CL release 2023-12-05 (#2238)

CL release 2023-12-05
obophenotype · Dec 5, 2023 · f76d14e · f76d14e
1 parent de6b195
commit f76d14e
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Showing 37 changed files with 161,049 additions and 10,971 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
@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/cl/patterns/definitions.owl>
-<http://purl.obolibrary.org/obo/cl/releases/2023-10-18/patterns/definitions.owl>
-Annotation(owl:versionInfo "2023-10-18")
+<http://purl.obolibrary.org/obo/cl/releases/2023-12-05/patterns/definitions.owl>
+Annotation(owl:versionInfo "2023-12-05")
 
 
 

diff --git a/src/ontology/diffs/cl-diff.md b/src/ontology/diffs/cl-diff.md
diff --git a/src/ontology/reports/cl-edit.owl-obo-report.tsv b/src/ontology/reports/cl-edit.owl-obo-report.tsv
@@ -7,7 +7,6 @@ WARN	missing_definition	CL:0000036	IAO:0000115
 WARN	missing_definition	CL:0000054	IAO:0000115	
 WARN	missing_definition	CL:0000069	IAO:0000115	
 WARN	missing_definition	CL:0000072	IAO:0000115	
-WARN	missing_definition	CL:0000073	IAO:0000115	
 WARN	missing_definition	CL:0000076	IAO:0000115	
 WARN	missing_definition	CL:0000078	IAO:0000115	
 WARN	missing_definition	CL:0000079	IAO:0000115	
@@ -59,7 +58,6 @@ WARN	missing_definition	CL:0000310	IAO:0000115
 WARN	missing_definition	CL:0000311	IAO:0000115	
 WARN	missing_definition	CL:0000314	IAO:0000115	
 WARN	missing_definition	CL:0000319	IAO:0000115	
-WARN	missing_definition	CL:0000321	IAO:0000115	
 WARN	missing_definition	CL:0000323	IAO:0000115	
 WARN	missing_definition	CL:0000324	IAO:0000115	
 WARN	missing_definition	CL:0000326	IAO:0000115	
@@ -151,7 +149,6 @@ WARN	missing_definition	CL:0002602	IAO:0000115
 WARN	missing_definition	CL:0002621	IAO:0000115	
 WARN	missing_definition	CL:0002631	IAO:0000115	
 WARN	missing_definition	CL:0002632	IAO:0000115	
-WARN	missing_definition	CL:0002681	IAO:0000115	
 WARN	missing_definition	CL:0007019	IAO:0000115	
 WARN	missing_definition	CL:0008021	IAO:0000115	
 WARN	missing_definition	CL:0008028	IAO:0000115	
@@ -189,15 +186,7 @@ WARN	missing_definition	CL:1000245	IAO:0000115
 WARN	missing_definition	CL:1000271	IAO:0000115	
 WARN	missing_definition	CL:1000272	IAO:0000115	
 WARN	missing_definition	CL:1000274	IAO:0000115	
-WARN	missing_definition	CL:1000497	IAO:0000115	
-WARN	missing_definition	CL:1000500	IAO:0000115	
-WARN	missing_definition	CL:1000504	IAO:0000115	
-WARN	missing_definition	CL:1000505	IAO:0000115	
-WARN	missing_definition	CL:1000507	IAO:0000115	
 WARN	missing_definition	CL:1000510	IAO:0000115	
-WARN	missing_definition	CL:1000546	IAO:0000115	
-WARN	missing_definition	CL:1000548	IAO:0000115	
-WARN	missing_definition	CL:1000549	IAO:0000115	
 WARN	missing_definition	CL:1000550	IAO:0000115	
 WARN	missing_definition	CL:1000596	IAO:0000115	
 WARN	missing_definition	CL:1000600	IAO:0000115	
