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NTR 'contains measured amount' #726

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merged 20 commits into from
Nov 6, 2023
Merged

NTR 'contains measured amount' #726

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8c10639
Adding RO_0017002 (contains amount) and dependencies
jmwhorton Jun 7, 2023
7677838
Merge pull request #1 from jmwhorton/ntr/contains-amount
jmwhorton Jun 7, 2023
3f6b507
Updating RO_0017002 annotations for consistency.
jmwhorton Jun 19, 2023
71b0bd2
Merge pull request #2 from jmwhorton/ntr/contains-amount
jmwhorton Jun 19, 2023
85d2858
Correcting RO_0017002 to RO_0017005
jmwhorton Jun 20, 2023
2379b07
correcting whitespace
jmwhorton Jun 20, 2023
5dc6571
Merge branch 'master' into master
jmwhorton Jul 6, 2023
bdf2d93
Updating label 'contains amount' to 'contains measured amount'
jmwhorton Jul 6, 2023
dcb48f9
Merge branch 'master' into master
Jul 12, 2023
f67ea0f
Merge branch 'master' into master
Jul 17, 2023
1b13773
Removed OBI terms from other_import, added to obi_terms
jmwhorton Jul 26, 2023
1cbf36b
Added example of usage for RO_0017005 'contains measured amount'
jmwhorton Jul 26, 2023
055d165
Merge branch 'master' into master
Aug 10, 2023
ec7ed63
Adjusting imports to meet standards
jmwhorton Aug 23, 2023
99cdeb5
Merge branch 'master' into master
jmwhorton Aug 23, 2023
7fe8f64
Removing unnecessary declarations
jmwhorton Aug 23, 2023
e2bcc8f
Replacing IAO_0000109 with COB_0000121
jmwhorton Aug 24, 2023
6028f32
Replacing 'dc' with 'terms'
jmwhorton Sep 12, 2023
2f0ec21
Merge branch 'master' into master
jmwhorton Nov 1, 2023
e36acf3
Merge branch 'master' into master
wdduncan Nov 6, 2023
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205 changes: 191 additions & 14 deletions src/ontology/imports/cob_import.owl
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@@ -1,14 +1,191 @@
<?xml version="1.0"?>
<rdf:RDF
xml:base="http://purl.obolibrary.org/obo/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:obo="http://purl.obolibrary.org/obo/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro/imports/cob_import.owl"/>

<!-- This is a placeholder, it will be regenerated when makefile is first executed -->
</rdf:RDF>
Prefix(:=<http://purl.obolibrary.org/obo/ro/imports/cob_import.owl#>)
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(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/ro/imports/cob_import.owl>
<http://purl.obolibrary.org/obo/ro/releases/2023-08-23/imports/cob_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/cob/releases/2023-05-12/cob.owl>)
Annotation(owl:versionInfo "2023-08-23"^^xsd:string)

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000016>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000017>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000020>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000023>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000034>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000141>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000000>))
Declaration(Class(<http://purl.obolibrary.org/obo/COB_0000121>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0003674>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005634>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0008150>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000054>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000066>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000067>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000052>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000053>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000056>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000057>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000058>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002333>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000117>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
Declaration(AnnotationProperty(<http://www.w3.org/2004/02/skos/core#exactMatch>))
############################
# Annotation Properties
############################

# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000115> (definition)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000115> "definition")


############################
# Object Properties
############################

# Object Property: <http://purl.obolibrary.org/obo/BFO_0000050> (part of)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000050> "part of")
InverseObjectProperties(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000051>)
TransitiveObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>)

# Object Property: <http://purl.obolibrary.org/obo/BFO_0000051> (has part)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000051> "has part")

# Object Property: <http://purl.obolibrary.org/obo/BFO_0000054> (realized in)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000054> "realized in"@en)

# Object Property: <http://purl.obolibrary.org/obo/BFO_0000066> (occurs in)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000066> "occurs in")
InverseObjectProperties(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000067>)
ObjectPropertyDomain(<http://purl.obolibrary.org/obo/BFO_0000066> <http://purl.obolibrary.org/obo/BFO_0000015>)

# Object Property: <http://purl.obolibrary.org/obo/BFO_0000067> (contains process)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000067> "contains process"@en)

# Object Property: <http://purl.obolibrary.org/obo/RO_0000052> (characteristic of)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0000052> "characteristic of"@en)
InverseObjectProperties(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/RO_0000053>)

