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obophenotype / cell-ontology

An ontology of cell types
https://obophenotype.github.io/cell-ontology/
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Fixes #2672 - textual and logical defs - parietal cell #2681

Closed Caroline-99 closed 1 month ago

Caroline-99 commented 1 month ago
Caroline-99 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/2024-10-18/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/2024-10-18/cl-simple.owl` - Loaded from: `file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl` ### Ontology imports ### Ontology annotations ### parietal cell `http://purl.obolibrary.org/obo/CL_0000162` #### Removed - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "oxyntic cell" - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651" #### Added - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "gastric parietal cell" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29263912" - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29263912" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31613538" - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "oxyntic cell" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Parietal_cell" - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by its pyramidal shape, abundant mitochondria, and a complex network of secretory canaliculi lined with microvilli. It secretes hydrochloric acid into the stomach lumen and produces intrinsic factor, essential for vitamin B12 absorption." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31670611" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31613538" - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) SubClassOf [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152)
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 ### parietal cell `http://purl.obolibrary.org/obo/CL_0000162` #### Removed - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "oxyntic cell" - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651" - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) SubClassOf [glandular secretory epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) SubClassOf [capable of](http://purl.obolibrary.org/obo/RO_0002215) some [acid secretion](http://purl.obolibrary.org/obo/GO_0046717) #### Added - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "gastric parietal cell" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29263912" - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29263912" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31613538" - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "oxyntic cell" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Parietal_cell" - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by its pyramidal shape, abundant mitochondria, and a complex network of secretory canaliculi lined with microvilli. It secretes hydrochloric acid into the stomach lumen and produces intrinsic factor, essential for vitamin B12 absorption." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31670611" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31613538" - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) SubClassOf [capable of](http://purl.obolibrary.org/obo/RO_0002215) some [gastric acid secretion](http://purl.obolibrary.org/obo/GO_0001696) - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) SubClassOf [part of](http://purl.obolibrary.org/obo/BFO_0000050) some [fundic gastric gland](http://purl.obolibrary.org/obo/UBERON_0010038) - [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [microvillus](http://purl.obolibrary.org/obo/GO_0005902)
Caroline-99 commented 1 month ago

'fundic gastric gland' doesn't appear to be a commonly used term, please change to gastric gland (refers to glands in all parts of stomach)or fundic gland (refers to gland specifically in the fundus of the stomach). Everything else looks great!

@JABelfiore I have just checked and there is no an uberon term for fundic gland. Fundic gland is used as a synonym to fundic gastric gland in Uberon and is defined as The fundus glands (or fundic glands, or gastric glands) are found in the body and fundus of the stomach. They are simple tubes, two or more of which open into a single duct. Would you be okay with me using the term fundic gastric gland? Or do you want me to change it to gastric gland ?

JABelfiore commented 1 month ago

'fundic gastric gland' doesn't appear to be a commonly used term, please change to gastric gland (refers to glands in all parts of stomach)or fundic gland (refers to gland specifically in the fundus of the stomach). Everything else looks great!

@JABelfiore I have just checked and there is no an uberon term for fundic gland. Fundic gland is used as a synonym to fundic gastric gland in Uberon and is defined as The fundus glands (or fundic glands, or gastric glands) are found in the body and fundus of the stomach. They are simple tubes, two or more of which open into a single duct. Would you be okay with me using the term fundic gastric gland? Or do you want me to change it to gastric gland ?

If its in uberon happy to keep as is