@@ -274,7 +263,6 @@ WARN	missing_definition	CL:1001220	IAO:0000115
 WARN	missing_definition	CL:1001221	IAO:0000115	
 WARN	missing_definition	CL:1001223	IAO:0000115	
 WARN	missing_definition	CL:1001224	IAO:0000115	
-WARN	missing_definition	CL:1001225	IAO:0000115	
 WARN	missing_definition	CL:1001286	IAO:0000115	
 WARN	missing_definition	CL:1001287	IAO:0000115	
 WARN	missing_definition	CL:1001319	IAO:0000115	
@@ -295,7 +283,6 @@ WARN	missing_definition	IAO:0000115	IAO:0000115
 WARN	missing_definition	IAO:0000424	IAO:0000115	
 WARN	missing_definition	IAO:0000700	IAO:0000115	
 WARN	missing_definition	IAO:0100001	IAO:0000115	
-WARN	missing_definition	obo:cl#abbreviation	IAO:0000115	
 WARN	missing_definition	obo:uberon#HUMAN_PREFERRED	IAO:0000115	
 WARN	missing_definition	obo:uberon#LATIN	IAO:0000115	
 WARN	missing_definition	obo:uberon#PLURAL	IAO:0000115	
@@ -312,6 +299,7 @@ WARN	missing_definition	oboInOwl:hasSynonymType	IAO:0000115
 WARN	missing_definition	oboInOwl:inSubset	IAO:0000115	
 WARN	missing_definition	oboInOwl:shorthand	IAO:0000115	
 WARN	missing_obsolete_label	CL:0000736	rdfs:label	embryonic gland hemocyte
+WARN	missing_synonymtype_declaration	OMO:0003000	rdfs:subPropertyOf	
 WARN	missing_synonymtype_declaration	OMO:0003004	rdfs:subPropertyOf	
 WARN	missing_synonymtype_declaration	obo:uberon/core#MISSPELLING	rdfs:subPropertyOf	
 INFO	lowercase_definition	CL:4023080	IAO:0000115	a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has stellate pyramidal morphology.
@@ -464,6 +452,7 @@ INFO	missing_superclass	CL:0002608	rdfs:subClassOf
 INFO	missing_superclass	CL:0002621	rdfs:subClassOf	
 INFO	missing_superclass	CL:0002634	rdfs:subClassOf	
 INFO	missing_superclass	CL:0002673	rdfs:subClassOf	
+INFO	missing_superclass	CL:0002681	rdfs:subClassOf	
 INFO	missing_superclass	CL:0003001	rdfs:subClassOf	
 INFO	missing_superclass	CL:0004246	rdfs:subClassOf	
 INFO	missing_superclass	CL:0004247	rdfs:subClassOf	
@@ -642,7 +631,14 @@ INFO	missing_superclass	CL:1000492	rdfs:subClassOf
 INFO	missing_superclass	CL:1000493	rdfs:subClassOf	
 INFO	missing_superclass	CL:1000494	rdfs:subClassOf	
 INFO	missing_superclass	CL:1000497	rdfs:subClassOf	
+INFO	missing_superclass	CL:1000500	rdfs:subClassOf	
+INFO	missing_superclass	CL:1000504	rdfs:subClassOf	
+INFO	missing_superclass	CL:1000505	rdfs:subClassOf	
+INFO	missing_superclass	CL:1000507	rdfs:subClassOf	
+INFO	missing_superclass	CL:1000546	rdfs:subClassOf	
+INFO	missing_superclass	CL:1000549	rdfs:subClassOf	
 INFO	missing_superclass	CL:1000692	rdfs:subClassOf	
+INFO	missing_superclass	CL:1001225	rdfs:subClassOf	
 INFO	missing_superclass	CL:1001428	rdfs:subClassOf	
 INFO	missing_superclass	CL:1001433	rdfs:subClassOf	
 INFO	missing_superclass	CL:1001516	rdfs:subClassOf	
@@ -817,7 +813,6 @@ INFO	missing_superclass	CL:4030005	rdfs:subClassOf
 INFO	missing_superclass	CL:4030015	rdfs:subClassOf	
