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WIP: Experiment in defining role hierarchy to structure participant relations #278

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WIP: Experiment in defining role hierarchy to structure participant relations #278

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98abd97
Added first pass at #277
cmungall Oct 23, 2018
645d29b
Refactored to be a mix of roles and functions, see #277
cmungall Oct 23, 2018
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274 changes: 274 additions & 0 deletions src/ontology/role-edit.owl
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Original file line number Diff line number Diff line change
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Prefix(:=<http://purl.obolibrary.org/obo/ro/role.owl/>)
Prefix(dc:=<http://purl.org/dc/elements/1.1/>)
Prefix(obo:=<http://purl.obolibrary.org/obo/>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(cito:=<http://purl.org/spar/cito/>)
Prefix(foaf:=<http://xmlns.com/foaf/0.1/>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Prefix(swrl:=<http://www.w3.org/2003/11/swrl#>)
Prefix(swrla:=<http://swrl.stanford.edu/ontologies/3.3/swrla.owl#>)
Prefix(swrlb:=<http://www.w3.org/2003/11/swrlb#>)
Prefix(subsets:=<http://purl.obolibrary.org/obo/ro/subsets#>)
Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)


Ontology(<http://purl.obolibrary.org/obo/ro/role.owl>
<http://purl.obolibrary.org/obo/ro/role-edit.owl>
Import(<http://purl.obolibrary.org/obo/ro.owl>)
Annotation(dc:description "ROle ontology."@en)

Declaration(Class(obo:RO_0040001))
Declaration(Class(obo:RO_0040002))
Declaration(Class(obo:RO_0040003))
Declaration(Class(obo:RO_0040004))
Declaration(Class(obo:RO_0040005))
Declaration(Class(obo:RO_0040006))
Declaration(Class(obo:RO_0040007))
Declaration(Class(obo:RO_0040008))
Declaration(Class(obo:RO_0040009))
Declaration(Class(obo:RO_0040010))
Declaration(Class(obo:RO_0040011))
Declaration(Class(obo:RO_0040012))
Declaration(Class(obo:RO_0040013))
Declaration(Class(obo:RO_0040014))
Declaration(Class(obo:RO_0040015))
Declaration(Class(obo:RO_0040016))
Declaration(Class(obo:RO_0040017))
Declaration(Class(obo:RO_0040018))
Declaration(Class(obo:RO_0040019))
Declaration(Class(obo:RO_0040020))
Declaration(Class(obo:RO_0040021))
Declaration(Class(obo:RO_0040022))
Declaration(Class(obo:RO_0040023))
Declaration(Class(obo:RO_0040024))
Declaration(Class(obo:RO_0040025))
Declaration(Class(obo:RO_0040026))
Declaration(Class(obo:RO_0040027))
Declaration(Class(obo:RO_0040032))
Declaration(Class(obo:RO_0040033))



############################
# Classes
############################

# Class: obo:RO_0040001 (participant disposition)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0040001 "A disposition played by a participant in a process.")
AnnotationAssertion(oboInOwl:created_by obo:RO_0040001 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040001 "2018-07-07T23:00:17Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040001 "participant disposition")
SubClassOf(obo:RO_0040001 obo:BFO_0000016)

# Class: obo:RO_0040002 (primary agent function)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0040002 "A disposition played by a participant that acts to achieve the objectives of the directed process.")
AnnotationAssertion(oboInOwl:created_by obo:RO_0040002 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040002 "2018-07-07T23:00:24Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0040002 "agent function")
AnnotationAssertion(rdfs:label obo:RO_0040002 "primary agent function")
EquivalentClasses(obo:RO_0040002 ObjectIntersectionOf(obo:BFO_0000034 obo:RO_0040013))
SubClassOf(obo:RO_0040002 obo:RO_0040013)

# Class: obo:RO_0040003 (input role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040003 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040003 "2018-07-07T23:00:38Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040003 "input role")
SubClassOf(obo:RO_0040003 obo:RO_0040021)
DisjointUnion(obo:RO_0040003 obo:RO_0040006 obo:RO_0040007)

# Class: obo:RO_0040004 (output role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040004 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040004 "2018-07-07T23:00:45Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040004 "output role")
SubClassOf(obo:RO_0040004 obo:RO_0040021)

# Class: obo:RO_0040005 (catalyst function)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040005 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040005 "2018-07-07T23:01:46Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040005 "catalyst function")
SubClassOf(obo:RO_0040005 obo:RO_0040002)

# Class: obo:RO_0040006 (targeted input role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040006 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040006 "2018-07-07T23:03:01Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040006 "targeted input role")
EquivalentClasses(obo:RO_0040006 ObjectIntersectionOf(obo:RO_0040003 obo:RO_0040020))

# Class: obo:RO_0040007 (non-targeted input role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040007 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040007 "2018-07-07T23:03:22Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040007 "non-targeted input role")
SubClassOf(obo:RO_0040007 obo:RO_0040003)

# Class: obo:RO_0040008 (substrate role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040008 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040008 "2018-07-07T23:04:11Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040008 "substrate role")
SubClassOf(obo:RO_0040008 obo:RO_0040006)

# Class: obo:RO_0040009 (transportee role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040009 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040009 "2018-07-07T23:05:01Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040009 "transportee role")
SubClassOf(obo:RO_0040009 obo:RO_0040006)

