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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Fixes #2652 - Added GO terms for colonocytes + Updated definition #2741

Closed Caroline-99 closed 3 weeks ago

Caroline-99 commented 3 weeks ago

Fixes #2652

Added the GO terms for colonocytes and updated the textual definition and references to align with the new logical axioms

Note: I have imported GO:0019626 - short-chain fatty acid catabolic process. However, I merged the imports into a different branch.

dosumis commented 3 weeks ago

gogoeditdiff

github-actions[bot] commented 3 weeks ago
Here's a diff of how these changes impact the classified ontology (on -base file): # Ontology comparison ## Left - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-base.owl` - Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-11-08/cl-base.owl` - Loaded from: `file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-master.owl/cl-base.owl` ## Right - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-base.owl` - Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-11-08/cl-base.owl` - Loaded from: `file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl` ### Ontology imports ### Ontology annotations ### GO_0019626 `http://purl.obolibrary.org/obo/GO_0019626` #### Added - Class: [GO_0019626](http://purl.obolibrary.org/obo/GO_0019626) ### GO_0035377 `http://purl.obolibrary.org/obo/GO_0035377` #### Added - Class: [GO_0035377](http://purl.obolibrary.org/obo/GO_0035377) ### colonocyte `http://purl.obolibrary.org/obo/CL_1000347` #### Removed - [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "A columnar cell of the colon that is part of the colonic epithelium." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) SubClassOf [enterocyte of epithelium of large intestine](http://purl.obolibrary.org/obo/CL_0002071) - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" #### Added - [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte (absorptive epithelial cell) of the colonic epithelium, characterized by a columnar shape. This cell is responsible for the absorption, transport, and metabolization of short-chain fatty acids (SCFAs) produced by gut bacteria, as well as the transport and absorption of water and electrolytes." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23821742" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16870803" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0035377](http://purl.obolibrary.org/obo/GO_0035377) - [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) SubClassOf [enterocyte of epithelium of large intestine](http://purl.obolibrary.org/obo/CL_0002071) - [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0019626](http://purl.obolibrary.org/obo/GO_0019626)
github-actions[bot] commented 3 weeks 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 ### GO_0019626 `http://purl.obolibrary.org/obo/GO_0019626` #### Added - Class: [GO_0019626](http://purl.obolibrary.org/obo/GO_0019626) ### colonocyte `http://purl.obolibrary.org/obo/CL_1000347` #### Removed - [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A columnar cell of the colon that is part of the colonic epithelium." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389" - [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) SubClassOf [enterocyte of epithelium of large intestine](http://purl.obolibrary.org/obo/CL_0002071) - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" #### Added - [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte (absorptive epithelial cell) of the colonic epithelium, characterized by a columnar shape. This cell is responsible for the absorption, transport, and metabolization of short-chain fatty acids (SCFAs) produced by gut bacteria, as well as the transport and absorption of water and electrolytes." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16870803" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23821742" - [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) SubClassOf [capable of](http://purl.obolibrary.org/obo/RO_0002215) some [transepithelial water transport](http://purl.obolibrary.org/obo/GO_0035377) - [colonocyte](http://purl.obolibrary.org/obo/CL_1000347) SubClassOf [capable of](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0019626](http://purl.obolibrary.org/obo/GO_0019626)