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Merge pull request #280 from oborel/object-property-characteristics
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Ready to merge: Additional axiomatization on existing relations
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@cmungall
cmungall authored Feb 2, 2019
2 parents 5925853 + 0217d9b commit 347fe5b
Showing 1 changed file with 36 additions and 2 deletions.
38 changes: 36 additions & 2 deletions src/ontology/ro-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -1026,6 +1026,8 @@ AnnotationAssertion(obo:IAO_0000114 obo:R0_0009004 obo:IAO_0000428)
AnnotationAssertion(obo:IAO_0000115 obo:R0_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:R0_0009004 "Damion Dooley")
AnnotationAssertion(rdfs:label obo:R0_0009004 "has consumer"@en)
ObjectPropertyDomain(obo:R0_0009004 obo:BFO_0000040)
ObjectPropertyRange(obo:R0_0009004 obo:CARO_0001010)

# Object Property: obo:RO_0000052 (inheres in)

Expand Down Expand Up @@ -1365,6 +1367,8 @@ AnnotationAssertion(oboInOwl:created_by obo:RO_0002018 "dos"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0002018 "2017-05-24T09:49:21Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0002018 "has component process")
SubObjectPropertyOf(obo:RO_0002018 obo:RO_0002180)
ObjectPropertyDomain(obo:RO_0002018 obo:BFO_0000015)
ObjectPropertyRange(obo:RO_0002018 obo:BFO_0000015)

# Object Property: obo:RO_0002019 (has ligand)

Expand Down Expand Up @@ -1568,6 +1572,8 @@ AnnotationAssertion(obo:IAO_0000424 obo:RO_0002104 "<http://purl.obolibrary.org/
AnnotationAssertion(obo:RO_0001900 obo:RO_0002104 obo:RO_0001901)
AnnotationAssertion(rdfs:label obo:RO_0002104 "has plasma membrane part"@en)
SubObjectPropertyOf(obo:RO_0002104 obo:BFO_0000051)
ObjectPropertyDomain(obo:RO_0002104 obo:CARO_0000006)
ObjectPropertyRange(obo:RO_0002104 obo:CARO_0000006)

# Object Property: obo:RO_0002105 (synapsed_via_type_Ib_bouton_to)

Expand Down Expand Up @@ -1660,6 +1666,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:RO_0002111 "has neurotransmitter")
AnnotationAssertion(rdfs:label obo:RO_0002111 "releases neurotransmitter"@en)
SubObjectPropertyOf(obo:RO_0002111 owl:topObjectProperty)
ObjectPropertyDomain(obo:RO_0002111 obo:CARO_0000003)
ObjectPropertyRange(obo:RO_0002111 obo:BFO_0000040)

# Object Property: obo:RO_0002112 (synapsed_by_via_type_Is_bouton)

Expand Down Expand Up @@ -2062,7 +2069,9 @@ AnnotationAssertion(rdfs:label obo:RO_0002204 "gene product of"@en)
SubObjectPropertyOf(obo:RO_0002204 obo:RO_0002330)
InverseObjectProperties(obo:RO_0002204 obo:RO_0002205)
ObjectPropertyDomain(obo:RO_0002204 obo:BFO_0000004)
ObjectPropertyDomain(obo:RO_0002204 ObjectUnionOf(obo:BFO_0000031 obo:BFO_0000040))
ObjectPropertyRange(obo:RO_0002204 obo:BFO_0000002)
ObjectPropertyRange(obo:RO_0002204 ObjectUnionOf(obo:BFO_0000031 obo:BFO_0000040))

# Object Property: obo:RO_0002205 (has gene product)

Expand All @@ -2086,6 +2095,7 @@ AnnotationAssertion(rdfs:label obo:RO_0002206 "expressed in"@en)
SubObjectPropertyOf(obo:RO_0002206 obo:RO_0002330)
InverseObjectProperties(obo:RO_0002206 obo:RO_0002292)
ObjectPropertyDomain(obo:RO_0002206 obo:BFO_0000002)
ObjectPropertyDomain(obo:RO_0002206 ObjectUnionOf(obo:BFO_0000031 obo:BFO_0000040))
ObjectPropertyRange(obo:RO_0002206 obo:CARO_0000006)

