kidney afferent arteriole cell and 2 subclasses text def added #2466

JABelfiore · 2024-07-25T14:33:07Z

text def added for grouping term kidney afferent arteriole cell and 2 subclasses

dosumis · 2024-07-25T16:03:52Z

#gogoeditdiff

github-actions · 2024-07-25T16:08:43Z

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/2024-08-09/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/2024-08-09/cl-simple.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

kidney afferent arteriole cell `http://purl.obolibrary.org/obo/CL_1001006`

Removed

kidney afferent arteriole cell definition "Any kidney arterial blood vessel cell that is part of some renal afferent arteriole."
- database_cross_reference "FBC:Autogenerated"

Added

kidney afferent arteriole cell definition "An endothelial cell which is part of the afferent arteriole in the kidney. This cell is responsible for maintaining renal blood flow and glomerular filtration rate."
- database_cross_reference "PMID:24066938"
- database_cross_reference "PMID:25834230"
- database_cross_reference "PMID:16990493"
- database_cross_reference "PMID:22733355"

kidney afferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001096`

Removed

kidney afferent arteriole endothelial cell definition "Any endothelial cell that is part of some renal afferent arteriole."
- database_cross_reference "FBC:Autogenerated"

Added

kidney afferent arteriole endothelial cell definition "An endothelial cell that lines the interior surface of the afferent arteriole and maintains vascular tone. This cell responds to changing ion concentrations and blood pressure by releasing vasoactive substances, in order to regulate blood flow into the glomeruli, which is essential for glomerular filtration."
- database_cross_reference "PMID:24066938"
- database_cross_reference "PMID:25834230"
- database_cross_reference "PMID:16990493"
- database_cross_reference "PMID:22733355"

kidney afferent arteriole smooth muscle cell `http://purl.obolibrary.org/obo/CL_1001097`

Removed

kidney afferent arteriole smooth muscle cell definition "Any smooth muscle cell that is part of some renal afferent arteriole."
- database_cross_reference "FBC:Autogenerated"

Added

kidney afferent arteriole smooth muscle cell definition "A smooth muscle cell found in the wall of the afferent arteriole. This cell contracts and relaxes in response to changes in blood pressure, a process known as a myogenic response, to alter artery diameter and regulate blood flow into the glomeruli."
- database_cross_reference "PMID:24066938"
- database_cross_reference "PMID:25834230"
- database_cross_reference "PMID:16990493"
- database_cross_reference "PMID:22733355"

github-actions · 2024-07-25T16:08:45Z

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

kidney afferent arteriole cell `http://purl.obolibrary.org/obo/CL_1001006`

Added

kidney afferent arteriole cell definition "An endothelial cell which is part of the afferent arteriole in the kidney. This cell is responsible for maintaining renal blood flow and glomerular filtration rate."
- database_cross_reference "PMID:24066938"
- database_cross_reference "PMID:25834230"
- database_cross_reference "PMID:16990493"
- database_cross_reference "PMID:22733355"

kidney afferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001096`

Added

kidney afferent arteriole endothelial cell definition "An endothelial cell that lines the interior surface of the afferent arteriole and maintains vascular tone. This cell responds to changing ion concentrations and blood pressure by releasing vasoactive substances, in order to regulate blood flow into the glomeruli, which is essential for glomerular filtration."
- database_cross_reference "PMID:24066938"
- database_cross_reference "PMID:25834230"
- database_cross_reference "PMID:16990493"
- database_cross_reference "PMID:22733355"

kidney afferent arteriole smooth muscle cell `http://purl.obolibrary.org/obo/CL_1001097`

Added

kidney afferent arteriole smooth muscle cell definition "A smooth muscle cell found in the wall of the afferent arteriole. This cell contracts and relaxes in response to changes in blood pressure, a process known as a myogenic response, to alter artery diameter and regulate blood flow into the glomeruli."
- database_cross_reference "PMID:24066938"
- database_cross_reference "PMID:25834230"
- database_cross_reference "PMID:16990493"
- database_cross_reference "PMID:22733355"

dosumis · 2024-07-25T16:09:42Z

Looks like qc fail is because date format is wrong for new terms. Can you check setup details in obook?

Update: as no new terms and no edits to dates, I don't know what is causing the date format QC error. @anitacaron - any ideas?

dosumis · 2024-07-25T17:28:05Z

On style: avoid typically especially in the genus/differentia part of the def.

The defs should refer specifically to the afferent arteriole - much more specific than renal vasculature. Linking to a good schematic image could help clarify.

The more general term is just a location based grouping term (we have too many of these in the Kidney), so can have a much less detailed Def.

Can you find a way to more cleanly distinguish between the two subtypes in their defs?

anitacaron

Could you please be more specific in the PR's title?

src/ontology/cl-edit.owl

AvolaAmg · 2024-07-26T12:29:08Z

src/ontology/cl-edit.owl

@@ -27225,6 +27227,7 @@ SubClassOf(obo:CL_1001068 obo:CL_1000893)

 # Class: obo:CL_1001096 (kidney afferent arteriole endothelial cell)

+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16990493") Annotation(oboInOwl:hasDbXref "PMID:22733355") Annotation(oboInOwl:hasDbXref "PMID:24066938") Annotation(oboInOwl:hasDbXref "PMID:25834230") obo:IAO_0000115 obo:CL_1001096 "An endothelial cell typically found in renal vasculature which is primarily responsible for maintaining renal blood flow and glomerular filtration rate. This cell type regulates blood pressure and fluid balance by controlling the expansion or contraction of the arteriole before the glomerulus through autoregulation mechanisms such as the myogenic response and tubuloglomerular feedback.")


