools/ontology-development-kit/ +# Fingerprint of the configuration file when this Makefile was last generated +CONFIG_HASH= 075dd4dff2b03ac15eb3fdc35033a80af4fec05442bc35f82dd3131f528c8209 + # ---------------------------------------- # Standard Constants @@ -44,7 +47,7 @@ REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE) OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by term-editor-uri dce obsolete-relation SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms -ODK_VERSION_MAKEFILE = v1.4.1 +ODK_VERSION_MAKEFILE = v1.5 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') @@ -59,6 +62,11 @@ FORMATS = $(sort owl obo json owl) FORMATS_INCL_TSV = $(sort $(FORMATS) tsv) RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full core ) +ifeq ($(ODK_DEBUG),yes) +ODK_DEBUG_FILE = debug.log +SHELL = $(SCRIPTSDIR)/run-command.sh +endif + # ---------------------------------------- # Top-level targets # ---------------------------------------- @@ -69,12 +77,16 @@ RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full core ) all: all_odk .PHONY: all_odk -all_odk: odkversion test all_assets +all_odk: odkversion config_check test custom_reports all_assets .PHONY: test test: odkversion reason_test sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt echo "Finished running all tests successfully." +.PHONY: test +test_fast: + $(MAKE_FAST) test + .PHONY: release_diff release_diff: $(REPORTDIR)/release-diff.md @@ -85,13 +97,52 @@ reason_test: $(EDIT_PREPROCESSED) .PHONY: odkversion odkversion: - echo "ODK Makefile version: $(ODK_VERSION_MAKEFILE) (this is the version of the ODK with which this Makefile was generated, \ - not the version of the ODK you are running)" &&\ - echo "ROBOT version (ODK): " && $(ROBOT) --version + @echo "ODK Makefile $(ODK_VERSION_MAKEFILE)" + @odk-info --tools +.PHONY: config_check +config_check: + @if [ "$$(sha256sum $(ONT)-odk.yaml | cut -c1-64)" = "$(CONFIG_HASH)" ]; then \ + echo "Repository is up-to-date." ; else \ + echo "Your ODK configuration has changed since this Makefile was generated. You may need to run 'make update_repo'." ; fi + $(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR): mkdir -p $@ +# ---------------------------------------- +# ODK-managed ROBOT plugins +# ---------------------------------------- + +# Make sure ROBOT knows where to find plugins +export ROBOT_PLUGINS_DIRECTORY=$(TMPDIR)/plugins + +# Override this rule in ro.Makefile to install custom plugins +.PHONY: custom_robot_plugins +custom_robot_plugins: + + +.PHONY: extra_robot_plugins +extra_robot_plugins: + + +# Install all ROBOT plugins to the runtime plugins directory +.PHONY: all_robot_plugins +all_robot_plugins: $(foreach plugin,$(notdir $(wildcard /tools/robot-plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + $(foreach plugin,$(notdir $(wildcard ../../plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + custom_robot_plugins extra_robot_plugins \ + +# Default rule to install plugins +$(ROBOT_PLUGINS_DIRECTORY)/%.jar: + @mkdir -p $(ROBOT_PLUGINS_DIRECTORY) + @if [ -f ../../plugins/$*.jar ]; then \ + ln ../../plugins/$*.jar $@ ; \ + elif [ -f /tools/robot-plugins/$*.jar ]; then \ + cp /tools/robot-plugins/$*.jar $@ ; \ + fi + +# Specific rules for supplementary plugins defined in configuration + + # ---------------------------------------- # Release assets # ---------------------------------------- @@ -181,10 +232,10 @@ validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql) -sparql_test: $(EDIT_PREPROCESSED) catalog-v001.xml | $(REPORTDIR) +sparql_test: $(EDIT_PREPROCESSED) | $(REPORTDIR) ifneq ($(SPARQL_VALIDATION_QUERIES),) - $(ROBOT) verify --catalog catalog-v001.xml -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) + $(ROBOT) verify -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) endif # ---------------------------------------- @@ -192,10 +243,18 @@ endif # ---------------------------------------- $(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR) - $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri http://purl.obolibrary.org/obo/RO_ --base-iri http://purl.obolibrary.org/obo/BFO_0000050 --base-iri http://purl.obolibrary.org/obo/BFO_0000051 --base-iri http://purl.obolibrary.org/obo/BFO_0000060 --print 5 -o $@ + $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri http://purl.obolibrary.org/obo/RO_ --base-iri http://purl.obolibrary.org/obo/BFO_0000050 --base-iri http://purl.obolibrary.org/obo/BFO_0000051 --base-iri http://purl.obolibrary.org/obo/BFO_0000060 --base-iri http://purl.obolibrary.org/obo/BFO_0000062 --base-iri http://purl.obolibrary.org/obo/BFO_0000063 --base-iri http://purl.obolibrary.org/obo/BFO_0000066 --base-iri http://purl.obolibrary.org/obo/BFO_0000067 --base-iri http://purl.obolibrary.org/obo/BFO_0000054 --base-iri http://purl.obolibrary.org/obo/BFO_0000055 --print 5 -o $@ $(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR) - $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri http://purl.obolibrary.org/obo/RO_ --base-iri http://purl.obolibrary.org/obo/BFO_0000050 --base-iri http://purl.obolibrary.org/obo/BFO_0000051 --base-iri http://purl.obolibrary.org/obo/BFO_0000060 --print 5 -o $@ + $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri http://purl.obolibrary.org/obo/RO_ --base-iri http://purl.obolibrary.org/obo/BFO_0000050 --base-iri http://purl.obolibrary.org/obo/BFO_0000051 --base-iri http://purl.obolibrary.org/obo/BFO_0000060 --base-iri http://purl.obolibrary.org/obo/BFO_0000062 --base-iri http://purl.obolibrary.org/obo/BFO_0000063 --base-iri http://purl.obolibrary.org/obo/BFO_0000066 --base-iri http://purl.obolibrary.org/obo/BFO_0000067 --base-iri http://purl.obolibrary.org/obo/BFO_0000054 --base-iri http://purl.obolibrary.org/obo/BFO_0000055 --print 5 -o $@ + +check_for_robot_updates: + @cut -f2 "/tools/robot_report_profile.txt" | sort > $(TMPDIR)/sorted_tsv2.txt + @cut -f2 "$(ROBOT_PROFILE)" | sort > $(TMPDIR)/sorted_tsv1.txt + @comm -23 $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/sorted_tsv1.txt > $(TMPDIR)/missing.txt + @echo "Missing tests:" + @cat $(TMPDIR)/missing.txt + @rm $(TMPDIR)/sorted_tsv1.txt $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/missing.txt $(TMPDIR)/report_profile_robot.txt # ---------------------------------------- # Release assets @@ -213,7 +272,7 @@ RELEASE_ASSETS = \ $(SUBSET_FILES) .PHONY: all_assets -all_assets: $(ASSETS) +all_assets: $(ASSETS) check_rdfxml_assets .PHONY: show_assets show_assets: @@ -221,7 +280,7 @@ show_assets: du -sh $(ASSETS) check_rdfxml_%: % - @check-rdfxml $< + @check-rdfxml $< .PHONY: check_rdfxml_assets check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl) @@ -319,9 +378,9 @@ $(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/pato_import.owl: $(MIRRORDIR)/pato.owl $(IMPORTDIR)/pato_terms_combined.txt if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ extract -T $(IMPORTDIR)/pato_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ - remove --base-iri $(URIBASE)/PATO --axioms external --preserve-structure false --trim false \ + remove --base-iri $(OBOBASE)/PATO --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)/pato_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115 -T $(IMPORTDIR)/pato_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ $(ANNOTATE_CONVERT_FILE); fi ## Module for ontology: cl @@ -329,9 +388,9 @@ $(IMPORTDIR)/pato_import.owl: $(MIRRORDIR)/pato.owl $(IMPORTDIR)/pato_terms_comb $(IMPORTDIR)/cl_import.owl: $(MIRRORDIR)/cl.owl $(IMPORTDIR)/cl_terms_combined.txt if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ extract -T $(IMPORTDIR)/cl_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ - remove --base-iri $(URIBASE)/CL --axioms external --preserve-structure false --trim false \ + remove --base-iri $(OBOBASE)/CL --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)/cl_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115 -T $(IMPORTDIR)/cl_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ $(ANNOTATE_CONVERT_FILE); fi ## Module for ontology: envo @@ -339,9 +398,9 @@ $(IMPORTDIR)/cl_import.owl: $(MIRRORDIR)/cl.owl $(IMPORTDIR)/cl_terms_combined.t $(IMPORTDIR)/envo_import.owl: $(MIRRORDIR)/envo.owl $(IMPORTDIR)/envo_terms_combined.txt if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ extract -T $(IMPORTDIR)/envo_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ - remove --base-iri $(URIBASE)/ENVO --axioms external --preserve-structure false --trim false \ + remove --base-iri $(OBOBASE)/ENVO --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)/envo_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115 -T $(IMPORTDIR)/envo_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ $(ANNOTATE_CONVERT_FILE); fi ## Module for ontology: go @@ -349,9 +408,9 @@ $(IMPORTDIR)/envo_import.owl: $(MIRRORDIR)/envo.owl $(IMPORTDIR)/envo_terms_comb $(IMPORTDIR)/go_import.owl: $(MIRRORDIR)/go.owl $(IMPORTDIR)/go_terms_combined.txt if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ extract -T $(IMPORTDIR)/go_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ - remove --base-iri $(URIBASE)/GO --axioms external --preserve-structure false --trim false \ + remove --base-iri $(OBOBASE)/GO --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)/go_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115 -T $(IMPORTDIR)/go_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ $(ANNOTATE_CONVERT_FILE); fi ## Module for ontology: other @@ -364,7 +423,7 @@ $(IMPORTDIR)/orcidio_import.owl: $(MIRRORDIR)/orcidio.owl $(IMPORTDIR)/orcidio_t if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ extract -T $(IMPORTDIR)/orcidio_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ remove --base-iri https://orcid.org/ --axioms external --preserve-structure false --trim false \ - remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/orcidio_terms_combined.txt --select complement \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115 -T $(IMPORTDIR)/orcidio_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 @@ -374,7 +433,7 @@ $(IMPORTDIR)/uberon_import.owl: $(MIRRORDIR)/uberon.owl $(IMPORTDIR)/uberon_term if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ extract -T $(IMPORTDIR)/uberon_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ remove --base-iri $(OBOBASE)/UBERON --axioms external --preserve-structure false --trim false \ - remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/uberon_terms_combined.txt --select complement \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115 -T $(IMPORTDIR)/uberon_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 @@ -384,7 +443,7 @@ $(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combine 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 \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115 -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 @@ -440,9 +499,9 @@ recreate-%: no-mirror-recreate-%: $(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=false PAT=true $(COMPONENTSDIR)/$*.owl -B -$(COMPONENTSDIR)/%: | $(COMPONENTSDIR) - touch $@ -.PRECIOUS: $(COMPONENTSDIR)/% +$(COMPONENTSDIR)/%.owl: | $(COMPONENTSDIR) + test -f $@ || touch $@ +.PRECIOUS: $(COMPONENTSDIR)/%.owl @@ -459,55 +518,47 @@ IMP=true # Global parameter to bypass import generation MIR=true # Global parameter to bypass mirror generation IMP_LARGE=true # Global parameter to bypass handling of large imports +ifeq ($(strip $(MIR)),true) ## ONTOLOGY: omo .PHONY: mirror-omo .PRECIOUS: $(MIRRORDIR)/omo.owl mirror-omo: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/omo.owl --create-dirs -o $(TMPDIR)/omo-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: pato .PHONY: mirror-pato .PRECIOUS: $(MIRRORDIR)/pato.owl mirror-pato: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pato.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PATO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/pato.owl --create-dirs -o $(TMPDIR)/pato-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/pato-download.owl --base-iri $(OBOBASE)/PATO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl ## ONTOLOGY: cl .PHONY: mirror-cl .PRECIOUS: $(MIRRORDIR)/cl.owl mirror-cl: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cl.owl --create-dirs -o $(MIRRORDIR)/cl.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/cl.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CL --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/cl.owl --create-dirs -o $(TMPDIR)/cl-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/cl-download.owl --base-iri $(OBOBASE)/CL --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl ## ONTOLOGY: envo .PHONY: mirror-envo .PRECIOUS: $(MIRRORDIR)/envo.owl mirror-envo: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/envo.owl --create-dirs -o $(MIRRORDIR)/envo.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/envo.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/ENVO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/envo.owl --create-dirs -o $(TMPDIR)/envo-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/envo-download.owl --base-iri $(OBOBASE)/ENVO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl ## ONTOLOGY: go .PHONY: mirror-go .PRECIOUS: $(MIRRORDIR)/go.owl mirror-go: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/go.