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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Fixes #2578 -NTR- fibroblastic reticular cell #2581

Closed Caroline-99 closed 6 days ago

Caroline-99 commented 1 week ago
Caroline-99 commented 1 week ago

gogoeditdiff

github-actions[bot] commented 1 week ago
Here's a diff of how these changes impact the classified ontology (on -simple file): # Ontology comparison ## Left - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-simple.owl` - Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-09-19/cl-simple.owl` - Loaded from: `file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl` ## Right - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-simple.owl` - Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-09-19/cl-simple.owl` - Loaded from: `file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl` ### Ontology imports ### Ontology annotations ### intestinal fibroblastic reticular cell `http://purl.obolibrary.org/obo/CL_4052004` #### Added - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal fibroblastic reticular cell" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "solitary intestinal lymphoid tissue (SILT) FRCs" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "doi:/10.1038/s41467-022-29734-2" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [date](http://purl.org/dc/terms/date) "2024-09-19T11:22:18Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "FRC" - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-022-29734-2" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "Ccl19-expressing FRCs" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-022-29734-2" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized fibroblastic reticular cell that is part of gut-associated lymphoid tissues(GALT), responsible for forming a structural network that facilitates immune cell interactions. This cell is found in Peyer's patches, cryptopatches, and isolated lymphoid follicles. It plays crucial roles in maintaining intestinal immunity by controlling innate lymphoid cell homeostasis and function, organizing lymphoid structures, and contributing to intestinal microbiome balance." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33707780" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-022-29734-2" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gut-associated secondary lymphoid organs (SLOs) FRCs" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-022-29734-2" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [description](http://purl.org/dc/terms/description) "Intestinal fibroblastic reticular cells (FRCs) develop from both perivascular and subepithelial progenitors during Peyer's patch formation. Intestinal fibroblastic reticular cells express key markers such as CCL19, CCL21, CXCL13, TNFSF13B (also known as BAFF), and produce IL-7, which are important for their immune regulatory functions and the organization of lymphoid structures." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33707780" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-022-29734-2" - Class: [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) SubClassOf [fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_0009101)
github-actions[bot] commented 1 week ago
Here's a diff of your edit file (unreasoned) # Ontology comparison ## Left - Ontology IRI: `http://purl.obolibrary.org/obo/cl.owl` - Version IRI: *None* - Loaded from: `file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl` ## Right - Ontology IRI: `http://purl.obolibrary.org/obo/cl.owl` - Version IRI: *None* - Loaded from: `file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl` ### Ontology imports ### Ontology annotations ### intestinal fibroblastic reticular cell `http://purl.obolibrary.org/obo/CL_4052004` #### Added - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal fibroblastic reticular cell" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "solitary intestinal lymphoid tissue (SILT) FRCs" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "doi:/10.1038/s41467-022-29734-2" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [date](http://purl.org/dc/terms/date) "2024-09-19T11:22:18Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "FRC" - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-022-29734-2" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "Ccl19-expressing FRCs" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-022-29734-2" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized fibroblastic reticular cell that is part of gut-associated lymphoid tissues(GALT), responsible for forming a structural network that facilitates immune cell interactions. This cell is found in Peyer's patches, cryptopatches, and isolated lymphoid follicles. It plays crucial roles in maintaining intestinal immunity by controlling innate lymphoid cell homeostasis and function, organizing lymphoid structures, and contributing to intestinal microbiome balance." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33707780" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-022-29734-2" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gut-associated secondary lymphoid organs (SLOs) FRCs" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-022-29734-2" - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [description](http://purl.org/dc/terms/description) "Intestinal fibroblastic reticular cells (FRCs) develop from both perivascular and subepithelial progenitors during Peyer's patch formation. Intestinal fibroblastic reticular cells express key markers such as CCL19, CCL21, CXCL13, TNFSF13B (also known as BAFF), and produce IL-7, which are important for their immune regulatory functions and the organization of lymphoid structures." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33707780" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-022-29734-2" - Class: [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) SubClassOf [fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_0009101) - [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) SubClassOf [part of](http://purl.obolibrary.org/obo/BFO_0000050) some [gut-associated lymphoid tissue](http://purl.obolibrary.org/obo/UBERON_0001962)