# Class: obo:RO_0040010 (transporter function)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040010 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040010 "2018-07-07T23:05:10Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040010 "transporter function")
SubClassOf(obo:RO_0040010 obo:RO_0040002)

# Class: obo:RO_0040011 (modified input role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040011 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040011 "2018-07-07T23:06:59Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040011 "modified input role")
SubClassOf(obo:RO_0040011 obo:RO_0040006)

# Class: obo:RO_0040012 (disassembled disposition)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040012 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040012 "2018-07-07T23:07:25Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040012 "disassembled disposition")
SubClassOf(obo:RO_0040012 obo:RO_0040011)

# Class: obo:RO_0040013 (directed process participant disposition)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0040013 "A disposition played in a process that is a realization of a function, or a causally connected set of function realizations.")
AnnotationAssertion(oboInOwl:created_by obo:RO_0040013 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040013 "2018-07-07T23:08:02Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040013 "directed process participant disposition")
EquivalentClasses(obo:RO_0040013 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:BFO_0000015 ObjectSomeValuesFrom(obo:BFO_0000055 obo:BFO_0000034))))
SubClassOf(obo:RO_0040013 obo:RO_0040001)
DisjointUnion(obo:RO_0040013 obo:RO_0040002 obo:RO_0040003 obo:RO_0040004)

# Class: obo:RO_0040014 (product role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040014 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040014 "2018-07-07T23:10:08Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040014 "product role")
SubClassOf(obo:RO_0040014 obo:RO_0040022)

# Class: obo:RO_0040015 (cofactor role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040015 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040015 "2018-07-07T23:12:34Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040015 "cofactor role")
SubClassOf(obo:RO_0040015 obo:RO_0040026)

# Class: obo:RO_0040016 (consumed disposition)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040016 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040016 "2018-07-07T23:16:16Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040016 "consumed disposition")
SubClassOf(obo:RO_0040016 obo:RO_0040011)

# Class: obo:RO_0040017 (barrier function)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040017 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040017 "2018-07-07T23:17:15Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0040017 "A function that is realized by influencing the flow of movement of a material entity, either directly through physical blocking or indirectly through fields, etc.")
AnnotationAssertion(rdfs:label obo:RO_0040017 "barrier function")
SubClassOf(obo:RO_0040017 obo:RO_0040002)

# Class: obo:RO_0040018 (intermediate output disposition)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040018 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040018 "2018-07-07T23:18:11Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040018 "intermediate output disposition")
SubClassOf(obo:RO_0040018 obo:RO_0040023)

# Class: obo:RO_0040019 (byproduct disposition)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040019 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040019 "2018-07-07T23:18:18Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040019 "byproduct disposition")
SubClassOf(obo:RO_0040019 obo:RO_0040023)

# Class: obo:RO_0040020 (targeted input or output role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040020 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040020 "2018-07-07T23:19:19Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040020 "targeted input or output role")
SubClassOf(obo:RO_0040020 obo:RO_0040021)

# Class: obo:RO_0040021 (input or output role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040021 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040021 "2018-07-07T23:19:56Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040021 "input or output role")
SubClassOf(obo:RO_0040021 obo:BFO_0000023)
SubClassOf(obo:RO_0040021 obo:RO_0040013)
DisjointUnion(obo:RO_0040021 obo:RO_0040003 obo:RO_0040004)

# Class: obo:RO_0040022 (targeted output role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040022 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040022 "2018-07-07T23:21:13Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040022 "targeted output role")
EquivalentClasses(obo:RO_0040022 ObjectIntersectionOf(obo:RO_0040004 obo:RO_0040020))

# Class: obo:RO_0040023 (non-targeted output disposition)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040023 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040023 "2018-07-07T23:22:45Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040023 "non-targeted output disposition")
SubClassOf(obo:RO_0040023 obo:RO_0040004)

# Class: obo:RO_0040024 (regulator function)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040024 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040024 "2018-07-07T23:24:08Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040024 "regulator function")
SubClassOf(obo:RO_0040024 obo:RO_0040002)

# Class: obo:RO_0040025 (binding function)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040025 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040025 "2018-07-07T23:26:26Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040025 "binding function")
SubClassOf(obo:RO_0040025 obo:RO_0040002)

# Class: obo:RO_0040026 (helper input role)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040026 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040026 "2018-07-07T23:28:32Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040026 "helper input role")
SubClassOf(obo:RO_0040026 obo:RO_0040007)

# Class: obo:RO_0040027 (consumed reactant disposition)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040027 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040027 "2018-07-07T23:36:14Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040027 "consumed reactant disposition")
SubClassOf(obo:RO_0040027 obo:RO_0040016)

# Class: obo:RO_0040032 (maintenance of state)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040032 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040032 "2018-07-25T20:40:21Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040032 "maintenance of state")
SubClassOf(obo:RO_0040032 obo:BFO_0000016)

# Class: obo:RO_0040033 (maintenance of shape)

AnnotationAssertion(oboInOwl:created_by obo:RO_0040033 "cjm"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0040033 "2018-07-25T20:40:52Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0040033 "maintenance of shape")
SubClassOf(obo:RO_0040033 obo:RO_0040032)


)