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Merge pull request #2036 from obophenotype/release-2023-06-22
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CL release 2023-06-22
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bvarner-ebi authored Jun 22, 2023
2 parents ca2ca1a + 77be629 commit a8c05ca
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Showing 30 changed files with 216,077 additions and 4,891 deletions.
1,386 changes: 1,274 additions & 112 deletions cl-base.owl
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2,120 changes: 1,776 additions & 344 deletions cl.obo
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4 changes: 2 additions & 2 deletions patterns/definitions.owl
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Expand Up @@ -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/2023-04-20/patterns/definitions.owl>
Annotation(owl:versionInfo "2023-04-20")
<http://purl.obolibrary.org/obo/cl/releases/2023-06-21/patterns/definitions.owl>
Annotation(owl:versionInfo "2023-06-21")



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4 changes: 2 additions & 2 deletions src/ontology/components/general_cell_types_upper_slim.owl
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Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/cl/components/general_cell_types_upper_slim.owl>
<http://purl.obolibrary.org/obo/cl/releases/2023-06-21/components/general_cell_types_upper_slim.owl>
Annotation(owl:versionInfo "2023-06-21")
<http://purl.obolibrary.org/obo/cl/releases/2023-06-22/components/general_cell_types_upper_slim.owl>
Annotation(owl:versionInfo "2023-06-22")

Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000034>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000039>))
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6,091 changes: 4,478 additions & 1,613 deletions src/ontology/diffs/cl-diff.md
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7 changes: 3 additions & 4 deletions src/ontology/reports/cl-edit.owl-obo-report.tsv
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Expand Up @@ -22,7 +22,6 @@ WARN missing_definition CL:0000109 IAO:0000115
WARN missing_definition CL:0000112 IAO:0000115
WARN missing_definition CL:0000114 IAO:0000115
WARN missing_definition CL:0000117 IAO:0000115
WARN missing_definition CL:0000120 IAO:0000115
WARN missing_definition CL:0000123 IAO:0000115
WARN missing_definition CL:0000130 IAO:0000115
WARN missing_definition CL:0000131 IAO:0000115
Expand Down Expand Up @@ -100,7 +99,6 @@ WARN missing_definition CL:0000423 IAO:0000115
WARN missing_definition CL:0000428 IAO:0000115
WARN missing_definition CL:0000435 IAO:0000115
WARN missing_definition CL:0000436 IAO:0000115
WARN missing_definition CL:0000441 IAO:0000115
WARN missing_definition CL:0000443 IAO:0000115
WARN missing_definition CL:0000445 IAO:0000115
WARN missing_definition CL:0000447 IAO:0000115
Expand Down Expand Up @@ -294,7 +292,6 @@ WARN missing_definition CL:1001286 IAO:0000115
WARN missing_definition CL:1001287 IAO:0000115
WARN missing_definition CL:1001319 IAO:0000115
WARN missing_definition CL:1001320 IAO:0000115
WARN missing_definition CL:1001428 IAO:0000115
WARN missing_definition CL:1001430 IAO:0000115
WARN missing_definition CL:1001431 IAO:0000115
WARN missing_definition CL:1001432 IAO:0000115
Expand Down Expand Up @@ -409,7 +406,6 @@ INFO missing_superclass CL:0001080 rdfs:subClassOf
INFO missing_superclass CL:0001081 rdfs:subClassOf
INFO missing_superclass CL:0001082 rdfs:subClassOf
INFO missing_superclass CL:0002062 rdfs:subClassOf
INFO missing_superclass CL:0002063 rdfs:subClassOf
INFO missing_superclass CL:0002067 rdfs:subClassOf
INFO missing_superclass CL:0002075 rdfs:subClassOf
INFO missing_superclass CL:0002089 rdfs:subClassOf
Expand Down Expand Up @@ -596,8 +592,10 @@ INFO missing_superclass CL:1000381 rdfs:subClassOf
INFO missing_superclass CL:1000382 rdfs:subClassOf
INFO missing_superclass CL:1000385 rdfs:subClassOf
INFO missing_superclass CL:1000398 rdfs:subClassOf
INFO missing_superclass CL:1000442 rdfs:subClassOf
INFO missing_superclass CL:1000494 rdfs:subClassOf
INFO missing_superclass CL:1000692 rdfs:subClassOf
INFO missing_superclass CL:1001428 rdfs:subClassOf
INFO missing_superclass CL:1001433 rdfs:subClassOf
INFO missing_superclass CL:1001516 rdfs:subClassOf
INFO missing_superclass CL:1001517 rdfs:subClassOf
Expand Down Expand Up @@ -793,5 +791,6 @@ INFO missing_superclass CL:4033021 rdfs:subClassOf
INFO missing_superclass CL:4033022 rdfs:subClassOf
INFO missing_superclass CL:4033025 rdfs:subClassOf
INFO missing_superclass CL:4033026 rdfs:subClassOf
INFO missing_superclass CL:4033040 rdfs:subClassOf
INFO missing_superclass CL:4033049 rdfs:subClassOf
INFO missing_superclass CL:4033050 rdfs:subClassOf
98 changes: 47 additions & 51 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" : "2023-05-22"
"val" : "2023-06-22"
} ],
"version" : "http://purl.obolibrary.org/obo/cl/releases/2023-05-22/subsets/blood_and_immune_upper_slim.owl"
"version" : "http://purl.obolibrary.org/obo/cl/releases/2023-06-22/subsets/blood_and_immune_upper_slim.owl"
