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DO NOT MERGE: Paralleling disease relations branch with a disorder branch #287

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DO NOT MERGE: Paralleling disease relations branch with a disorder branch #287

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153 changes: 145 additions & 8 deletions src/ontology/ro-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -18,17 +18,17 @@ Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
Ontology(<http://purl.obolibrary.org/obo/ro.owl>
<http://purl.obolibrary.org/obo/ro-edit.owl>
Import(<http://purl.obolibrary.org/obo/ro/annotations.owl>)
Import(<http://purl.obolibrary.org/obo/ro/chemical.owl>)
Import(<http://purl.obolibrary.org/obo/ro/core.owl>)
Import(<http://purl.obolibrary.org/obo/ro/el-constraints.owl>)
Import(<http://purl.obolibrary.org/obo/ro/generated-axioms.owl>)
Import(<http://purl.obolibrary.org/obo/ro/pato_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/temporal-intervals.owl>)
Import(<http://purl.obolibrary.org/obo/ro/go-biotic.owl>)
Import(<http://purl.obolibrary.org/obo/ro/go_cc_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/chemical.owl>)
Import(<http://purl.obolibrary.org/obo/ro/go_mf_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/core.owl>)
Import(<http://purl.obolibrary.org/obo/ro/rohom.owl>)
Import(<http://purl.obolibrary.org/obo/ro/other_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/go-biotic.owl>)
Import(<http://purl.obolibrary.org/obo/ro/el-constraints.owl>)
Import(<http://purl.obolibrary.org/obo/ro/pato_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/rohom.owl>)
Import(<http://purl.obolibrary.org/obo/ro/temporal-intervals.owl>)
Annotation(dc:description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies."@en)
Annotation(dc:source <http://obofoundry.org/ro>)
Annotation(dc:title "OBO Relations Ontology"@en)
Expand All @@ -39,6 +39,7 @@ Annotation(foaf:homepage " https://github.com/oborel/obo-relations/"^^xsd:anyURI
Declaration(Class(obo:CARO_0001010))
Declaration(Class(obo:GO_0004872))
Declaration(Class(obo:GO_0048018))
Declaration(Class(obo:OGMS_0000045))
Declaration(Class(obo:RO_0002310))
Declaration(Class(obo:RO_0002532))
Declaration(Class(obo:RO_0002533))
Expand Down Expand Up @@ -484,6 +485,18 @@ Declaration(ObjectProperty(obo:RO_0004034))
Declaration(ObjectProperty(obo:RO_0004035))
Declaration(ObjectProperty(obo:RO_0004046))
Declaration(ObjectProperty(obo:RO_0004047))
Declaration(ObjectProperty(obo:RO_0005019))
Declaration(ObjectProperty(obo:RO_0005020))
Declaration(ObjectProperty(obo:RO_0005021))
Declaration(ObjectProperty(obo:RO_0005022))
Declaration(ObjectProperty(obo:RO_0005023))
Declaration(ObjectProperty(obo:RO_0005024))
Declaration(ObjectProperty(obo:RO_0005025))
Declaration(ObjectProperty(obo:RO_0005026))
Declaration(ObjectProperty(obo:RO_0005027))
Declaration(ObjectProperty(obo:RO_0005028))
Declaration(ObjectProperty(obo:RO_0005029))
Declaration(ObjectProperty(obo:RO_0005030))
Declaration(ObjectProperty(obo:RO_0008501))
Declaration(ObjectProperty(obo:RO_0008502))
Declaration(ObjectProperty(obo:RO_0008503))
Expand Down Expand Up @@ -5414,6 +5427,130 @@ AnnotationAssertion(oboInOwl:creation_date obo:RO_0004047 "2018-03-13T23:55:19Z"
AnnotationAssertion(rdfs:label obo:RO_0004047 "causally upstream of or within, positive effect")
SubObjectPropertyOf(obo:RO_0004047 obo:RO_0002418)

# Object Property: obo:RO_0005019 (disorder has basis in)

AnnotationAssertion(oboInOwl:created_by obo:RO_0005019 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005019 "2018-11-09T03:26:47Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005019 "disorder has basis in")
SubObjectPropertyOf(obo:RO_0005019 obo:RO_0004017)
SubObjectPropertyOf(obo:RO_0005019 obo:RO_0005023)
ObjectPropertyDomain(obo:RO_0005019 obo:OGMS_0000045)

