From 896d3ed70d895b828526e9cf2dcfed73c4305ec1 Mon Sep 17 00:00:00 2001 From: cmungall Date: Thu, 20 Jun 2019 13:53:12 -0700 Subject: [PATCH 1/2] Adding molecular-part-of. See aslo #328 Making active-in subproperty of located-in --- src/ontology/ro-edit.owl | 54 ++++++++++++++++++++++++++-------------- 1 file changed, 36 insertions(+), 18 deletions(-) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 842d8a7e..cb32431d 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -46,7 +46,6 @@ Declaration(Class(obo:RO_0002534)) Declaration(Class(foaf:image)) Declaration(ObjectProperty(obo:BFO_0000050)) Declaration(ObjectProperty(obo:BFO_0000051)) -Declaration(ObjectProperty(obo:RO_0009004)) Declaration(ObjectProperty(obo:RO_0000300)) Declaration(ObjectProperty(obo:RO_0000301)) Declaration(ObjectProperty(obo:RO_0000302)) @@ -498,12 +497,15 @@ Declaration(ObjectProperty(obo:RO_0008508)) Declaration(ObjectProperty(obo:RO_0009001)) Declaration(ObjectProperty(obo:RO_0009002)) Declaration(ObjectProperty(obo:RO_0009003)) +Declaration(ObjectProperty(obo:RO_0009004)) Declaration(ObjectProperty(obo:RO_0009005)) Declaration(ObjectProperty(obo:RO_0009501)) Declaration(ObjectProperty(obo:RO_0010001)) Declaration(ObjectProperty(obo:RO_0010002)) Declaration(ObjectProperty(obo:RO_0040035)) Declaration(ObjectProperty(obo:RO_0040036)) +Declaration(ObjectProperty(:RO_0004095)) +Declaration(ObjectProperty(:RO_0004096)) Declaration(ObjectProperty(owl:topObjectProperty)) Declaration(DataProperty(obo:RO_0002029)) Declaration(AnnotationProperty(obo:IAO_0000232)) @@ -1019,17 +1021,6 @@ AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000062 subsets:ro-eco) AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000063 subsets:ro-eco) SubObjectPropertyOf(obo:BFO_0000063 obo:RO_0002222) -# Object Property: obo:RO_0009004 (has consumer) - -AnnotationAssertion(obo:IAO_0000112 obo:RO_0009004 "sardine has consumer some homo sapiens"@en) -AnnotationAssertion(obo:IAO_0000114 obo:RO_0009004 obo:IAO_0000428) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0009004 "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect."@en) -AnnotationAssertion(obo:IAO_0000117 obo:RO_0009004 "Damion Dooley") -AnnotationAssertion(rdfs:label obo:RO_0009004 "has consumer"@en) -ObjectPropertyDomain(obo:RO_0009004 obo:BFO_0000040) -ObjectPropertyRange(obo:RO_0009004 obo:CARO_0001010) - - # Object Property: obo:RO_0000052 (inheres in) SubObjectPropertyOf(obo:RO_0000052 obo:RO_0002314) @@ -3561,13 +3552,13 @@ SubObjectPropertyOf(obo:RO_0002431 obo:RO_0002500) # Object Property: obo:RO_0002432 (is active in) AnnotationAssertion(obo:IAO_0000112 obo:RO_0002432 "A protein that enables activity in a cytosol.") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:cjm") Annotation(oboInOwl:hasDbXref "GOC:dos") obo:IAO_0000115 obo:RO_0002432 "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.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:cjm") Annotation(oboInOwl:hasDbXref "GOC:dos") obo:IAO_0000115 obo:RO_0002432 "A relationship between two continuants c and d, where c enables some process p, and p occurs in d.