juxtaglomerular complex cell merged with kidney granular cell #3109

JABelfiore · 2025-05-02T12:57:20Z

Merge juxtaglomerular complex cell into kidney granular cell
Equivalent to will be combined in the following way: 'kidney cortical cell' and ('part of' some 'juxtaglomerular apparatus') and ('capable of' some 'renin secretion into blood stream') and keep also SubClassOf smooth muscle cell. All other logical axioms should be inferred.
JG exact synonym should be changed to related with annotation property abbreviation and with a reference.
New exact synonym: juxtaglomerular complex cell
Remove juxtaglomerular complex cell from the kidney_slim, checking if it affects any other term

aleixpuigb

Changes in the slim needs to be done in src/templates/kidney_upper_slim.csv, not in the owl file directly.

This reverts commit 0d5cdd0.

This reverts commit d9172ce.

aleixpuigb · 2025-05-21T14:16:59Z

#gogoeditdiff

github-actions · 2025-05-21T14:23:17Z

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/2025-05-21/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/2025-05-21/cl-base.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

OMO_0003000 `http://purl.obolibrary.org/obo/OMO_0003000`

Added

AnnotationProperty: OMO_0003000

extraglomerular mesangial cell `http://purl.obolibrary.org/obo/CL_0002173`

Removed

extraglomerular mesangial cell SubClassOf obsolete juxtaglomerular complex cell
- is_inferred "true"

Added

extraglomerular mesangial cell SubClassOf kidney granular cell
- is_inferred "true"

kidney granular cell `http://purl.obolibrary.org/obo/CL_0000648`

Removed

kidney granular cell hasExactSynonym "JG cell"
kidney granular cell EquivalentTo secretory cell and (BFO_0000050 some UBERON_0002113) and (RO_0002215 some GO_0002001)
kidney granular cell SubClassOf obsolete juxtaglomerular complex cell

Added

kidney granular cell hasExactSynonym "juxtaglomerulus cell"
- hasDbXref "GO:0072052"
kidney granular cell hasExactSynonym "juxtaglomerular complex cell"
kidney granular cell hasRelatedSynonym "JG cell"
- hasDbXref "doi:10.1007/s00424-012-1126-7"
- OMO_0003000 ""
kidney granular cell contributor 0009-0005-7919-4905
kidney granular cell hasDbXref "KUPO:0001028"
kidney granular cell date "2025-05-02T12:33:27Z"^^dateTime
kidney granular cell EquivalentTo kidney cortical cell and (BFO_0000050 some UBERON_0002303) and (RO_0002215 some GO_0002001)
kidney granular cell SubClassOf kidney cortical cell
kidney granular cell SubClassOf BFO_0000050 some UBERON_0002303

macula densa epithelial cell `http://purl.obolibrary.org/obo/CL_1000850`

Removed

macula densa epithelial cell SubClassOf obsolete juxtaglomerular complex cell
- is_inferred "true"

Added

macula densa epithelial cell SubClassOf secretory epithelial cell
macula densa epithelial cell SubClassOf kidney granular cell
- is_inferred "true"

obsolete juxtaglomerular complex cell `http://purl.obolibrary.org/obo/CL_1000618`

Removed

obsolete juxtaglomerular complex cell IAO_0000115 "Any kidney cortical cell that is part of some juxtaglomerular apparatus."
- hasDbXref "FBC:Autogenerated"
obsolete juxtaglomerular complex cell label "juxtaglomerular complex cell"
obsolete juxtaglomerular complex cell hasExactSynonym "juxtaglomerulus cell"
- hasDbXref "GO:0072052"
obsolete juxtaglomerular complex cell inSubset kidney_upper_slim
obsolete juxtaglomerular complex cell EquivalentTo kidney cortical cell and (BFO_0000050 some UBERON_0002303)
obsolete juxtaglomerular complex cell SubClassOf kidney cortical cell
- is_inferred "true"
obsolete juxtaglomerular complex cell SubClassOf BFO_0000050 some UBERON_0002303

Added

obsolete juxtaglomerular complex cell IAO_0000233 "[Text def] expanding the definition of the juxtaglomerular complex cells #2471"
obsolete juxtaglomerular complex cell comment "merged with kidney granular cell"
obsolete juxtaglomerular complex cell IAO_0100001 kidney granular cell
obsolete juxtaglomerular complex cell label "obsolete juxtaglomerular complex cell"
obsolete juxtaglomerular complex cell deprecated true

github-actions · 2025-05-21T14:23:20Z

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

extraglomerular mesangial cell `http://purl.obolibrary.org/obo/CL_0002173`

Removed

extraglomerular mesangial cell SubClassOf obsolete juxtaglomerular complex cell
- is_inferred "true"