},
"nodes" : [ {
"id" : "http://purl.obolibrary.org/obo/BFO_0000002",
Expand Down Expand Up @@ -947,7 +947,7 @@
"xrefs" : [ "GOC:tfm", "MESH:D013234" ]
},
"comments" : [ "This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’." ],
"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "animal stem cell"
Expand Down Expand Up @@ -1295,13 +1295,15 @@
"xrefs" : [ "ISBN:0517223651", "MESH:D005347", "http://en.wikipedia.org/wiki/Fibroblast" ]
},
"comments" : [ "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative." ],
"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"xrefs" : [ {
"val" : "BTO:0000452"
}, {
"val" : "CALOHA:TS-0362"
}, {
"val" : "FMA:63877"
}, {
"val" : "NCIT:C12482"
}, {
"val" : "VHOG:0001482"
} ],
Expand All @@ -1319,7 +1321,7 @@
"val" : "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.",
"xrefs" : [ "FB:ma", "GOC:tfm", "MESH:D004847" ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "epitheliocyte"
Expand Down Expand Up @@ -1389,6 +1391,7 @@
"val" : "A cell found predominately in the blood.",
"xrefs" : [ "GOC:add", "GOC:tfm" ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim" ],
"xrefs" : [ {
"val" : "FMA:62844"
}, {
Expand All @@ -1404,7 +1407,7 @@
"val" : "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.",
"xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0781735149" ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "T lymphocyte"
Expand Down Expand Up @@ -1956,7 +1959,7 @@
"xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "PMID:16213494", "PMID:1919437" ]
},
"comments" : [ "Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid." ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "histiocyte"
Expand Down Expand Up @@ -1986,7 +1989,7 @@
"val" : "A lymphocyte of B lineage that is capable of B cell mediated immunity.",
"xrefs" : [ "GOC:add", "GOC:tfm", "GO_REF:0000031", "ISBN:0781735149" ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "B lymphocyte"
Expand Down Expand Up @@ -2120,7 +2123,7 @@
"val" : "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).",
"xrefs" : [ "GOC:add", "ISBN:0781735149" ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"synonyms" : [ {
"pred" : "hasRelatedSynonym",
"val" : "interdigitating cell"
Expand Down Expand Up @@ -2173,10 +2176,6 @@
"xrefs" : [ "JB:jb" ]
}
}
}, {
"id" : "http://purl.obolibrary.org/obo/CL_0000530",
"lbl" : "primary neuron",
"type" : "CLASS"
}, {
"id" : "http://purl.obolibrary.org/obo/CL_0000540",
"lbl" : "neuron",
Expand All @@ -2187,7 +2186,7 @@
"xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ]
},
"comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma." ],
"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"synonyms" : [ {
"pred" : "hasExactSynonym",
"val" : "nerve cell"
Expand Down Expand Up @@ -2582,7 +2581,7 @@
"xrefs" : [ "GO_REF:0000031", "MESH:D009000" ]
},
"comments" : [ "Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid." ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"xrefs" : [ {
"val" : "BTO:0000876"
}, {
Expand Down Expand Up @@ -2690,6 +2689,8 @@
"val" : "FMA:62852"
}, {
"val" : "MESH:D007962"
}, {
"val" : "NCIT:C12529"
} ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/RO_0002175",
Expand Down Expand Up @@ -3611,7 +3612,7 @@
"val" : "A connective tissue cell found in bone.",
"xrefs" : [ "GOC:add", "GO_REF:0000034" ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"subsets" : [ "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/RO_0002175",
"val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606"
Expand Down Expand Up @@ -8952,6 +8953,9 @@
"val" : "vesicle trafficking"
} ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
"val" : "https:/geneontology/go-ontology/issues/25421"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
"val" : "GO:0006899"
}, {
Expand Down Expand Up @@ -9038,6 +9042,9 @@
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
"val" : "https:/geneontology/go-ontology/issues/24787"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0002161",
"val" : "http://purl.obolibrary.org/obo/NCBITaxon_4890"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
"val" : "biological_process"
Expand Down Expand Up @@ -14955,6 +14962,9 @@
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
"val" : "external"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
"val" : "uberon"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level",
"val" : "true"
Expand Down Expand Up @@ -34982,7 +34992,7 @@
"val" : "Anatomical system that consists of all blood and lymph vessels.",
"xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ],
"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ],
"xrefs" : [ {
"val" : "BTO:0001085"
}, {
Expand All @@ -35001,9 +35011,6 @@
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "consider merging with vasculature"
}, {
"pred" : "http://purl.obolibrary.org/obo/RO_0002175",
"val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606"
}, {
"pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001",
"val" : "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]."