# Object Property: obo:RO_0005020 (disorder has basis in dysfunction of)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0005020 "A relation that holds between the disorder and a material entity where the physical basis of the disorder is a disorder of that material entity that affects its function.")
AnnotationAssertion(obo:IAO_0000589 obo:RO_0005020 "disorder has basis in dysfunction of (disorder to anatomical structure)")
AnnotationAssertion(oboInOwl:created_by obo:RO_0005020 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005020 "2018-11-09T03:29:32Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005020 "disorder has basis in dysfunction of")
SubObjectPropertyOf(obo:RO_0005020 obo:RO_0005019)
ObjectPropertyRange(obo:RO_0005020 obo:CARO_0000006)

# Object Property: obo:RO_0005021 (disorder has basis in disruption of)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0005021 "A relation that holds between the disorder and a process where the physical basis of the disorder disrupts execution of a key biological process.")
AnnotationAssertion(obo:IAO_0000589 obo:RO_0005021 "disorder has basis in disruption of (disorder to process)")
AnnotationAssertion(oboInOwl:created_by obo:RO_0005021 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005021 "2018-11-09T03:37:52Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005021 "disorder has basis in disruption of")
SubObjectPropertyOf(obo:RO_0005021 obo:RO_0005019)
ObjectPropertyRange(obo:RO_0005021 obo:BFO_0000015)

# Object Property: obo:RO_0005022 (disorder has basis in feature)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0005022 "A relation that holds between the disorder and a feature (a phenotype or other disorder) where the physical basis of the disorder is the feature.")
AnnotationAssertion(oboInOwl:created_by obo:RO_0005022 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005022 "2018-11-09T03:46:07Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005022 "disorder has basis in feature")
SubObjectPropertyOf(obo:RO_0005022 obo:RO_0002200)
SubObjectPropertyOf(obo:RO_0005022 obo:RO_0005019)
ObjectPropertyDomain(obo:RO_0005022 obo:OGMS_0000045)
ObjectPropertyRange(obo:RO_0005022 ObjectUnionOf(obo:OGMS_0000045 obo:UPHENO_0001001))

# Object Property: obo:RO_0005023 (causal relationship with disorder as subject)

AnnotationAssertion(obo:IAO_0000116 obo:RO_0005023 "After import upper level from OGMS, make domain more specific.")
AnnotationAssertion(obo:IAO_0000232 obo:RO_0005023 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disorder as the subject.")
AnnotationAssertion(oboInOwl:created_by obo:RO_0005023 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005023 "2018-11-09T03:50:54Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005023 "causal relationship with disorder as subject")
SubObjectPropertyOf(obo:RO_0005023 obo:RO_0002410)
SubObjectPropertyOf(obo:RO_0005023 obo:RO_0040035)
ObjectPropertyDomain(obo:RO_0005023 obo:OGMS_0000045)

# Object Property: obo:RO_0005024 (disorder causes disruption of)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0005024 "A relationship between a disorder and a process where the disorder process disrupts the execution of the process.")
AnnotationAssertion(obo:IAO_0000589 obo:RO_0005024 "disorder causes disruption of (disorder to process)")
AnnotationAssertion(oboInOwl:created_by obo:RO_0005024 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005024 "2018-11-09T03:51:09Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005024 "disorder causes disruption of")
SubObjectPropertyOf(obo:RO_0005024 obo:RO_0005023)
ObjectPropertyDomain(obo:RO_0005024 obo:OGMS_0000045)
ObjectPropertyRange(obo:RO_0005024 obo:BFO_0000015)

# Object Property: obo:RO_0005025 (disorder causes dysfunction of)

AnnotationAssertion(obo:IAO_0000589 obo:RO_0005025 "disorder causes dysfunction of (disorder to anatomical entity)")
AnnotationAssertion(oboInOwl:created_by obo:RO_0005025 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005025 "2018-11-09T03:58:20Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005025 "disorder causes dysfunction of")
SubObjectPropertyOf(obo:RO_0005025 obo:RO_0005023)
ObjectPropertyDomain(obo:RO_0005025 obo:OGMS_0000045)
ObjectPropertyRange(obo:RO_0005025 obo:CARO_0000006)

# Object Property: obo:RO_0005026 (disorder has location)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0005026 "A relationship between a disorder and an anatomical entity where the disorder has one or more features that are located in that entity.")
AnnotationAssertion(obo:IAO_0000116 obo:RO_0005026 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology")
AnnotationAssertion(obo:IAO_0000232 obo:RO_0005026 "This relation is intentionally very general, and covers isolated disorders, where the disorder is realized as a process occurring in the location, and syndromic disorders, where one or more of the features may be present in that location. Thus any given disorder can have multiple locations in the sense defined here.")
AnnotationAssertion(oboInOwl:created_by obo:RO_0005026 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005026 "2018-11-09T04:06:02Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005026 "disorder has location")
SubObjectPropertyOf(obo:RO_0005026 obo:RO_0040035)
ObjectPropertyDomain(obo:RO_0005026 obo:OGMS_0000045)
ObjectPropertyRange(obo:RO_0005026 obo:BFO_0000004)
ObjectPropertyRange(obo:RO_0005026 ObjectUnionOf(obo:CARO_0000006 obo:CARO_0000007))

