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measures characteristic #717

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merged 26 commits into from
Apr 4, 2024
Merged

measures characteristic #717

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3ef2ed4
measures characteristic
ddooley May 23, 2023
3bbc2f5
fixed 'has characteristic' ref.
ddooley May 23, 2023
f40c1e9
Merge remote-tracking branch 'upstream/master' into issue#658
ddooley May 26, 2023
a1bb58d
includes obi import file
ddooley May 26, 2023
e0f11b3
COB import of planned process
ddooley May 27, 2023
69e7509
Adding OBI assay
ddooley Jun 12, 2023
f1145f1
revising "measures characteristic" label
ddooley Jun 12, 2023
c2963f7
catalogue tweak
ddooley Jun 12, 2023
05d7066
Merge branch 'master' into issue#658
ddooley Jun 13, 2023
87f6905
Merge branch 'master' into issue#658
anitacaron Jul 7, 2023
e504f90
update repo
anitacaron Jul 7, 2023
6f4f06d
remove cob import
anitacaron Jul 7, 2023
8909673
Merge branch 'master' into issue#658
Jul 12, 2023
06e10e1
rename process measures characteristic
ddooley Jul 18, 2023
3c59171
Merge branch 'master' into issue#658
Aug 10, 2023
1d199b1
import characteristic (BFO:0000020) from COB
anitacaron Aug 10, 2023
4665ec7
update to domain/range 'specifically dependent continuant' / COB char…
ddooley Aug 10, 2023
bce72c0
Merge branch 'master' into issue#658
ddooley Jan 22, 2024
c7216be
terms prefix fix
ddooley Jan 22, 2024
322d1c4
tweak inverse defn
ddooley Feb 26, 2024
8129630
Merge branch 'master' into issue#658
ddooley Feb 26, 2024
ab2f8ff
annotation tweaks
ddooley Feb 26, 2024
919a63a
Merge branch 'issue#658' of https://github.com/ddooley/obo-relations …
ddooley Feb 26, 2024
5f3073b
Merge branch 'master' into issue#658
Mar 1, 2024
6931c96
fix typo in characteristic measured by assay definition
Mar 28, 2024
5b3d94d
Merge branch 'master' into issue#658
Mar 28, 2024
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56 changes: 38 additions & 18 deletions src/ontology/ro-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,8 @@ Import(<http://purl.obolibrary.org/obo/ro/imports/orcidio_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/imports/other_import.owl>)
Import(<http://purl.obolibrary.org/obo/ro/imports/pato_import.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:title "OBO Relations Ontology"@en)
Annotation(dc:license <https://creativecommons.org/publicdomain/zero/1.0/>)
Annotation(dc:title "OBO Relations Ontology"@en)
Annotation(foaf:homepage " https://github.com/oborel/obo-relations/"^^xsd:anyURI)

Declaration(Class(obo:BFO_0000019))
Expand Down Expand Up @@ -508,6 +508,8 @@ Declaration(ObjectProperty(obo:RO_0009002))
Declaration(ObjectProperty(obo:RO_0009003))
Declaration(ObjectProperty(obo:RO_0009004))
Declaration(ObjectProperty(obo:RO_0009005))
Declaration(ObjectProperty(obo:RO_0009006))
Declaration(ObjectProperty(obo:RO_0009007))
Declaration(ObjectProperty(obo:RO_0009501))
Declaration(ObjectProperty(obo:RO_0010001))
Declaration(ObjectProperty(obo:RO_0010002))
Expand Down Expand Up @@ -666,10 +668,10 @@ Declaration(AnnotationProperty(obo:valid_for_go_gp2term))
Declaration(AnnotationProperty(obo:valid_for_go_ontology))
Declaration(AnnotationProperty(obo:valid_for_gocam))
Declaration(AnnotationProperty(subsets:ro-eco))
Declaration(AnnotationProperty(dc:date))
Declaration(AnnotationProperty(dc:conformsTo))
Declaration(AnnotationProperty(dc:contributor))
Declaration(AnnotationProperty(dc:creator))
Declaration(AnnotationProperty(dc:date))
Declaration(AnnotationProperty(dc:description))
Declaration(AnnotationProperty(dc:license))
Declaration(AnnotationProperty(dc:source))
Expand Down Expand Up @@ -5953,6 +5955,24 @@ AnnotationAssertion(rdfs:label obo:RO_0009005 "has primary substance added"@en)
SubObjectPropertyOf(obo:RO_0009005 obo:RO_0009001)
IrreflexiveObjectProperty(obo:RO_0009005)

