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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Fixes #2705 Textual and logical defs - ureter and urethra urothelial cell #2734

Closed Caroline-99 closed 2 weeks ago

Caroline-99 commented 2 weeks ago

Added textual definition for the two terms + references AND removed redundant axioms

Caroline-99 commented 2 weeks ago

gogoeditdiff

github-actions[bot] commented 2 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/2024-11-06/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/2024-11-06/cl-base.owl` - Loaded from: `file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl` ### Ontology imports ### Ontology annotations ### ureter urothelial cell `http://purl.obolibrary.org/obo/CL_1000706` #### Removed - [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "Any urothelial cell that is part of some urothelium of ureter." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated" - [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) SubClassOf [ureteral cell](http://purl.obolibrary.org/obo/CL_1000601) - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" - [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) SubClassOf [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" #### Added - [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "A urothelial cell that is part of the urothelium of ureter." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36180582" - [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) SubClassOf [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) - [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) SubClassOf [ureteral cell](http://purl.obolibrary.org/obo/CL_1000601) ### urethra urothelial cell `http://purl.obolibrary.org/obo/CL_1001430` #### Removed - [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "Any urothelial cell that is part of some urethra urothelium." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated" - [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) SubClassOf [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" #### Added - [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) [IAO_0000115](http://purl.obolibrary.org/obo/IAO_0000115) "A urothelial cell that is part of the urethra urothelium. This cell plays a crucial role in maintaining the urethral barrier function, protecting against toxic substances in urine, sensing environmental changes, and defending against pathogen entry." - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23589830" - [hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36180582" - [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) SubClassOf [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731)
github-actions[bot] commented 2 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 ### ureter urothelial cell `http://purl.obolibrary.org/obo/CL_1000706` #### Removed - [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) SubClassOf [part of](http://purl.obolibrary.org/obo/BFO_0000050) some [urothelium of ureter](http://purl.obolibrary.org/obo/UBERON_0001254) - [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) SubClassOf [ureteral cell](http://purl.obolibrary.org/obo/CL_1000601) - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" - [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) SubClassOf [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" #### Added - [ureter urothelial cell](http://purl.obolibrary.org/obo/CL_1000706) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A urothelial cell that is part of the urothelium of ureter." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36180582" ### urethra urothelial cell `http://purl.obolibrary.org/obo/CL_1001430` #### Removed - [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) SubClassOf [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" - [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) SubClassOf [part of](http://purl.obolibrary.org/obo/BFO_0000050) some [urethra urothelium](http://purl.obolibrary.org/obo/UBERON_0004787) - [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) SubClassOf [urethra cell](http://purl.obolibrary.org/obo/CL_1001320) - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" #### Added - [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A urothelial cell that is part of the urethra urothelium. This cell plays a crucial role in maintaining the urethral barrier function, protecting against toxic substances in urine, sensing environmental changes, and defending against pathogen entry." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23589830" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36180582"