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl && \ - $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/GO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/go.owl --create-dirs -o $(TMPDIR)/go-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/go-download.owl --base-iri $(OBOBASE)/GO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl ## ONTOLOGY: other @@ -518,41 +569,41 @@ mirror-go: | $(TMPDIR) .PHONY: mirror-orcidio .PRECIOUS: $(MIRRORDIR)/orcidio.owl mirror-orcidio: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://w3id.org/orcidio/orcidio.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + $(ROBOT) convert -I https://w3id.org/orcidio/orcidio.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: uberon .PHONY: mirror-uberon .PRECIOUS: $(MIRRORDIR)/uberon.owl mirror-uberon: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/uberon.owl --create-dirs -o $(MIRRORDIR)/uberon.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/uberon.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/uberon.owl --create-dirs -o $(TMPDIR)/uberon-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/uberon-download.owl -o $(TMPDIR)/$@.owl ## 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 + curl -L $(OBOBASE)/obi.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/obi-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: cob .PHONY: mirror-cob .PRECIOUS: $(MIRRORDIR)/cob.owl mirror-cob: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cob.owl --create-dirs -o $(MIRRORDIR)/cob.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/cob.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/cob.owl --create-dirs -o $(TMPDIR)/cob-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/cob-download.owl -o $(TMPDIR)/$@.owl $(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." &&\ + if [ -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 +else # MIR=false +$(MIRRORDIR)/%.owl: + @echo "Not refreshing $@ because the mirrorring pipeline is disabled (MIR=$(MIR))." +endif @@ -641,9 +692,13 @@ ROBOT_RELEASE_IMPORT_MODE=$(ROBOT) merge --input $< # ROBOT pipeline that removes imports, then merges components. This is for release artefacts that start from "base" ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --trim false merge $(patsubst %, -i %, $(OTHER_SRC)) -# base: All the axioms as they are editted by the editors, excluding reasoning -$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) - $(ROBOT_RELEASE_IMPORT_MODE_BASE) \ +# base: A version of the ontology that does not include any externally imported axioms. +$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \ + relax \ + reduce -r ELK \ + remove --base-iri http://purl.obolibrary.org/obo/RO_ --base-iri http://purl.obolibrary.org/obo/BFO_0000050 --base-iri http://purl.obolibrary.org/obo/BFO_0000051 --base-iri http://purl.obolibrary.org/obo/BFO_0000060 --base-iri http://purl.obolibrary.org/obo/BFO_0000062 --base-iri http://purl.obolibrary.org/obo/BFO_0000063 --base-iri http://purl.obolibrary.org/obo/BFO_0000066 --base-iri http://purl.obolibrary.org/obo/BFO_0000067 --base-iri http://purl.obolibrary.org/obo/BFO_0000054 --base-iri http://purl.obolibrary.org/obo/BFO_0000055 --axioms external --preserve-structure false --trim false \ $(SHARED_ROBOT_COMMANDS) \ annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ @@ -711,13 +766,16 @@ update_repo: -# Note to future generations: prepending ./ is a safety measure to ensure that -# the environment does not malicously set `CLEANFILES` to `\`. +# Note to future generations: computing the real path relative to the +# current directory is a way to ensure we only clean up directories that +# are located below the current directory, regardless of the contents of +# the *DIR variables. .PHONY: clean clean: - [ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/* - [ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/* - [ -n "$(UPDATEREPODIR)" ] && [ $(UPDATEREPODIR) != "." ] && [ $(UPDATEREPODIR) != "/" ] && [ $(UPDATEREPODIR) != ".." ] && [ -d ./$(UPDATEREPODIR) ] && rm -rf ./$(UPDATEREPODIR)/* + for dir in $(MIRRORDIR) $(TMPDIR) $(UPDATEREPODIR) ; do \ + reldir=$$(realpath --relative-to=$$(pwd) $$dir) ; \ + case $$reldir in .