References all good!
Just as a suggestion I would change a bit the text definition and remove 'typically found' but substitute it with cell location
for instance:

An endothelial cell which is part of the arteriole in the renal vasculature
or something similar

AvolaAmg · 2024-07-26T13:02:00Z

src/ontology/cl-edit.owl

@@ -30948,7 +30952,7 @@ SubClassOf(obo:CL_4030039 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0070006))

 # Class: obo:CL_4030040 (endometrial ciliated epithelial cell)

-AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(oboInOwl:hasDbXref "PMID:37999981") Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") Annotation(oboInOwl:hasDbXref "doi:10.1016/j.coemr.2024.100503") obo:IAO_0000115 obo:CL_4030040 "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of 9+2 motile cilia on its apical surface, which facilitates the movement of mucus across the endometrial surface.")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31290979") Annotation(oboInOwl:hasDbXref "PMID:37999981") Annotation(oboInOwl:hasDbXref "doi:10.1016/j.coemr.2024.100503") Annotation(oboInOwl:hasDbXref "doi:10.1038/s41591-020-1040-z") Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells") obo:IAO_0000115 obo:CL_4030040 "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of 9+2 motile cilia on its apical surface, which facilitates the movement of mucus across the endometrial surface.")


you can change this reference DOI: 10.1016/j.coemr.2024.100503 for its respective PMID: 38293616 and this reference DOI: 10.1038/s41591-020-1040-z for its respective PMID: 32929266

dosumis · 2024-08-01T21:17:33Z

#gogoeditdiff

github-actions · 2024-08-01T21:18:43Z

Your branch is 2 commit/s behind, please update your branch.

Caroline-99 · 2024-08-09T13:45:09Z

#gogoeditdiff

text def added

52bba85

text def added for grouping term kidney afferent arteriole cell and 2 subclasses

JABelfiore linked an issue Jul 25, 2024 that may be closed by this pull request

[Text def] kidney afferent arteriole cell #2264

Closed

JABelfiore self-assigned this Jul 25, 2024

JABelfiore requested review from AvolaAmg and Caroline-99 July 25, 2024 14:33

anitacaron requested changes Jul 26, 2024

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AvolaAmg reviewed Jul 26, 2024

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JABelfiore changed the title ~~text def added~~ text def added kidney afferent arteriole cell and 2 subclasses Jul 29, 2024

JABelfiore changed the title ~~text def added kidney afferent arteriole cell and 2 subclasses~~ kidney afferent arteriole cell and 2 subclasses text def added Jul 29, 2024

JABelfiore added 3 commits August 8, 2024 10:35

subclass text defs refined

c1e6ef2

removed 'type' and glomerulus specification in general def

8f59459

plurals removed for alignment

03bfc6c

Merge branch 'master' into 2264-text-def-kidney-afferent-arteriole-cell

4706e52

Caroline-99 approved these changes Aug 9, 2024

View reviewed changes

anitacaron approved these changes Aug 13, 2024

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JABelfiore merged commit 1c70c07 into master Aug 13, 2024
1 check passed

JABelfiore deleted the 2264-text-def-kidney-afferent-arteriole-cell branch August 13, 2024 12:59

		@@ -27225,6 +27227,7 @@ SubClassOf(obo:CL_1001068 obo:CL_1000893)

		# Class: obo:CL_1001096 (kidney afferent arteriole endothelial cell)

		AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16990493") Annotation(oboInOwl:hasDbXref "PMID:22733355") Annotation(oboInOwl:hasDbXref "PMID:24066938") Annotation(oboInOwl:hasDbXref "PMID:25834230") obo:IAO_0000115 obo:CL_1001096 "An endothelial cell typically found in renal vasculature which is primarily responsible for maintaining renal blood flow and glomerular filtration rate. This cell type regulates blood pressure and fluid balance by controlling the expansion or contraction of the arteriole before the glomerulus through autoregulation mechanisms such as the myogenic response and tubuloglomerular feedback.")

kidney afferent arteriole cell and 2 subclasses text def added #2466

kidney afferent arteriole cell and 2 subclasses text def added #2466

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JABelfiore commented Jul 25, 2024

dosumis commented Jul 25, 2024

github-actions bot commented Jul 25, 2024 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

kidney afferent arteriole cell http://purl.obolibrary.org/obo/CL_1001006

Removed

Added

kidney afferent arteriole endothelial cell http://purl.obolibrary.org/obo/CL_1001096

Removed

Added

kidney afferent arteriole smooth muscle cell http://purl.obolibrary.org/obo/CL_1001097

Removed

Added

github-actions bot commented Jul 25, 2024 • edited Loading

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

kidney afferent arteriole cell http://purl.obolibrary.org/obo/CL_1001006

Added

kidney afferent arteriole endothelial cell http://purl.obolibrary.org/obo/CL_1001096

Added

kidney afferent arteriole smooth muscle cell http://purl.obolibrary.org/obo/CL_1001097

Added

dosumis commented Jul 25, 2024 • edited Loading

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dosumis commented Aug 1, 2024

github-actions bot commented Aug 1, 2024

Caroline-99 commented Aug 9, 2024

github-actions bot commented Jul 25, 2024 •

edited

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kidney afferent arteriole cell `http://purl.obolibrary.org/obo/CL_1001006`

kidney afferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001096`

kidney afferent arteriole smooth muscle cell `http://purl.obolibrary.org/obo/CL_1001097`

github-actions bot commented Jul 25, 2024 •

edited

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kidney afferent arteriole cell `http://purl.obolibrary.org/obo/CL_1001006`

kidney afferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001096`

kidney afferent arteriole smooth muscle cell `http://purl.obolibrary.org/obo/CL_1001097`

dosumis commented Jul 25, 2024 •

edited

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