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002432 "Chris Mungall") AnnotationAssertion(obo:IAO_0000118 obo:RO_0002432 "executes activity in") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002432 "enables activity in") AnnotationAssertion(rdfs:comment obo:RO_0002432 "") AnnotationAssertion(rdfs:label obo:RO_0002432 "is active in") -SubObjectPropertyOf(obo:RO_0002432 obo:RO_0002131) +SubObjectPropertyOf(obo:RO_0002432 obo:RO_0001025) SubObjectPropertyOf(obo:RO_0002432 obo:RO_0002328) # Object Property: obo:RO_0002433 (contributes to morphology of) @@ -5040,13 +5031,13 @@ AnnotationAssertion(obo:IAO_0000116 obo:RO_0003003 "Logical axioms to be added a AnnotationAssertion(rdfs:label obo:RO_0003003 "increases expression of") SubObjectPropertyOf(obo:RO_0003003 obo:RO_0002450) -# Object Property: obo:RO_0003301 (is model of) +# Object Property: obo:RO_0003301 (has role in modeling) AnnotationAssertion(obo:IAO_0000115 obo:RO_0003301 "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0003301 "Matthew Brush") +AnnotationAssertion(obo:IAO_0000118 obo:RO_0003301 "is used to study"@en) AnnotationAssertion(rdfs:comment obo:RO_0003301 "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate.") AnnotationAssertion(rdfs:label obo:RO_0003301 "has role in modeling"@en) -AnnotationAssertion(obo:IAO_0000118 obo:RO_0003301 "is used to study"@en) AsymmetricObjectProperty(obo:RO_0003301) IrreflexiveObjectProperty(obo:RO_0003301) @@ -5570,6 +5561,16 @@ IrreflexiveObjectProperty(obo:RO_0009003) ObjectPropertyDomain(obo:RO_0009003 obo:BFO_0000040) ObjectPropertyRange(obo:RO_0009003 obo:BFO_0000040) +# Object Property: obo:RO_0009004 (has consumer) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0009004 "sardine has consumer some homo sapiens"@en) +AnnotationAssertion(obo:IAO_0000114 obo:RO_0009004 obo:IAO_0000428) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0009004 "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect."@en) +AnnotationAssertion(obo:IAO_0000117 obo:RO_0009004 "Damion Dooley") +AnnotationAssertion(rdfs:label obo:RO_0009004 "has consumer"@en) +ObjectPropertyDomain(obo:RO_0009004 obo:BFO_0000040) +ObjectPropertyRange(obo:RO_0009004 obo:CARO_0001010) + # Object Property: obo:RO_0009005 (has primary substance added) AnnotationAssertion(obo:IAO_0000112 obo:RO_0009005 "bread 'has primary substance added' some 'flour'"@en) @@ -5654,6 +5655,23 @@ SubObjectPropertyOf(obo:RO_HOM0000001 obo:RO_0002158) SubObjectPropertyOf(obo:RO_HOM0000003 obo:RO_0002320) +# Object Property: :RO_0004095 (continuant part of) + +AnnotationAssertion(obo:IAO_0000115 :RO_0004095 "A part of relationship that holds between two continuants.") +AnnotationAssertion(rdfs:label :RO_0004095 "continuant part of"@en) +SubObjectPropertyOf(:RO_0004095 obo:BFO_0000050) +TransitiveObjectProperty(:RO_0004095) +ObjectPropertyDomain(:RO_0004095 obo:BFO_0000002) +ObjectPropertyRange(:RO_0004095 obo:BFO_0000002) + +# Object Property: :RO_0004096 (molecular part of) + +AnnotationAssertion(obo:IAO_0000115 :RO_0004096 "A part of relationship that holds between two molecular entities. An example is the part of relationship between a protein and a protein complex.") +AnnotationAssertion(obo:IAO_0000232 :RO_0004096 "Once stable URIs are added to OBO-Core we will add domain and range constraints.") +AnnotationAssertion(rdfs:label :RO_0004096 "molecular part of"@en) +SubObjectPropertyOf(:RO_0004096 :RO_0004095) +TransitiveObjectProperty(:RO_0004096) + ############################ # Data Properties @@ -5907,7 +5925,7 @@ DLSafeRule(Annotation(rdfs:comment "This rule is dubious: added as a quick fix f DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() 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 "From has_ligand to ligand activity") Body(ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002019 Variable() Variable()))Head(ClassAtom(obo:GO_0048018 Variable()) ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "From has_ligand to ligand activity") Body(ObjectPropertyAtom(obo:RO_0002019 