# Object Property: obo:RO_0002207 (directly develops from)
Expand Down Expand Up @@ -2179,6 +2189,7 @@ AnnotationAssertion(obo:IAO_0000112 obo:RO_0002214 "heart SubClassOf 'has protot
AnnotationAssertion(obo:IAO_0000114 obo:RO_0002214 obo:IAO_0000125)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0002214 "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation.")
AnnotationAssertion(obo:IAO_0000116 obo:RO_0002214 "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)")
AnnotationAssertion(obo:IAO_0000116 obo:RO_0002214 "TODO: add homeomorphy axiom")
AnnotationAssertion(obo:IAO_0000116 obo:RO_0002214 "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002214 "Chris Mungall")
AnnotationAssertion(rdfs:label obo:RO_0002214 "has prototype"@en)
Expand Down Expand Up @@ -2455,6 +2466,8 @@ AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:RO_0002248 "has active pharma
AnnotationAssertion(rdfs:label obo:RO_0002248 "has active ingredient")
SubObjectPropertyOf(obo:RO_0002248 obo:BFO_0000051)
InverseObjectProperties(obo:RO_0002248 obo:RO_0002249)
ObjectPropertyDomain(obo:RO_0002248 obo:BFO_0000040)
ObjectPropertyRange(obo:RO_0002248 obo:BFO_0000040)

# Object Property: obo:RO_0002249 (active ingredient in')

Expand Down Expand Up @@ -2921,6 +2934,8 @@ AnnotationAssertion(obo:IAO_0000119 obo:RO_0002332 <http://purl.obolibrary.org/o
AnnotationAssertion(obo:IAO_0000589 obo:RO_0002332 "regulates levels of (process to entity)")
AnnotationAssertion(rdfs:label obo:RO_0002332 "regulates levels of"@en)
SubObjectPropertyOf(obo:RO_0002332 obo:RO_0002328)
ObjectPropertyDomain(obo:RO_0002332 obo:BFO_0000015)
ObjectPropertyRange(obo:RO_0002332 obo:BFO_0000040)

# Object Property: obo:RO_0002333 (enabled by)

Expand Down Expand Up @@ -2962,6 +2977,7 @@ SubObjectPropertyOf(obo:RO_0002336 obo:RO_0002334)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0002337 "A relationship that holds via some process of localization")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002337 "Chris Mungall")
AnnotationAssertion(obo:IAO_0000232 obo:RO_0002337 "Do not use this relation directly. It is a grouping relation.")
AnnotationAssertion(rdfs:label obo:RO_0002337 "related via localization to"@en)
ObjectPropertyDomain(obo:RO_0002337 obo:BFO_0000015)
ObjectPropertyRange(obo:RO_0002337 obo:BFO_0000002)
Expand Down Expand Up @@ -3770,6 +3786,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002452 "A relation that holds betwee
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002452 "Chris Mungall")
AnnotationAssertion(rdfs:label obo:RO_0002452 "has symptom")
SubObjectPropertyOf(obo:RO_0002452 obo:RO_0002200)
ObjectPropertyDomain(obo:RO_0002452 obo:OGMS_0000031)

# Object Property: obo:RO_0002453 (host of)

Expand Down Expand Up @@ -3871,7 +3888,6 @@ SubObjectPropertyOf(obo:RO_0002463 obo:RO_0002461)

# Object Property: obo:RO_0002464 (helper property (not for use in curation))

AnnotationAssertion(obo:IAO_0000114 obo:RO_0002464 obo:IAO_0000428)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002464 "Chris Mungall")
AnnotationAssertion(obo:IAO_0000232 obo:RO_0002464 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.")
AnnotationAssertion(rdfs:label obo:RO_0002464 "helper property (not for use in curation)")
Expand Down Expand Up @@ -3944,6 +3960,8 @@ AnnotationAssertion(obo:RO_0001900 obo:RO_0002473 obo:RO_0001901)
AnnotationAssertion(oboInOwl:inSubset obo:RO_0002473 subsets:ro-eco)
AnnotationAssertion(rdfs:label obo:RO_0002473 "composed primarily of")
SubObjectPropertyOf(obo:RO_0002473 obo:BFO_0000051)
ObjectPropertyDomain(obo:RO_0002473 obo:BFO_0000040)
ObjectPropertyRange(obo:RO_0002473 obo:BFO_0000040)