# Object Property: obo:RO_0005027 (disorder has inflammation site)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0005027 "A relationship between a disorder and an anatomical entity where the disorder is triggered by an inflammatory response to stimuli occurring in the anatomical entity")
AnnotationAssertion(oboInOwl:created_by obo:RO_0005027 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005027 "2018-11-09T19:37:31Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005027 "disorder has inflammation site")
SubObjectPropertyOf(obo:RO_0005027 obo:RO_0005026)
ObjectPropertyDomain(obo:RO_0005027 obo:OGMS_0000045)
ObjectPropertyRange(obo:RO_0005027 obo:CARO_0000003)

# Object Property: obo:RO_0005028 (realized in response to stimulus)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0005028 "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.")
AnnotationAssertion(oboInOwl:created_by obo:RO_0005028 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005028 "2018-11-09T19:45:49Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005028 "realized in response to stimulus")
SubObjectPropertyOf(obo:RO_0005028 obo:RO_0002410)
ObjectPropertyDomain(obo:RO_0005028 obo:BFO_0000017)
ObjectPropertyRange(obo:RO_0005028 obo:BFO_0000040)

# Object Property: obo:RO_0005029 (disorder has feature)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0005029 "A relationship between a disorder and some feature of that disorder, where the feature is either a phenotype or an isolated disorder.")
AnnotationAssertion(oboInOwl:created_by obo:RO_0005029 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005029 "2018-11-09T19:50:53Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005029 "disorder has feature")
SubObjectPropertyOf(obo:RO_0005029 obo:RO_0040035)
ObjectPropertyDomain(obo:RO_0005029 obo:OGMS_0000045)
ObjectPropertyRange(obo:RO_0005029 ObjectUnionOf(obo:OGMS_0000045 obo:UPHENO_0001001))

# Object Property: obo:RO_0005030 (disorder arises from structure)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0005030 "A relationship between a disorder and an anatomical structure where the material basis of the disorder is some pathological change in the structure.")
AnnotationAssertion(oboInOwl:created_by obo:RO_0005030 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0005030 "2018-11-09T19:58:44Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0005030 "disorder arises from structure")
SubObjectPropertyOf(obo:RO_0005030 obo:RO_0005019)
ObjectPropertyRange(obo:RO_0005030 obo:CARO_0000003)

# Object Property: obo:RO_0008501 (epiphyte of)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0008501 "An interaction relationship wherein a plant or algae is living on the outside surface of another plant.")
Expand Down Expand Up @@ -5842,7 +5979,7 @@ 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(<urn:swrl#B>) Variable(<urn:swrl#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#A>) Variable(<urn:swrl#B>)) ObjectPropertyAtom(obo:RO_0002013 Variable(<urn:swrl#D>) Variable(<urn:swrl#C>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#A>) Variable(<urn:swrl#D>))))
DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl#B>) Variable(<urn:swrl#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#A>) Variable(<urn:swrl#B>)) ObjectPropertyAtom(obo:RO_0002014 Variable(<urn:swrl#D>) Variable(<urn:swrl#C>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#A>) Variable(<urn:swrl#D>))))
DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable(<urn:swrl#B>) Variable(<urn:swrl#C>)) ObjectPropertyAtom(obo:RO_0002333 Variable(<urn:swrl#A>) Variable(<urn:swrl#B>)) ObjectPropertyAtom(obo:RO_0002015 Variable(<urn:swrl#D>) Variable(<urn:swrl#C>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#A>) Variable(<urn:swrl#D>))))
DLSafeRule(Annotation(rdfs:label "From has_ligand to ligand activity") Body(ObjectPropertyAtom(obo:RO_0002019 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)))Head(ClassAtom(obo:GO_0048018 Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#z>) Variable(<urn:swrl#x>))))
DLSafeRule(Annotation(rdfs:label "From has_ligand to ligand activity") Body(ObjectPropertyAtom(obo:RO_0002327 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002019 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(obo:GO_0048018 Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#z>) Variable(<urn:swrl#x>))))
DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#eff>) Variable(<urn:swrl#in>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#mf>) Variable(<urn:swrl#in>))))
DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#mf>) Variable(<urn:swrl#in>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#eff>) Variable(<urn:swrl#in>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
Expand Down