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CL release v2024-08-16 #2500

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Aug 16, 2024
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CL release v2024-08-16 #2500

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1,848 changes: 1,570 additions & 278 deletions cl-base.owl
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2,278 changes: 1,823 additions & 455 deletions cl.obo
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239 changes: 237 additions & 2 deletions patterns/definitions.owl
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15 changes: 15 additions & 0 deletions patterns/pattern.owl
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Expand Up @@ -12,20 +12,26 @@ Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000000>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000003>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005886>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0008150>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0022402>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_1>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000001>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0002354>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001062>))
Declaration(Class(<http://purl.obolibrary.org/obo/cl/cellBearerOfQuality>))
Declaration(Class(<http://purl.obolibrary.org/obo/cl/cellCapableOfBiologicalProcess>))
Declaration(Class(<http://purl.obolibrary.org/obo/cl/cellHasPlasmaMembranePartX>))
Declaration(Class(<http://purl.obolibrary.org/obo/cl/cellPartOfAnatomicalEntity>))
Declaration(Class(<http://purl.obolibrary.org/obo/cl/cyclingCellStates.yaml>))
Declaration(Class(<http://purl.obolibrary.org/obo/cl/taxonSpecific>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))
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_0000086>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002104>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002162>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002215>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
Declaration(AnnotationProperty(<http://purl.org/dc/terms/date>))
Declaration(AnnotationProperty(<http://purl.org/dc/terms/title>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))
Expand Down Expand Up @@ -66,6 +72,15 @@ AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/cl/cellPartOfAnatomicalEntity> "'cell' of 'anatomical entity'"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/cl/cellPartOfAnatomicalEntity> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/CL_0000000> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0001062>)))

# Class: <http://purl.obolibrary.org/obo/cl/cyclingCellStates.yaml> (cycling 'cell')

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "xsd:string"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/cl/cyclingCellStates.yaml> "A(n) 'cell' that is cycling."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/date> <http://purl.obolibrary.org/obo/cl/cyclingCellStates.yaml> "xsd:string"^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/cl/cyclingCellStates.yaml> "cyclingCellStates"^^xsd:string)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "xsd:string"^^xsd:string) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/cl/cyclingCellStates.yaml> "proliferating 'cell'"^^xsd:string)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/cl/cyclingCellStates.yaml> "cycling 'cell'"^^xsd:string)
EquivalentClasses(<http://purl.obolibrary.org/obo/cl/cyclingCellStates.yaml> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/CL_0000000> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000056> <http://purl.obolibrary.org/obo/GO_0022402>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000086> <http://purl.obolibrary.org/obo/PATO_0002354>)))