Expand Down Expand Up @@ -36127,6 +36134,13 @@
"meta" : {
"comments" : [ "a subset of general classes related to specific cell types in the eye." ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim",
"lbl" : "general_cell_types_upper_slim",
"type" : "PROPERTY",
"meta" : {
"comments" : [ "a subset of general classes of cell types in the cell ontology." ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount",
"lbl" : "obsolete has_high_plasma_membrane_amount",
Expand Down Expand Up @@ -37428,7 +37442,7 @@
"obj" : "http://purl.obolibrary.org/obo/CL_0000556"
}, {
"sub" : "http://purl.obolibrary.org/obo/CL_0000233",
"pred" : "http://purl.obolibrary.org/obo/RO_0002215",
"pred" : "http://purl.obolibrary.org/obo/RO_0002216",
"obj" : "http://purl.obolibrary.org/obo/GO_0007596"
}, {
"sub" : "http://purl.obolibrary.org/obo/CL_0000234",
Expand Down Expand Up @@ -37610,10 +37624,6 @@
"sub" : "http://purl.obolibrary.org/obo/CL_0000473",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/CL_0000003"
}, {
"sub" : "http://purl.obolibrary.org/obo/CL_0000530",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/CL_0000540"
}, {
"sub" : "http://purl.obolibrary.org/obo/CL_0000540",
"pred" : "is_a",
Expand Down Expand Up @@ -39926,6 +39936,10 @@
"sub" : "http://purl.obolibrary.org/obo/GO_0001775",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/GO_0032501"
}, {
"sub" : "http://purl.obolibrary.org/obo/GO_0001775",
"pred" : "http://purl.obolibrary.org/obo/RO_0002160",
"obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208"
}, {
"sub" : "http://purl.obolibrary.org/obo/GO_0001816",
"pred" : "is_a",
Expand Down Expand Up @@ -41204,6 +41218,10 @@
"sub" : "http://purl.obolibrary.org/obo/GO_0016192",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/GO_0006810"
}, {
"sub" : "http://purl.obolibrary.org/obo/GO_0016192",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/GO_0009987"
}, {
"sub" : "http://purl.obolibrary.org/obo/GO_0016192",
"pred" : "http://purl.obolibrary.org/obo/RO_0002608",
Expand Down Expand Up @@ -45576,16 +45594,6 @@
"sub" : "http://purl.obolibrary.org/obo/UBERON_0002346",
"pred" : "http://purl.obolibrary.org/obo/BFO_0000051",
"obj" : "http://purl.obolibrary.org/obo/CL_0000133"
}, {
"sub" : "http://purl.obolibrary.org/obo/UBERON_0002346",
"pred" : "http://purl.obolibrary.org/obo/BFO_0000051",
"obj" : "http://purl.obolibrary.org/obo/CL_0000530",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://www.geneontology.org/formats/oboInOwl#source",
"val" : "ZFA"
} ]
}
}, {
"sub" : "http://purl.obolibrary.org/obo/UBERON_0002371",
"pred" : "is_a",
Expand Down Expand Up @@ -49405,22 +49413,6 @@
"propertyId" : "http://purl.obolibrary.org/obo/RO_0002215",
"fillerId" : "http://purl.obolibrary.org/obo/GO_0015671"
} ]
}, {
"definedClassId" : "http://purl.obolibrary.org/obo/CL_0000233",
"genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000763" ],
"restrictions" : [ {
"propertyId" : "http://purl.obolibrary.org/obo/RO_0000053",
"fillerId" : "http://purl.obolibrary.org/obo/PATO_0001405"
}, {
"propertyId" : "http://purl.obolibrary.org/obo/RO_0000053",
"fillerId" : "http://purl.obolibrary.org/obo/PATO_0001874"
}, {
"propertyId" : "http://purl.obolibrary.org/obo/RO_0002215",
"fillerId" : "http://purl.obolibrary.org/obo/GO_0007596"
}, {
"propertyId" : "http://purl.obolibrary.org/obo/RO_0002215",
"fillerId" : "http://purl.obolibrary.org/obo/GO_0008015"
} ]
}, {
"definedClassId" : "http://purl.obolibrary.org/obo/CL_0000234",
"genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000003" ],
Expand Down Expand Up @@ -52693,6 +52685,10 @@
"sub" : "http://purl.obolibrary.org/obo/GO_0000278",
"pred" : "http://purl.obolibrary.org/obo/RO_0002162",
"obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759"
}, {
"sub" : "http://purl.obolibrary.org/obo/GO_0001775",
"pred" : "http://purl.obolibrary.org/obo/RO_0002162",
"obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208"
}, {
"sub" : "http://purl.obolibrary.org/obo/GO_0002250",
"pred" : "http://purl.obolibrary.org/obo/RO_0002162",
Expand Down
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