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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Fixes #2586 NTR-enteroendocrine progenitor #2588

Closed Caroline-99 closed 1 month ago

Caroline-99 commented 1 month ago

Added a new term with textual and logical defs, synonyms and references

dosumis commented 1 month ago

gogoeditdiff

github-actions[bot] commented 1 month 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/2024-09-23/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/2024-09-23/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 enteroendocrine progenitor `http://purl.obolibrary.org/obo/CL_4052006` #### Added - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal enteroendocrine progenitor" - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [date](http://purl.org/dc/terms/date) "2024-09-20T12:13:26Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "EEC progenitor is also present in other organisms ie. flies have EEC progenitors but don't have intestinal crypts and don't express the same markers - instead they are Dl+ Pros+." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25670791" - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "EEC Progenitor" - [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) "PMID:31756561" - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the crypt of Lieberkuhn, originating from intestinal stem cells and giving rise to enteroendocrine cells (EECs). In mouse and human, it expresses markers like Neurog3, and has the ability to proliferate and differentiate into various EEC subtypes. Its proliferative potential supports both crypt growth and cell proliferation, distinguishing it from fully differentiated EECs." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32531023" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35913117" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-021-27901-5" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31756561" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38260422" - Class: [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563)
github-actions[bot] commented 1 month 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 enteroendocrine progenitor `http://purl.obolibrary.org/obo/CL_4052006` #### Added - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal enteroendocrine progenitor" - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [date](http://purl.org/dc/terms/date) "2024-09-20T12:13:26Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "EEC progenitor is also present in other organisms ie. flies have EEC progenitors but don't have intestinal crypts and don't express the same markers - instead they are Dl+ Pros+." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25670791" - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "EEC Progenitor" - [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) "PMID:31756561" - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the crypt of Lieberkuhn, originating from intestinal stem cells and giving rise to enteroendocrine cells (EECs). In mouse and human, it expresses markers like Neurog3, and has the ability to proliferate and differentiate into various EEC subtypes. Its proliferative potential supports both crypt growth and cell proliferation, distinguishing it from fully differentiated EECs." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32531023" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35913117" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-021-27901-5" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31756561" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38260422" - Class: [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [part of](http://purl.obolibrary.org/obo/BFO_0000050) some [epithelium of crypt of Lieberkuhn](http://purl.obolibrary.org/obo/UBERON_0011184) - [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563)
Caroline-99 commented 1 month ago

gogoeditdiff