# Object Property: <http://purl.obolibrary.org/obo/RO_0000053> (has characteristic)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0000053> "has characteristic")
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/RO_0000053> "https://github.com/oborel/obo-relations/pull/284")
InverseFunctionalObjectProperty(<http://purl.obolibrary.org/obo/RO_0000053>)
ObjectPropertyRange(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/BFO_0000020>)

# Object Property: <http://purl.obolibrary.org/obo/RO_0000056> (participates in)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0000056> "participates in"@en)
InverseObjectProperties(<http://purl.obolibrary.org/obo/RO_0000056> <http://purl.obolibrary.org/obo/RO_0000057>)

# Object Property: <http://purl.obolibrary.org/obo/RO_0000057> (has participant)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0000057> "has participant")
ObjectPropertyDomain(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/BFO_0000015>)

# Object Property: <http://purl.obolibrary.org/obo/RO_0000058> (is concretized as)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0000058> "is concretized as"@en)

# Object Property: <http://purl.obolibrary.org/obo/RO_0002333> (enabled by)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002333> "enabled by")
SubObjectPropertyOf(<http://purl.obolibrary.org/obo/RO_0002333> <http://purl.obolibrary.org/obo/RO_0000057>)



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

# Class: <http://purl.obolibrary.org/obo/BFO_0000015> (process)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000015> "process"@en)
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000015> ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000015>))

# Class: <http://purl.obolibrary.org/obo/BFO_0000016> (disposition)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000016> "disposition"@en)
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000016> <http://purl.obolibrary.org/obo/BFO_0000017>)

# Class: <http://purl.obolibrary.org/obo/BFO_0000017> (realizable)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000017> "realizable"@en)
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000017> <http://purl.obolibrary.org/obo/BFO_0000020>)

# Class: <http://purl.obolibrary.org/obo/BFO_0000020> (characteristic)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000020> "characteristic"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/BFO_0000020> "https://github.com/OBOFoundry/COB/issues/65")
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/BFO_0000020> "https://github.com/oborel/obo-relations/pull/284")
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000020> ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/BFO_0000020>))

# Class: <http://purl.obolibrary.org/obo/BFO_0000023> (role)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000023> "role"@en)
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000023> <http://purl.obolibrary.org/obo/BFO_0000017>)

# Class: <http://purl.obolibrary.org/obo/BFO_0000034> (function)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000034> "function"@en)
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000034> <http://purl.obolibrary.org/obo/BFO_0000016>)

# Class: <http://purl.obolibrary.org/obo/BFO_0000040> (material entity)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000040> "material entity"@en)

# Class: <http://purl.obolibrary.org/obo/BFO_0000141> (immaterial entity)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000141> "immaterial entity"@en)

# Class: <http://purl.obolibrary.org/obo/CL_0000000> (cell)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0000000> "A material entity that has a plasma membrane and results from cellular division.")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/CL_0000000> "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/CL_0000000> "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_0000000> "cell"@en)
SubClassOf(<http://purl.obolibrary.org/obo/CL_0000000> <http://purl.obolibrary.org/obo/BFO_0000040>)

# Class: <http://purl.obolibrary.org/obo/COB_0000121> (measurement datum)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/COB_0000121> "measurement datum")

# Class: <http://purl.obolibrary.org/obo/GO_0003674> (gene product or complex activity)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0003674> "This is the same as GO molecular function")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0003674> "gene product or complex activity"@en)
SubClassOf(<http://purl.obolibrary.org/obo/GO_0003674> <http://purl.obolibrary.org/obo/BFO_0000015>)
DisjointClasses(<http://purl.obolibrary.org/obo/GO_0003674> <http://purl.obolibrary.org/obo/GO_0008150>)

# Class: <http://purl.obolibrary.org/obo/GO_0005634> (cell nucleus)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0005634> "cell nucleus"@en)
SubClassOf(<http://purl.obolibrary.org/obo/GO_0005634> <http://purl.obolibrary.org/obo/BFO_0000040>)

# Class: <http://purl.obolibrary.org/obo/GO_0008150> (biological process)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/GO_0008150> "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0008150> "A biological process is an evolved process")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0008150> "biological process"@en)
SubClassOf(<http://purl.obolibrary.org/obo/GO_0008150> <http://purl.obolibrary.org/obo/BFO_0000015>)
SubClassOf(<http://purl.obolibrary.org/obo/GO_0008150> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/GO_0003674>))


)
2 changes: 1 addition & 1 deletion src/ontology/imports/cob_terms.txt
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@@ -1 +1 @@

COB:0000121
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