# Object Property: obo:RO_0002476 (child nucleus of)

Expand Down Expand Up @@ -4208,6 +4226,8 @@ AnnotationAssertion(obo:IAO_0000119 obo:RO_0002510 "http://www.ncbi.nlm.nih.gov/
AnnotationAssertion(rdfs:label obo:RO_0002510 "transcribed from")
SubObjectPropertyOf(obo:RO_0002510 obo:RO_0002330)
InverseObjectProperties(obo:RO_0002510 obo:RO_0002511)
ObjectPropertyDomain(obo:RO_0002510 ObjectUnionOf(obo:BFO_0000031 obo:BFO_0000040))
ObjectPropertyRange(obo:RO_0002510 ObjectUnionOf(obo:BFO_0000031 obo:BFO_0000040))

# Object Property: obo:RO_0002511 (transcribed to)

Expand All @@ -4225,6 +4245,9 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002512 "Chris Mungall")
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002512 "http://www.ncbi.nlm.nih.gov/pubmed/20226267"^^xsd:anyURI)
AnnotationAssertion(rdfs:label obo:RO_0002512 "ribosomal translation of")
SubObjectPropertyOf(obo:RO_0002512 obo:RO_0002330)
InverseObjectProperties(obo:RO_0002512 obo:RO_0002513)
ObjectPropertyDomain(obo:RO_0002512 ObjectUnionOf(obo:BFO_0000031 obo:BFO_0000040))
ObjectPropertyRange(obo:RO_0002512 ObjectUnionOf(obo:BFO_0000031 obo:BFO_0000040))

# Object Property: obo:RO_0002513 (ribosomally translates to)

Expand All @@ -4233,6 +4256,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002513 "Chris Mungall")
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002513 "http://www.ncbi.nlm.nih.gov/pubmed/20226267"^^xsd:anyURI)
AnnotationAssertion(rdfs:label obo:RO_0002513 "ribosomally translates to")
SubObjectPropertyOf(obo:RO_0002513 obo:RO_0002330)
ObjectPropertyDomain(obo:RO_0002513 ObjectUnionOf(obo:BFO_0000031 obo:BFO_0000040))
ObjectPropertyRange(obo:RO_0002513 ObjectUnionOf(obo:BFO_0000031 obo:BFO_0000040))

# Object Property: obo:RO_0002514 (sequentially related to)

Expand Down Expand Up @@ -4446,6 +4471,10 @@ AnnotationAssertion(obo:IAO_0000232 obo:RO_0002551 "The skeleton of a structure
AnnotationAssertion(rdfs:label obo:RO_0002551 "has skeleton")
SubObjectPropertyOf(obo:RO_0002551 obo:BFO_0000051)
InverseObjectProperties(obo:RO_0002551 obo:RO_0002576)
AsymmetricObjectProperty(obo:RO_0002551)
IrreflexiveObjectProperty(obo:RO_0002551)
ObjectPropertyDomain(obo:RO_0002551 obo:CARO_0000003)
ObjectPropertyRange(Annotation(obo:IAO_0000116 "This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.") obo:RO_0002551 obo:CARO_0000006)

# Object Property: obo:RO_0002552 (results in ending of)

Expand Down Expand Up @@ -4831,6 +4860,7 @@ InverseObjectProperties(obo:RO_0002615 obo:RO_0003301)

# Object Property: obo:RO_0002616 (related via evidence or inference to)

AnnotationAssertion(obo:IAO_0000232 obo:RO_0002616 "Do not use this relation directly. It is a grouping relation.")
AnnotationAssertion(rdfs:label obo:RO_0002616 "related via evidence or inference to")

