CL release c2024-08-16 (#2500)

CL release c2024-08-16
obophenotype · Aug 16, 2024 · 1b3ae70 · 1b3ae70
1 parent 30ea87b
commit 1b3ae70
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Showing 38 changed files with 11,370 additions and 5,491 deletions.
diff --git a/cl-base.owl b/cl-base.owl
diff --git a/cl.obo b/cl.obo
diff --git a/patterns/definitions.owl b/patterns/definitions.owl
diff --git a/patterns/pattern.owl b/patterns/pattern.owl
@@ -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>))
@@ -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)

diff --git a/src/ontology/reports/cl-base-diff.md b/src/ontology/reports/cl-base-diff.md
diff --git a/src/ontology/reports/cl-edit.owl-obo-report.tsv b/src/ontology/reports/cl-edit.owl-obo-report.tsv
@@ -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	
@@ -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	
@@ -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	
@@ -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	
@@ -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	
diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.json b/src/ontology/subsets/blood_and_immune_upper_slim.json
@@ -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",
@@ -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"
         } ]
       }
     }, {
@@ -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"
         } ]
       }
     }, {

diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.obo b/src/ontology/subsets/blood_and_immune_upper_slim.obo
@@ -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 ""
@@ -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
@@ -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
@@ -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]

diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.owl b/src/ontology/subsets/blood_and_immune_upper_slim.owl
@@ -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>
 
 
@@ -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"/>
@@ -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"/>