Added

extraglomerular mesangial cell SubClassOf kidney granular cell
- is_inferred "true"

kidney granular cell `http://purl.obolibrary.org/obo/CL_0000648`

Removed

kidney granular cell has exact synonym "JG cell"
kidney granular cell EquivalentTo secretory cell and (part of some kidney) and (capable of some renin secretion into blood stream)
kidney granular cell SubClassOf part of some juxtaglomerular apparatus

Added

kidney granular cell has exact synonym "juxtaglomerulus cell"
- database_cross_reference "GO:0072052"
kidney granular cell has exact synonym "juxtaglomerular complex cell"
kidney granular cell has_related_synonym "JG cell"
- abbreviation ""
- database_cross_reference "doi:10.1007/s00424-012-1126-7"
kidney granular cell contributor 0009-0005-7919-4905
kidney granular cell database_cross_reference "KUPO:0001028"
kidney granular cell date "2025-05-02T12:33:27Z"^^dateTime
kidney granular cell EquivalentTo kidney cortical cell and (part of some juxtaglomerular apparatus) and (capable of some renin secretion into blood stream)

macula densa epithelial cell `http://purl.obolibrary.org/obo/CL_1000850`

Removed

macula densa epithelial cell SubClassOf obsolete juxtaglomerular complex cell
- is_inferred "true"

Added

macula densa epithelial cell SubClassOf kidney granular cell
- is_inferred "true"

obsolete juxtaglomerular complex cell `http://purl.obolibrary.org/obo/CL_1000618`

Removed

obsolete juxtaglomerular complex cell label "juxtaglomerular complex cell"
obsolete juxtaglomerular complex cell has exact synonym "juxtaglomerulus cell"
- database_cross_reference "GO:0072052"
obsolete juxtaglomerular complex cell EquivalentTo kidney cortical cell and (part of some juxtaglomerular apparatus)
obsolete juxtaglomerular complex cell SubClassOf kidney cortical cell
- is_inferred "true"
obsolete juxtaglomerular complex cell SubClassOf part of some juxtaglomerular apparatus

Added

obsolete juxtaglomerular complex cell term tracker item "[Text def] expanding the definition of the juxtaglomerular complex cells #2471"
obsolete juxtaglomerular complex cell comment "merged with kidney granular cell"
obsolete juxtaglomerular complex cell term replaced by kidney granular cell
obsolete juxtaglomerular complex cell label "obsolete juxtaglomerular complex cell"
obsolete juxtaglomerular complex cell deprecated true

aleixpuigb

Please, see inline comments.

aleixpuigb · 2025-05-21T14:34:27Z

src/ontology/cl-edit.owl

+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GO:0072052") oboInOwl:hasExactSynonym obo:CL_0000648 "juxtaglomerulus cell")
 AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000648 "renin secreting cell")
+AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000648 "juxtaglomerular complex cell")
+AnnotationAssertion(Annotation(obo:OMO_0003000 "") Annotation(oboInOwl:hasDbXref "doi:10.1007/s00424-012-1126-7") oboInOwl:hasRelatedSynonym obo:CL_0000648 "JG cell")


The annotation property for abbreviation is not used correctly.

aleixpuigb · 2025-05-21T14:44:44Z

src/ontology/cl-edit.owl

+AnnotationAssertion(Annotation(obo:OMO_0003000 "") Annotation(oboInOwl:hasDbXref "doi:10.1007/s00424-012-1126-7") oboInOwl:hasRelatedSynonym obo:CL_0000648 "JG cell")
 AnnotationAssertion(rdfs:label obo:CL_0000648 "kidney granular cell")
-EquivalentClasses(obo:CL_0000648 ObjectIntersectionOf(obo:CL_0000151 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002113) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0002001)))
+EquivalentClasses(obo:CL_0000648 ObjectIntersectionOf(obo:CL_0002681 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002303) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0002001)))


I agree with the change since it is a cortical cell, and 'secreting cell' is reasoned. In the textual definition, people who know kidney anatomy will know that the glomerulus is part of the cortex. However, there might be people that don't know and might want to have it included in the textual definition (maybe in bracket after glomerulus). What do you think?

