Addresses #1892 NTR for respiratory new terms #1896
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Addresses #1892 NTR for respiratory new terms
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#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -simple file):Ontology comparisonLeft
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Ontology importsOntology annotationsCL_4033016
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationsCL_4033016
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| AnnotationAssertion(rdfs:label obo:CL_4033025 "perichondrial fibroblast") | ||
| EquivalentClasses(obo:CL_4033025 ObjectIntersectionOf(obo:CL_0000057 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008305))) | ||
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| # Class: obo:CL_4033026 (lung perichondrial fibroblast) |
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Unsure if there is a specific reason "lung" is used here and "airway" used in other terms. Ref describes "PC-fibro around the airway cartilage".
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Thank you for your comment, @bvarner-ebi. Initially I was considering airway for this same reason, however in the text you are quoting it is describing the localisation of PC-fibro in an image showing an airway. That doesn't exclude that it is also present in other pulmonary parts, as this cell is "enriched in the airways", but that doesn't mean it is exclusive, as cartilage it is not exclusive around the airways: "Cartilage (hyaline type) has the function of maintaining airway patency and it also serves for the attachment of local muscle and connective tissue."
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If this cell type does exist in lung tissue, would you please add that reference to the term. The quote mentioned above refers to the airways as well.
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Looking at the scRNA-seq data, the majority of cells identified as PC-fibro came from airway tissue, but a small proportion (~0'4%) was found in parenchymal tissue:
Of course the number of cells is very small and they can be false positives (in the umap they don't map with the PC-fibro cluster) or a different kind of perichondrial cells. In the later case, it makes more sense to use 'lung perichondrial fibroblast' to encompass all PC-fibro found in the lung.
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If that is from the dbxref, and if Par stands for parenchyma, it seems reasonable.
Thank you for all your comments , @bvarner-ebi. |
This commit removes 'serous secreting cell of trachea gland' as this cell type is already present in the ontology
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'serous secreting cell of trachea gland' will no longer be a new term as this cell type exists as CL:1000330 "serous cell of epithelium of trachea". All serous cells in airways are found in submucosal gland. Therefore, a separate ticket will be issued to update names, textual definitions and logical definitions for serous cells. |
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Thank you, @bvarner-ebi. I was waiting to see if there were more edits to do everything together. |
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#gogoeditdiff |
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Addresses #1892 NTR for respiratory new terms