Merge pull request #3909 from mgijax/create-pull-request/patch

Update all imports and components
mgijax · Feb 3, 2024 · b80e0ae · b80e0ae
2 parents fb0c10d + d8466cd
commit b80e0ae
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Showing 10 changed files with 6,910 additions and 7,046 deletions.
diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/mp/imports/chebi_import.owl>
-<http://purl.obolibrary.org/obo/mp/releases/2023-12-19/imports/chebi_import.owl>
-Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/chebi/obophenotype/releases/2023-11-17/chebi_slim.owl>)
-Annotation(owl:versionInfo "2023-12-19")
+<http://purl.obolibrary.org/obo/mp/releases/2024-02-02/imports/chebi_import.owl>
+Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/chebi/obophenotype/releases/2024-01-21/chebi_slim.owl>)
+Annotation(owl:versionInfo "2024-02-02")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10545>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_11955>))
@@ -7991,14 +7991,13 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/charge> <http://purl.o
 AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/formula> <http://purl.obolibrary.org/obo/CHEBI_18140> "HX")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/mass> <http://purl.obolibrary.org/obo/CHEBI_18140> "1.008")
 AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/monoisotopicmass> <http://purl.obolibrary.org/obo/CHEBI_18140> "1.00783")
-AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/smiles> <http://purl.obolibrary.org/obo/CHEBI_18140> "[F,Cl,Br,I]")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/chebi/smiles> <http://purl.obolibrary.org/obo/CHEBI_18140> "*[H]")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> <http://purl.obolibrary.org/obo/CHEBI_18140> "CHEBI:13368")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> <http://purl.obolibrary.org/obo/CHEBI_18140> "CHEBI:37140")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> <http://purl.obolibrary.org/obo/CHEBI_18140> "CHEBI:5599")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "IUPAC") <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CHEBI_18140> "hydrogen halide")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "IUPAC") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/chebi#IUPAC_NAME>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CHEBI_18140> "hydrogen halides")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CHEBI_18140> "chebi_ontology")
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "UniProt") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_18140> "HX")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_18140> "hydrogen halides")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/CHEBI_18140> "CHEBI:18140")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CHEBI_18140> <http://purl.obolibrary.org/obo/chebi#3_STAR>)
@@ -27877,8 +27876,7 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/CHEBI_83813> "CHEBI:83813")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CHEBI_83813> <http://purl.obolibrary.org/obo/chebi#3_STAR>)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CHEBI_83813> "proteinogenic amino acid")
-SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_83813> <http://purl.obolibrary.org/obo/CHEBI_33575>)
-SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_83813> <http://purl.obolibrary.org/obo/CHEBI_35352>)
+SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_83813> <http://purl.obolibrary.org/obo/CHEBI_33709>)
 
 # Class: <http://purl.obolibrary.org/obo/CHEBI_83820> (non-proteinogenic amino acid)
 
@@ -28228,6 +28226,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_88184> ObjectSomeValuesFrom(<ht
 # Class: <http://purl.obolibrary.org/obo/CHEBI_90710> (receptor modulator)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CHEBI_90710> "A drug that acts as an antagonist, agonist, reverse agonist, or in some other fashion when interacting with cellular receptors.")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId> <http://purl.obolibrary.org/obo/CHEBI_90710> "CHEBI:189678")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CHEBI_90710> "Wikipedia:Receptor_modulator")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/CHEBI_90710> "chebi_ontology")
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ChEBI") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CHEBI_90710> "receptor modulators")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/CHEBI_90710> "CHEBI:90710")

diff --git a/src/ontology/imports/cl_import.owl b/src/ontology/imports/cl_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/mp/imports/cl_import.owl>
-<http://purl.obolibrary.org/obo/mp/releases/2023-12-19/imports/cl_import.owl>
-Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/cl/releases/2023-12-05/cl-simple.owl>)
-Annotation(owl:versionInfo "2023-12-19")
+<http://purl.obolibrary.org/obo/mp/releases/2024-02-02/imports/cl_import.owl>
+Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/cl/releases/2024-01-04/cl-simple.owl>)
+Annotation(owl:versionInfo "2024-02-02")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000000>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000006>))
@@ -2080,15 +2080,13 @@ SubClassOf(<http://purl.obolibrary.org/obo/CL_0000123> ObjectSomeValuesFrom(<htt
 # Class: <http://purl.obolibrary.org/obo/CL_0000125> (glial cell)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MESH:D009457") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0000125> "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.")
-AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_0002175> <http://purl.obolibrary.org/obo/CL_0000125> <http://purl.obolibrary.org/obo/NCBITaxon_9606>)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CL_0000125> "BTO:0002606")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CL_0000125> "CALOHA:TS-0415")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CL_0000125> "FBbt:00005144")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CL_0000125> "FMA:54536")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CL_0000125> "neuroglial cell")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/CL_0000125> "neuroglia")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_0000125> <http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim>)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_0000125> <http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas>)
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/CL_0000125> "Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_0000125> "glial cell")
 SubClassOf(<http://purl.obolibrary.org/obo/CL_0000125> <http://purl.obolibrary.org/obo/CL_0000095>)
@@ -3145,8 +3143,6 @@ SubClassOf(<http://purl.obolibrary.org/obo/CL_0000412> <http://purl.obolibrary.o
 # Class: <http://purl.obolibrary.org/obo/CL_0000413> (haploid cell)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FB:ma") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:tfm") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0000413> "A cell whose nucleus contains a single haploid genome.")
-AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_0002175> <http://purl.obolibrary.org/obo/CL_0000413> <http://purl.obolibrary.org/obo/NCBITaxon_9606>)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_0000413> <http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas>)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_0000413> "haploid cell")
 SubClassOf(<http://purl.obolibrary.org/obo/CL_0000413> <http://purl.obolibrary.org/obo/CL_0000000>)
 
@@ -5319,10 +5315,12 @@ DisjointClasses(<http://purl.obolibrary.org/obo/CL_0000838> <http://purl.obolibr
 # Class: <http://purl.obolibrary.org/obo/CL_0000839> (myeloid lineage restricted progenitor cell)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:add") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:tfm") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:19022770") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_0000839> "A progenitor cell restricted to the myeloid lineage.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/RO_0002175> <http://purl.obolibrary.org/obo/CL_0000839> <http://purl.obolibrary.org/obo/NCBITaxon_9606>)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/CL_0000839> "myeloid progenitor cell")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CL_0000839> "BTO:0004730")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CL_0000839> "CALOHA:TS-2099")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/CL_0000839> "FMA:70339")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_0000839> <http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas>)
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/CL_0000839> "Note that this is a class of cell types, not an identified single cell type.")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_0000839> "myeloid lineage restricted progenitor cell")
 SubClassOf(Annotation(<http://www.geneontology.org/formats/oboInOwl#is_inferred> "true") <http://purl.obolibrary.org/obo/CL_0000839> <http://purl.obolibrary.org/obo/CL_0002031>)