# Class: <http://purl.obolibrary.org/obo/cl/taxonSpecific> ('cell', 'taxon')

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/cl/taxonSpecific> "Any 'cell' that is part of a 'taxon'."^^xsd:string)
Expand Down
1,976 changes: 1,748 additions & 228 deletions src/ontology/reports/cl-base-diff.md
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25 changes: 25 additions & 0 deletions src/ontology/reports/cl-edit.owl-obo-report.tsv
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Expand Up @@ -255,6 +255,8 @@ INFO missing_superclass CL:0002078 rdfs:subClassOf
INFO missing_superclass CL:0002089 rdfs:subClassOf
INFO missing_superclass CL:0002132 rdfs:subClassOf
INFO missing_superclass CL:0002148 rdfs:subClassOf
INFO missing_superclass CL:0002152 rdfs:subClassOf
INFO missing_superclass CL:0002181 rdfs:subClassOf
INFO missing_superclass CL:0002200 rdfs:subClassOf
INFO missing_superclass CL:0002202 rdfs:subClassOf
INFO missing_superclass CL:0002205 rdfs:subClassOf
Expand All @@ -265,6 +267,7 @@ INFO missing_superclass CL:0002235 rdfs:subClassOf
INFO missing_superclass CL:0002236 rdfs:subClassOf
INFO missing_superclass CL:0002237 rdfs:subClassOf
INFO missing_superclass CL:0002242 rdfs:subClassOf
INFO missing_superclass CL:0002244 rdfs:subClassOf
INFO missing_superclass CL:0002262 rdfs:subClassOf
INFO missing_superclass CL:0002275 rdfs:subClassOf
INFO missing_superclass CL:0002315 rdfs:subClassOf
Expand Down Expand Up @@ -309,6 +312,7 @@ INFO missing_superclass CL:0002632 rdfs:subClassOf
INFO missing_superclass CL:0002633 rdfs:subClassOf
INFO missing_superclass CL:0002634 rdfs:subClassOf
INFO missing_superclass CL:0002652 rdfs:subClassOf
INFO missing_superclass CL:0002659 rdfs:subClassOf
INFO missing_superclass CL:0002673 rdfs:subClassOf
INFO missing_superclass CL:0002681 rdfs:subClassOf
INFO missing_superclass CL:0003001 rdfs:subClassOf
Expand Down Expand Up @@ -499,6 +503,7 @@ INFO missing_superclass CL:1000746 rdfs:subClassOf
INFO missing_superclass CL:1001005 rdfs:subClassOf
INFO missing_superclass CL:1001009 rdfs:subClassOf
INFO missing_superclass CL:1001099 rdfs:subClassOf
INFO missing_superclass CL:1001123 rdfs:subClassOf
INFO missing_superclass CL:1001124 rdfs:subClassOf
INFO missing_superclass CL:1001225 rdfs:subClassOf
INFO missing_superclass CL:1001428 rdfs:subClassOf
Expand Down Expand Up @@ -723,4 +728,24 @@ INFO missing_superclass CL:4033054 rdfs:subClassOf
INFO missing_superclass CL:4033055 rdfs:subClassOf
INFO missing_superclass CL:4033061 rdfs:subClassOf
INFO missing_superclass CL:4033064 rdfs:subClassOf
INFO missing_superclass CL:4033068 rdfs:subClassOf
INFO missing_superclass CL:4033069 rdfs:subClassOf
INFO missing_superclass CL:4033070 rdfs:subClassOf
INFO missing_superclass CL:4033071 rdfs:subClassOf
INFO missing_superclass CL:4033072 rdfs:subClassOf
INFO missing_superclass CL:4033073 rdfs:subClassOf
INFO missing_superclass CL:4033074 rdfs:subClassOf
INFO missing_superclass CL:4033075 rdfs:subClassOf
INFO missing_superclass CL:4033076 rdfs:subClassOf
INFO missing_superclass CL:4033077 rdfs:subClassOf
INFO missing_superclass CL:4033078 rdfs:subClassOf
INFO missing_superclass CL:4033079 rdfs:subClassOf
INFO missing_superclass CL:4033080 rdfs:subClassOf
INFO missing_superclass CL:4033081 rdfs:subClassOf
INFO missing_superclass CL:4033082 rdfs:subClassOf
INFO missing_superclass CL:4040004 rdfs:subClassOf
INFO missing_superclass CL:4047001 rdfs:subClassOf
INFO missing_superclass CL:4047002 rdfs:subClassOf
INFO missing_superclass CL:4047003 rdfs:subClassOf
INFO missing_superclass CL:4047004 rdfs:subClassOf
INFO missing_superclass CL:4047005 rdfs:subClassOf
15 changes: 6 additions & 9 deletions src/ontology/subsets/blood_and_immune_upper_slim.json
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Expand Up @@ -4,9 +4,9 @@
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2024-07-10"
"val" : "2024-08-16"
} ],
"version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/blood_and_immune_upper_slim.owl"
"version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/blood_and_immune_upper_slim.owl"
},
"nodes" : [ {
"id" : "http://purl.obolibrary.org/obo/CL_0000000",
Expand Down Expand Up @@ -21768,13 +21768,10 @@
"val" : "uberon"
}, {
"pred" : "http://xmlns.com/foaf/0.1/depiction",
"val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb"
"val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb"
}, {
"pred" : "http://xmlns.com/foaf/0.1/depiction",
"val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb"
}, {
"pred" : "http://xmlns.com/foaf/0.1/depiction",
"val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb"
"val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb"
} ]
}
}, {
Expand Down Expand Up @@ -25311,10 +25308,10 @@
"val" : "uberon"
}, {
"pred" : "http://xmlns.com/foaf/0.1/depiction",
"val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb"
"val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb"
}, {
"pred" : "http://xmlns.com/foaf/0.1/depiction",
"val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb"
"val" : "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb"
} ]
}
}, {
Expand Down
13 changes: 6 additions & 7 deletions src/ontology/subsets/blood_and_immune_upper_slim.obo
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@@ -1,5 +1,5 @@
format-version: 1.2
data-version: cl/releases/2024-07-10/subsets/blood_and_immune_upper_slim.owl
data-version: cl/releases/2024-08-16/subsets/blood_and_immune_upper_slim.owl
subsetdef: abnormal_slim ""
subsetdef: added_for_HCA ""
subsetdef: attribute_slim ""
Expand Down Expand Up @@ -95,7 +95,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
idspace: sssom https://w3id.org/sssom/
idspace: terms http://purl.org/dc/terms/
ontology: cl/subsets/blood_and_immune_upper_slim
property_value: owl:versionInfo "2024-07-10" xsd:string
property_value: owl:versionInfo "2024-08-16" xsd:string