 INFO	missing_superclass	CL:4030016	rdfs:subClassOf	
 INFO	missing_superclass	CL:4030017	rdfs:subClassOf	
-INFO	missing_superclass	CL:4030018	rdfs:subClassOf	
 INFO	missing_superclass	CL:4030020	rdfs:subClassOf	
 INFO	missing_superclass	CL:4030021	rdfs:subClassOf	
 INFO	missing_superclass	CL:4030022	rdfs:subClassOf	
@@ -828,6 +823,16 @@ INFO	missing_superclass	CL:4030029	rdfs:subClassOf
 INFO	missing_superclass	CL:4030031	rdfs:subClassOf	
 INFO	missing_superclass	CL:4030033	rdfs:subClassOf	
 INFO	missing_superclass	CL:4030040	rdfs:subClassOf	
+INFO	missing_superclass	CL:4030058	rdfs:subClassOf	
+INFO	missing_superclass	CL:4030059	rdfs:subClassOf	
+INFO	missing_superclass	CL:4030060	rdfs:subClassOf	
+INFO	missing_superclass	CL:4030061	rdfs:subClassOf	
+INFO	missing_superclass	CL:4030062	rdfs:subClassOf	
+INFO	missing_superclass	CL:4030063	rdfs:subClassOf	
+INFO	missing_superclass	CL:4030064	rdfs:subClassOf	
+INFO	missing_superclass	CL:4030065	rdfs:subClassOf	
+INFO	missing_superclass	CL:4030067	rdfs:subClassOf	
+INFO	missing_superclass	CL:4030068	rdfs:subClassOf	
 INFO	missing_superclass	CL:4032001	rdfs:subClassOf	
 INFO	missing_superclass	CL:4033000	rdfs:subClassOf	
 INFO	missing_superclass	CL:4033001	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" : "2023-11-22"
+        "val" : "2023-12-05"
       } ],
-      "version" : "http://purl.obolibrary.org/obo/cl/releases/2023-11-22/subsets/blood_and_immune_upper_slim.owl"
+      "version" : "http://purl.obolibrary.org/obo/cl/releases/2023-12-05/subsets/blood_and_immune_upper_slim.owl"
     },
     "nodes" : [ {
       "id" : "http://purl.obolibrary.org/obo/BFO_0000002",
@@ -816,8 +816,6 @@
           "val" : "BTO:0000725"
         }, {
           "val" : "CALOHA:TS-0448"
-        }, {
-          "val" : "FMA:70337"
         }, {
           "val" : "FMA:86475"
         }, {
@@ -2509,8 +2507,6 @@
         },
         "xrefs" : [ {
           "val" : "CALOHA:TS-2086"
-        }, {
-          "val" : "FMA:63368"
         }, {
           "val" : "MESH:D053687"
         } ]
@@ -3894,8 +3890,6 @@
           "val" : "CALOHA:TS-0263"
         }, {
           "val" : "FMA:82840"
-        }, {
-          "val" : "FMA:82841"
         }, {
           "val" : "WBbt:0007028"
         } ],
@@ -4324,9 +4318,6 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.org/dc/terms/contributor",
-          "val" : "https://orcid.org/0000-0002-1773-2692"
-        }, {
           "pred" : "http://purl.org/dc/terms/date",
           "val" : "2022-11-04T14:40:00Z"
         } ]
@@ -36660,7 +36651,7 @@
         "deprecated" : true
       }
     }, {
-      "id" : "http://purl.obolibrary.org/obo/cl#kidney_slim",
+      "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim",
       "lbl" : "kidney_upper_slim",
       "type" : "PROPERTY",
       "meta" : {