# Object Property: obo:RO_0009006 (measures characteristic)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0009006 "A relation between a process and a characteristic, in which the process generates a data item which is a measure of a characteristic."@en)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0009006 <https://orcid.org/0000-0002-8844-9165>)
AnnotationAssertion(dc:date obo:RO_0009006 "2023-05-23T15:24:15Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0009006 "measures characteristic"@en)
ObjectPropertyDomain(obo:RO_0009006 obo:BFO_0000015)
ObjectPropertyRange(obo:RO_0009006 obo:BFO_0000020)

# Object Property: obo:RO_0009007 (characteristic measured by)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0009007 "Inverse of 'has characteristic'"@en)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0009007 <https://orcid.org/0000-0002-8844-9165>)
AnnotationAssertion(dc:date obo:RO_0009007 "2023-05-23T15:29:50Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0009007 "characteristic measured by"@en)
ObjectPropertyDomain(obo:RO_0009007 obo:BFO_0000020)
ObjectPropertyRange(obo:RO_0009007 obo:BFO_0000015)

# Object Property: obo:RO_0009501 (realized in response to)

AnnotationAssertion(obo:IAO_0000112 obo:RO_0009501 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.")
Expand Down Expand Up @@ -6734,16 +6754,16 @@ DataPropertyRange(obo:RO_0002029 DatatypeRestriction(xsd:short xsd:minInclusive
# Classes
############################

# Class: obo:BFO_0000002 (continuant)
# Class: obo:BFO_0000002 (obo:BFO_0000002)

SubClassOf(obo:BFO_0000002 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000002))
SubClassOf(obo:BFO_0000002 ObjectAllValuesFrom(obo:RO_HOM0000000 obo:BFO_0000002))

# Class: obo:BFO_0000003 (occurrent)
# Class: obo:BFO_0000003 (obo:BFO_0000003)

SubClassOf(obo:BFO_0000003 ObjectAllValuesFrom(obo:RO_HOM0000000 obo:BFO_0000003))

# Class: obo:BFO_0000015 (process)
# Class: obo:BFO_0000015 (obo:BFO_0000015)

SubClassOf(obo:BFO_0000015 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000015))

Expand Down Expand Up @@ -7019,19 +7039,19 @@ DLSafeRule(Annotation(rdfs:seeAlso <https://github.com/oborel/obo-relations/issu
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 "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>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
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(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl#x>)) ClassAtom(owl:Nothing Variable(<urn:swrl#y>))))
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(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002131 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl#x>)) ClassAtom(owl:Nothing Variable(<urn:swrl#y>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)) ObjectPropertyAtom(obo:RO_0002211 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)))Head(ObjectPropertyAtom(obo:RO_0012012 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0019002 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ObjectPropertyAtom(obo:RO_0019001 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002264 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)))Head(ObjectPropertyAtom(obo:RO_0002263 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#q>) Variable(<urn:swrl:var#u>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)))Head(ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#u>))))
DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#eff>) Variable(<urn:swrl#in>)))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_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002233 Variable(<urn:swrl#mf>) Variable(<urn:swrl#in>)))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_0002578 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002578 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)) ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)))Head(ObjectPropertyAtom(obo:RO_0002629 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#mf>) Variable(<urn:swrl#mf2>)) ObjectPropertyAtom(obo:RO_0002025 Variable(<urn:swrl#mf>) Variable(<urn:swrl#eff>)))Head(ObjectPropertyAtom(obo:RO_0002630 Variable(<urn:swrl#eff>) Variable(<urn:swrl#mf2>))))
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(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002404 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl#y>)) ClassAtom(owl:Nothing Variable(<urn:swrl#x>))))
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(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ClassAtom(owl:Nothing Variable(<urn:swrl#y>)) ClassAtom(owl:Nothing Variable(<urn:swrl#x>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002211 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)) ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)))Head(ObjectPropertyAtom(obo:RO_0012012 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)) ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#y>) Variable(<urn:swrl#z>)) ObjectPropertyAtom(obo:RO_0002213 Variable(<urn:swrl#x>) Variable(<urn:swrl#y>)))Head(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl#x>) Variable(<urn:swrl#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)) ObjectPropertyAtom(obo:RO_0019002 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)))Head(ObjectPropertyAtom(obo:RO_0019001 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#y>) Variable(<urn:swrl:var#z>)) ObjectPropertyAtom(obo:RO_0002264 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#y>)))Head(ObjectPropertyAtom(obo:RO_0002263 Variable(<urn:swrl:var#x>) Variable(<urn:swrl:var#z>))))
DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#q>)) ObjectPropertyAtom(obo:RO_0002411 Variable(<urn:swrl:var#q>) Variable(<urn:swrl:var#u>)))Head(ObjectPropertyAtom(obo:RO_0012011 Variable(<urn:swrl:var#p>) Variable(<urn:swrl:var#u>))))
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)
Expand Down