*|"") ;; *) rm -rf $$reldir/* ;; esac \ + done rm -f $(CLEANFILES) .PHONY: help @@ -736,6 +794,7 @@ Core commands: * prepare_release_fast: Run the entire release pipeline without refreshing imports, recreating components or recompiling patterns. * update_repo: Update the ODK repository setup using the config file ro-odk.yaml * test: Running all validation tests +* test_fast: Runs the test suite, but without updating imports or components * odkversion: Show the current version of the ODK Makefile and ROBOT. * clean: Delete all temporary files * help: Print ODK Usage information @@ -753,7 +812,7 @@ Imports management: Editor utilities: * validate_idranges: Make sure your ID ranges file is formatted correctly -* normalize_src: Load and safe your ro-edit file after you to make sure its serialised correctly +* normalize_src: Load and save your ro-edit file after you to make sure its serialised correctly * explain_unsat: If you have unsatisfiable classes, this command will create a markdown file (tmp/explain_unsat.md) which will explain all your unsatisfiable classes * validate-all-tsv: Check all your tsv files for possible problems in syntax. Use ALL_TSV_FILES variable to list files * validate-tsv: Check a tsv file for syntactic problems with tsvalid. Use TSV variable to pass filepath, e.g. make TSV=../my.tsv validate-tsv. diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl index 7e5506bf..9f5d2164 100644 --- a/src/ontology/imports/cob_import.owl +++ b/src/ontology/imports/cob_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-02-09") +Annotation(owl:versionInfo "2024-03-02") Declaration(Class()) Declaration(Class()) @@ -57,23 +57,17 @@ AnnotationAssertion(rdfs:label "def # Object Properties ############################ -# Object Property: (part of) +# Object Property: () -AnnotationAssertion(rdfs:label "part of") InverseObjectProperties( ) TransitiveObjectProperty() -# Object Property: (has part) - -AnnotationAssertion(rdfs:label "has part") - # Object Property: (realized in) AnnotationAssertion(rdfs:label "realized in"@en) -# Object Property: (occurs in) +# Object Property: () -AnnotationAssertion(rdfs:label "occurs in") InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -81,35 +75,25 @@ ObjectPropertyDomain( "contains process"@en) -# Object Property: (characteristic of) +# Object Property: () -AnnotationAssertion(rdfs:label "characteristic of"@en) InverseObjectProperties( ) -# Object Property: (has characteristic) +# Object Property: () -AnnotationAssertion(rdfs:label "has characteristic") -AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") InverseFunctionalObjectProperty() ObjectPropertyRange( ) -# Object Property: (participates in) +# Object Property: () -AnnotationAssertion(rdfs:label "participates in"@en) InverseObjectProperties( ) -# Object Property: (has participant) +# Object Property: () -AnnotationAssertion(rdfs:label "has participant") ObjectPropertyDomain( ) -# Object Property: (is concretized as) - -AnnotationAssertion(rdfs:label "is concretized as"@en) - -# Object Property: (enabled by) +# Object Property: () -AnnotationAssertion(rdfs:label "enabled by") SubObjectPropertyOf( ) diff --git a/src/ontology/ro-odk.yaml b/src/ontology/ro-odk.yaml index dbc8e4ab..8f454173 100644 --- a/src/ontology/ro-odk.yaml +++ b/src/ontology/ro-odk.yaml @@ -1,6 +1,7 @@ id: ro title: "OBO Relations Ontology" github_org: oborel +git_main_branch: master repo: obo-relations report_fail_on: Error edit_format: owl @@ -18,6 +19,12 @@ namespaces: - http://purl.obolibrary.org/obo/BFO_0000050 - http://purl.obolibrary.org/obo/BFO_0000051 - http://purl.obolibrary.org/obo/BFO_0000060 + - http://purl.obolibrary.org/obo/BFO_0000062 + - http://purl.obolibrary.org/obo/BFO_0000063 + - http://purl.obolibrary.org/obo/BFO_0000066 + - http://purl.obolibrary.org/obo/BFO_0000067 + - http://purl.obolibrary.org/obo/BFO_0000054 + - http://purl.obolibrary.org/obo/BFO_0000055 import_group: annotation_properties: - rdfs:label diff --git a/src/ontology/ro.Makefile b/src/ontology/ro.Makefile index 38c327f5..f8d11d12 100644 --- a/src/ontology/ro.Makefile +++ b/src/ontology/ro.Makefile @@ -53,9 +53,34 @@ $(IMPORTDIR)/cob_import.owl: $(MIRRORDIR)/cob.owl $(IMPORTDIR)/cob_terms_combine if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ extract -T $(IMPORTDIR)/cob_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/cob_terms_combined.txt --select complement \ + remove --select "RO:* BFO:0000050* BFO:0000051* BFO:0000060* BFO:0000066*" --axioms "annotation" \ query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ $(ANNOTATE_CONVERT_FILE); fi +# ======================================== +# Custom imports +# ======================================== + +# This filter contains all property characteristic related to RO entities +# Note: For some reason, IrreflexiveObjectProperty is not supported +tmp/missing-base.owl: $(EDIT_PREPROCESSED) $(ONTOLOGYTERMS) + $(ROBOT) merge -i $(EDIT_PREPROCESSED) \ + filter -T $(ONTOLOGYTERMS) --trim false --axioms "AsymmetricObjectProperty FunctionalObjectProperty FunctionalDataProperty InverseFunctionalObjectProperty SymmetricObjectProperty TransitiveObjectProperty InverseObjectProperties ObjectPropertyDomain DataPropertyDomain DataPropertyRange ObjectPropertyRange" \ + -o $@.tmp.owl && mv $@.tmp.owl $@ + +# TODO: This goal (and tmp/missing-base.owl) can be removed once https://github.com/ontodev/robot/issues/1108 is resolved +$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) tmp/missing-base.owl + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \ + relax \ + reduce -r ELK \ + remove --base-iri http://purl.obolibrary.org/obo/RO_ --base-iri http://purl.obolibrary.org/obo/BFO_0000050 --base-iri http://purl.obolibrary.org/obo/BFO_0000051 --base-iri http://purl.obolibrary.org/obo/BFO_0000060 --base-iri http://purl.obolibrary.org/obo/BFO_0000062 --base-iri http://purl.obolibrary.org/obo/BFO_0000063 --base-iri http://purl.obolibrary.org/obo/BFO_0000066 --base-iri http://purl.obolibrary.org/obo/BFO_0000067 --base-iri http://purl.obolibrary.org/obo/BFO_0000054 --base-iri http://purl.obolibrary.org/obo/BFO_0000055 --axioms external --preserve-structure false --trim false \ + merge -i tmp/missing-base.owl \ + $(SHARED_ROBOT_COMMANDS) \ + annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ + --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + --output $@.tmp.owl && mv $@.tmp.owl $@ + # ======================================== # DOCUMENTATION diff --git a/src/ontology/run.sh b/src/ontology/run.sh index 2718ff67..873e9bdf 100755 --- a/src/ontology/run.sh +++ b/src/ontology/run.sh @@ -14,6 +14,8 @@ # # See README-editors.md for more details. +set -e + if [ -f run.sh.conf ]; then . ./run.sh.conf fi @@ -29,6 +31,22 @@ elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/tok GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token") fi +# SSH agent socket +# On macOS, we cannot use $SSH_AUTH_SOCK directly, +# we need to use a "magic" socket instead. +case "$(uname)" in +Darwin) + ODK_SSH_AUTH_SOCKET=/run/host-services/ssh-auth.sock + ;; +*) + ODK_SSH_AUTH_SOCKET=$SSH_AUTH_SOCK + ;; +esac +ODK_SSH_BIND= +if [ -n "$ODK_SSH_AUTH_SOCKET" ]; then + ODK_SSH_BIND=",$ODK_SSH_AUTH_SOCKET:/run/host-services/ssh-auth.sock" +fi + ODK_IMAGE=${ODK_IMAGE:-odkfull} TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }') if [ -n "$TAG_IN_IMAGE" ]; then @@ -40,16 +58,28 @@ ODK_TAG=${ODK_TAG:-latest} ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx8G} ODK_DEBUG=${ODK_DEBUG:-no} +ODK_USER_ID=${ODK_USER_ID:-$(id -u)} +ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)} + +# Convert OWLAPI_* environment variables to the OWLAPI as Java options +# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html +# for a list of allowed options +OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions +for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do + ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}" +done + TIMECMD= if [ x$ODK_DEBUG = xyes ]; then # If you wish to change the format string, take care of using # non-breaking spaces (U+00A0) instead of normal spaces, to # prevent the shell from tokenizing the format string. - echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps." + echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps." TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb" fi +rm -f tmp/debug.log -VOLUME_BIND=$PWD/../../:/work +VOLUME_BIND=$PWD/../../:/work$ODK_SSH_BIND WORK_DIR=/work/src/ontology if [ -n "$ODK_BINDS" ]; then @@ -59,14 +89,14 @@ fi if [ -n "$USE_SINGULARITY" ]; then singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \ - --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \ + --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS,SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock,ODK_USER_ID=$ODK_USER_ID,ODK_GROUP_ID=$ODK_GROUP_ID,ODK_DEBUG=$ODK_DEBUG" \ --bind $VOLUME_BIND \ -W $WORK_DIR \ docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" else BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')" docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \ - -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \ + -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" -e SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock -e ODK_USER_ID=$ODK_USER_ID -e ODK_GROUP_ID=$ODK_GROUP_ID -e ODK_DEBUG=$ODK_DEBUG \ --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" fi diff --git a/src/scripts/run-command.sh b/src/scripts/run-command.sh new file mode 100755 index 00000000..45d431d1 --- /dev/null +++ b/src/scripts/run-command.sh @@ -0,0 +1,4 @@ +#!/bin/sh +ODK_DEBUG_FILE=${ODK_DEBUG_FILE:-debug.log} +echo "Command: sh $@" >> $ODK_DEBUG_FILE +/usr/bin/time -a -o $ODK_DEBUG_FILE -f "Elapsed time: %E\nPeak memory: %M kb" /bin/sh "$@" diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh index 395ee647..372412e8 100644 --- a/src/scripts/update_repo.sh +++ b/src/scripts/update_repo.sh @@ -21,10 +21,11 @@ cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/ cp -r target/$OID/src/sparql/* $SRCDIR/sparql/ mkdir -p $ROOTDIR/.github mkdir -p $ROOTDIR/.github/workflows -cp -n target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml +cp target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml + echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)" -echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml." + echo "Ontology repository update successfully completed." \ No newline at end of file diff --git a/src/sparql/iri-range-violation.sparql b/src/sparql/iri-range-violation.sparql index 66d8e919..2316f96c 100644 --- a/src/sparql/iri-range-violation.sparql +++ b/src/sparql/iri-range-violation.sparql @@ -13,7 +13,7 @@ WHERE { oboInOwl:inSubset dcterms:contributor } ?term ?property ?value . - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000062") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000063") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000066") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000067") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000054") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000055"))) FILTER (!isIRI(?value)) } diff --git a/src/sparql/label-with-iri-violation.sparql b/src/sparql/label-with-iri-violation.sparql index 7f701bcb..8f092090 100644 --- a/src/sparql/label-with-iri-violation.sparql +++ b/src/sparql/label-with-iri-violation.sparql @@ -4,6 +4,6 @@ SELECT ?term ?value WHERE { ?term rdfs:label ?value . FILTER (REGEX(?value, "http[s]?[:]")) - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000062") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000063") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000066") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000067") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000054") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000055"))) } diff --git a/src/sparql/owldef-self-reference-violation.sparql b/src/sparql/owldef-self-reference-violation.sparql index 1efed040..a9fa013a 100644 --- a/src/sparql/owldef-self-reference-violation.sparql +++ b/src/sparql/owldef-self-reference-violation.sparql @@ -7,6 +7,6 @@ SELECT ?term WHERE { { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] } UNION { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] } - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000062") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000063") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000066") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000067") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000054") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000055"))) } diff --git a/src/sparql/ro_terms.sparql b/src/sparql/ro_terms.sparql index 40179a04..52a4dd44 100644 --- a/src/sparql/ro_terms.sparql +++ b/src/sparql/ro_terms.sparql @@ -3,5 +3,5 @@ WHERE { { ?s1 ?p1 ?term . } UNION { ?term ?p2 ?o2 . } - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000062") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000063") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000066") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000067") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000054") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000055"))) }