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/2023-11-22/subsets/blood_and_immune_upper_slim.owl
+data-version: cl/releases/2023-12-05/subsets/blood_and_immune_upper_slim.owl
 subsetdef: abnormal_slim ""
 subsetdef: added_for_HCA ""
 subsetdef: attribute_slim ""
@@ -41,7 +41,7 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
 subsetdef: human_reference_atlas ""
 subsetdef: inconsistent_with_fma ""
-subsetdef: kidney_slim "a subset of general classes related to specific cell types in the kidney"
+subsetdef: kidney_upper_slim "a subset of general classes related to specific cell types in the kidney"
 subsetdef: location_grouping ""
 subsetdef: major_organ ""
 subsetdef: mpath_slim ""
@@ -88,7 +88,7 @@ synonymtypedef: synonym ""
 synonymtypedef: SYSTEMATIC ""
 synonymtypedef: systematic_synonym ""
 ontology: cl/subsets/blood_and_immune_upper_slim
-property_value: owl:versionInfo "2023-11-22" xsd:string
+property_value: owl:versionInfo "2023-12-05" xsd:string
 
 [Term]
 id: BFO:0000002
@@ -196,7 +196,6 @@ synonym: "hemopoietic stem cell" EXACT []
 synonym: "HSC" RELATED OMO:0003000 []
 xref: BTO:0000725
 xref: CALOHA:TS-0448
-xref: FMA:70337
 xref: FMA:86475
 xref: MESH:D006412
 xref: VHOG:0001485
@@ -1447,7 +1446,6 @@ id: CL:0000723
 name: somatic stem cell
 def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103]
 xref: CALOHA:TS-2086
-xref: FMA:63368
 xref: MESH:D053687
 is_a: CL:0000034 ! stem cell
 intersection_of: CL:0000034 ! stem cell
@@ -2529,7 +2527,6 @@ name: embryonic cell (metazoa)
 def: "A cell of the embryo." [FMA:0618947256]
 xref: CALOHA:TS-0263
 xref: FMA:82840
-xref: FMA:82841
 xref: WBbt:0007028
 is_a: CL:0000000 ! cell
 relationship: dc-contributor https://orcid.org/0000-0003-1980-3228
@@ -2801,7 +2798,6 @@ is_a: CL:0000542 ! lymphocyte
 is_a: CL:2000001 ! peripheral blood mononuclear cell
 intersection_of: CL:0000542 ! lymphocyte
 intersection_of: part_of UBERON:0000178 ! blood
-relationship: dc-contributor https://orcid.org/0000-0002-1773-2692
 property_value: dcterms-date "2022-11-04T14:40:00Z" xsd:dateTime
 
 [Term]

diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.owl b/src/ontology/subsets/blood_and_immune_upper_slim.owl
@@ -29,8 +29,8 @@
      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/2023-11-22/subsets/blood_and_immune_upper_slim.owl"/>
-        <owl:versionInfo>2023-11-22</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2023-12-05/subsets/blood_and_immune_upper_slim.owl"/>
+        <owl:versionInfo>2023-12-05</owl:versionInfo>
     </owl:Ontology>
 
 
@@ -723,9 +723,9 @@ WHERE {
 
 
 
-    <!-- http://purl.obolibrary.org/obo/cl#kidney_slim -->
+    <!-- http://purl.obolibrary.org/obo/cl#kidney_upper_slim -->
 
-    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/cl#kidney_slim">
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/cl#kidney_upper_slim">
         <terms:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2023-11-22T11:18:57Z</terms:date>
         <rdfs:comment>a subset of general classes related to specific cell types in the kidney</rdfs:comment>
         <rdfs:label>kidney_upper_slim</rdfs:label>
@@ -1818,12 +1818,6 @@ WHERE {
 
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#seeAlso -->
-
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#seeAlso"/>
-
-
-
     <!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand">
@@ -8175,7 +8169,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
         <oboInOwl:hasDbXref>BTO:0000725</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>CALOHA:TS-0448</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FMA:70337</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:86475</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MESH:D006412</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>VHOG:0001485</oboInOwl:hasDbXref>
@@ -12287,7 +12280,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         </rdfs:subClassOf>
         <obo:IAO_0000115>A stem cell that can give rise to cell types of the body other than those of the germ-line.</obo:IAO_0000115>
         <oboInOwl:hasDbXref>CALOHA:TS-2086</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FMA:63368</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>MESH:D053687</oboInOwl:hasDbXref>
         <rdfs:label>somatic stem cell</rdfs:label>
     </owl:Class>
@@ -16000,7 +15992,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         <oboInOwl:creation_date>2010-09-15T03:39:21Z</oboInOwl:creation_date>
         <oboInOwl:hasDbXref>CALOHA:TS-0263</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>FMA:82840</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>FMA:82841</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>WBbt:0007028</oboInOwl:hasDbXref>
         <rdfs:label>embryonic cell (metazoa)</rdfs:label>
     </owl:Class>
@@ -16796,7 +16787,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000542"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_2000001"/>
         <obo:IAO_0000115>A lymphocyte located in blood.</obo:IAO_0000115>
-        <terms:contributor rdf:resource="https://orcid.org/0000-0002-1773-2692"/>
         <terms:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-11-04T14:40:00Z</terms:date>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim"/>
         <rdfs:label>blood lymphocyte</rdfs:label>