[Term]
id: CL:0000000
Expand Down Expand Up @@ -12030,9 +12030,8 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium
relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata <vertebrates>
relationship: RO:0002202 UBERON:0004141 ! develops from heart tube
relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system
property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI
property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI
property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI
property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI
property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb" xsd:anyURI
property_value: RO:0002161 NCBITaxon:6239
property_value: RO:0002161 NCBITaxon:7227
property_value: RO:0002175 NCBITaxon:9606
Expand Down Expand Up @@ -13930,8 +13929,8 @@ is_a: UBERON:0002049 ! vasculature
intersection_of: UBERON:0002049 ! vasculature
intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel
relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel
property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI
property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI
property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb" xsd:anyURI
property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb" xsd:anyURI
property_value: RO:0002175 NCBITaxon:9606

[Term]
Expand Down
13 changes: 6 additions & 7 deletions src/ontology/subsets/blood_and_immune_upper_slim.owl
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Expand Up @@ -22,8 +22,8 @@
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cl/subsets/blood_and_immune_upper_slim.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/blood_and_immune_upper_slim.owl"/>
<owl:versionInfo>2024-07-10</owl:versionInfo>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/blood_and_immune_upper_slim.owl"/>
<owl:versionInfo>2024-08-16</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -37884,9 +37884,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#vertebrate_core"/>
<rdfs:comment>Taxon notes:&quot; the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)&quot; DOI:10.1101/gad.1485706</rdfs:comment>
<rdfs:label>heart</rdfs:label>
<foaf:depiction rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb</foaf:depiction>
<foaf:depiction rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb</foaf:depiction>
<foaf:depiction rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb</foaf:depiction>
<foaf:depiction rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb</foaf:depiction>
<foaf:depiction rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb</foaf:depiction>
</owl:Class>
<owl:Restriction rdf:nodeID="genid4248">
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
Expand Down Expand Up @@ -42861,8 +42860,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different
<oboInOwl:id>UBERON:0004537</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
<rdfs:label>blood vasculature</rdfs:label>
<foaf:depiction rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb</foaf:depiction>
<foaf:depiction rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb</foaf:depiction>
<foaf:depiction rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb</foaf:depiction>
<foaf:depiction rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb</foaf:depiction>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0004537"/>
Expand Down
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