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()))Head(ClassAtom(obo:GO_0048018 Variable()) ObjectPropertyAtom(obo:RO_0002578 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()))) @@ -5931,4 +5949,4 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002089 subsets:ro-eco) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002091 subsets:ro-eco) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002093 subsets:ro-eco) AnnotationAssertion(Annotation(rdfs:comment "This is an experimental annotation") obo:IAO_0000589 rdfs:isDefinedBy "is defined by") -) +) \ No newline at end of file From bfb55bd0c2419f92a88d8e518a764b7e27c0f95d Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Fri, 19 Mar 2021 16:56:02 +0000 Subject: [PATCH 2/2] Update ro-edit.owl --- src/ontology/ro-edit.owl | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index e0fede08..766b6364 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -535,8 +535,8 @@ Declaration(ObjectProperty(obo:RO_0013007)) Declaration(ObjectProperty(obo:RO_0014001)) Declaration(ObjectProperty(obo:RO_0040035)) Declaration(ObjectProperty(obo:RO_0040036)) -Declaration(ObjectProperty(:RO_0004095)) -Declaration(ObjectProperty(:RO_0004096)) +Declaration(ObjectProperty(obo:RO_0004095)) +Declaration(ObjectProperty(obo:RO_0004096)) Declaration(ObjectProperty(owl:topObjectProperty)) Declaration(DataProperty(obo:RO_0002029)) Declaration(AnnotationProperty(obo:IAO_0000232)) @@ -6100,22 +6100,22 @@ SubObjectPropertyOf(obo:RO_HOM0000001 obo:RO_0002158) SubObjectPropertyOf(obo:RO_HOM0000003 obo:RO_0002320) -# Object Property: :RO_0004095 (continuant part of) +# Object Property: obo:RO_0004095 (continuant part of) -AnnotationAssertion(obo:IAO_0000115 :RO_0004095 "A part of relationship that holds between two continuants.") -AnnotationAssertion(rdfs:label :RO_0004095 "continuant part of"@en) -SubObjectPropertyOf(:RO_0004095 obo:BFO_0000050) -TransitiveObjectProperty(:RO_0004095) -ObjectPropertyDomain(:RO_0004095 obo:BFO_0000002) -ObjectPropertyRange(:RO_0004095 obo:BFO_0000002) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0004095 "A part of relationship that holds between two continuants.") +AnnotationAssertion(rdfs:label obo:RO_0004095 "continuant part of"@en) +SubObjectPropertyOf(obo:RO_0004095 obo:BFO_0000050) +TransitiveObjectProperty(obo:RO_0004095) +ObjectPropertyDomain(obo:RO_0004095 obo:BFO_0000002) +ObjectPropertyRange(obo:RO_0004095 obo:BFO_0000002) -# Object Property: :RO_0004096 (molecular part of) +# Object Property: obo:RO_0004096 (molecular part of) -AnnotationAssertion(obo:IAO_0000115 :RO_0004096 "A part of relationship that holds between two molecular entities. An example is the part of relationship between a protein and a protein complex.") -AnnotationAssertion(obo:IAO_0000232 :RO_0004096 "Once stable URIs are added to OBO-Core we will add domain and range constraints.") -AnnotationAssertion(rdfs:label :RO_0004096 "molecular part of"@en) -SubObjectPropertyOf(:RO_0004096 :RO_0004095) -TransitiveObjectProperty(:RO_0004096) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0004096 "A part of relationship that holds between two molecular entities. An example is the part of relationship between a protein and a protein complex.") +AnnotationAssertion(obo:IAO_0000232 obo:RO_0004096 "Once stable URIs are added to OBO-Core we will add domain and range constraints.") +AnnotationAssertion(rdfs:label obo:RO_0004096 "molecular part of"@en) +SubObjectPropertyOf(obo:RO_0004096 obo:RO_0004095) +TransitiveObjectProperty(obo:RO_0004096) ############################