# Object Property: obo:RO_0002618 (visits)
Expand Down Expand Up @@ -5017,6 +5047,8 @@ AnnotationAssertion(obo:IAO_0000116 obo:RO_0003301 "To Do: decide on scope of th
AnnotationAssertion(obo:IAO_0000117 obo:RO_0003301 "Matthew Brush")
AnnotationAssertion(rdfs:comment obo:RO_0003301 "The driving 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.")
AnnotationAssertion(rdfs:label obo:RO_0003301 "is model of"@en)
AsymmetricObjectProperty(obo:RO_0003301)
IrreflexiveObjectProperty(obo:RO_0003301)

# Object Property: obo:RO_0003302 (causes or contributes to condition)

Expand Down Expand Up @@ -5300,7 +5332,6 @@ ObjectPropertyRange(obo:RO_0004022 ObjectUnionOf(obo:OGMS_0000031 obo:UPHENO_000

# Object Property: obo:RO_0004023 (causal relationship with disease as subject)

AnnotationAssertion(obo:IAO_0000116 obo:RO_0004023 "After import upper level from OGMS, make domain more specific.")
AnnotationAssertion(obo:IAO_0000232 obo:RO_0004023 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.")
AnnotationAssertion(oboInOwl:created_by obo:RO_0004023 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0004023 "2017-11-05T03:50:54Z"^^xsd:dateTime)
Expand Down Expand Up @@ -5611,6 +5642,7 @@ ObjectPropertyRange(obo:RO_0040036 ObjectUnionOf(obo:CARO_0000006 obo:CARO_00000

# Object Property: obo:RO_HOM0000000 (in similarity relationship with)

AnnotationAssertion(obo:IAO_0000116 obo:RO_HOM0000000 "TODO: Add homeomorphy axiom")
AnnotationAssertion(obo:RO_0040042 obo:RO_HOM0000000 obo:BFO_0000002)
AnnotationAssertion(obo:RO_0040042 obo:RO_HOM0000000 obo:BFO_0000003)

Expand Down Expand Up @@ -5860,9 +5892,11 @@ SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0002593 obo:BFO_0000050) obo:RO_0
SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0002593 obo:BFO_0000063 ObjectInverseOf(obo:RO_0002593)) obo:RO_0002497)
SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0004024 obo:BFO_0000050) obo:RO_0004024)
SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0004025 obo:BFO_0000050) obo:RO_0004025)
SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0004025 obo:RO_0002215) obo:RO_0004024)
SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0009501 obo:RO_0002233) obo:RO_0004028)
SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf(obo:BFO_0000066) obo:RO_0002234) obo:RO_0003000)
SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf(obo:RO_0002176) obo:RO_0002176) obo:RO_0002170)
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002180 Variable(<urn:swrl#w>) Variable(<urn:swrl#p>)) ClassAtom(obo:BFO_0000015 Variable(<urn:swrl#p>)) ClassAtom(obo:BFO_0000015 Variable(<urn:swrl#w>)))Head(ObjectPropertyAtom(obo:RO_0002018 Variable(<urn:swrl#w>) Variable(<urn:swrl#p>))))
DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z"^^xsd:string) Annotation(rdfs:label "infer input from direct reg"^^xsd:string) Body(ObjectPropertyAtom(obo:RO_0002327 Variable(<http://purl.obolibrary.org/obo/ro.owl#z>) Variable(<http://purl.obolibrary.org/obo/ro.owl#y>)) ObjectPropertyAtom(obo:RO_0002578 Variable(<http://purl.obolibrary.org/obo/ro.owl#x>) Variable(<http://purl.obolibrary.org/obo/ro.owl#y>)) ClassAtom(obo:GO_0003674 Variable(<http://purl.obolibrary.org/obo/ro.owl#x>)) ClassAtom(obo:GO_0003674 Variable(<http://purl.obolibrary.org/obo/ro.owl#y>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<http://purl.obolibrary.org/obo/ro.owl#x>) Variable(<http://purl.obolibrary.org/obo/ro.owl#z>))))
DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom(obo:GO_0003674 Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:BFO_0000051 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)))Head(ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
Expand Down

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