aleixpuigb · 2025-05-22T14:28:01Z

src/ontology/cl-edit.owl


-AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:cvs") Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:11457727") obo:IAO_0000115 obo:CL_0000648 "A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation.")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:cvs") Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:11457727") obo:IAO_0000115 obo:CL_0000648 "A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus (a structure within the renal cortex). While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation.")
+AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1007/s00424-012-1126-7") obo:OMO_0003000 obo:CL_0000648 "JG cell")


Please, add this term (JG cell) as related synonym, and add the AP has_synonym_type 'abbreviation' (entity IRI).

…-merge" This reverts commit 3bd0091, reversing changes made to e17b36e.

aleixpuigb · 2025-06-19T09:12:32Z

I would recommend to close this PR and start again, it has too many unrelated changes.

github-actions · 2025-07-20T03:00:11Z

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so.

juxtaglomerular complex cell merged with kidney granular cell

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JABelfiore linked an issue May 2, 2025 that may be closed by this pull request

[Text def] expanding the definition of the juxtaglomerular complex cells #2471

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JABelfiore added 2 commits May 2, 2025 14:20

Update kidney_upper_slim.owl

50cb90e

" issue amend

e9a3431

JABelfiore removed a link to an issue May 2, 2025

[Text def] expanding the definition of the juxtaglomerular complex cells #2471

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JABelfiore linked an issue May 2, 2025 that may be closed by this pull request

[Text def] expanding the definition of the juxtaglomerular complex cells #2471

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JABelfiore added 2 commits May 2, 2025 15:00

Update cl-edit.owl

d2d8261

deprecated true

c7de84a

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JABelfiore requested a review from aleixpuigb May 2, 2025 14:28

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JABelfiore and others added 9 commits May 8, 2025 11:25

Update kidney_upper_slim.owl

0d5cdd0

Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge

f0cb94c

Update kidney_upper_slim.tsv

d9172ce

Revert "Update kidney_upper_slim.owl"

51e8251

This reverts commit 0d5cdd0.

Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge

4e07d99

Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge

c340c06

Revert "Update kidney_upper_slim.tsv"

8fd6c3a

This reverts commit d9172ce.

Update kidney_upper_slim.csv

5e47f45

update slims

bb0c612

JABelfiore requested a review from aleixpuigb May 12, 2025 15:24

JABelfiore and others added 2 commits May 15, 2025 13:34

Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge

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Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge

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aleixpuigb requested changes May 21, 2025

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JABelfiore and others added 2 commits May 22, 2025 14:00

Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge

099f5bb

glomerulus update and abbreviation fix

90bef01

JABelfiore requested a review from aleixpuigb May 22, 2025 14:24

aleixpuigb reviewed May 22, 2025

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JABelfiore added 3 commits June 16, 2025 13:51

updated to related synonym

e17b36e

Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge

3bd0091

Revert "Merge branch 'master' into 2471-juxtaglomerular-complex-cells…

45a075b

…-merge" This reverts commit 3bd0091, reversing changes made to e17b36e.

JABelfiore requested a review from aleixpuigb June 17, 2025 09:21

github-actions bot added the unreviewed label Jul 20, 2025

juxtaglomerular complex cell merged with kidney granular cell #3109

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Ontology comparison

Left

Right

Ontology imports

Ontology annotations

OMO_0003000 http://purl.obolibrary.org/obo/OMO_0003000

Added

extraglomerular mesangial cell http://purl.obolibrary.org/obo/CL_0002173

Removed

Added

kidney granular cell http://purl.obolibrary.org/obo/CL_0000648

Removed

Added

macula densa epithelial cell http://purl.obolibrary.org/obo/CL_1000850

Removed

Added

obsolete juxtaglomerular complex cell http://purl.obolibrary.org/obo/CL_1000618

Removed

Added

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github-actions bot commented May 21, 2025

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

extraglomerular mesangial cell http://purl.obolibrary.org/obo/CL_0002173

Removed

Added

kidney granular cell http://purl.obolibrary.org/obo/CL_0000648

Removed

Added

macula densa epithelial cell http://purl.obolibrary.org/obo/CL_1000850

Removed

Added

obsolete juxtaglomerular complex cell http://purl.obolibrary.org/obo/CL_1000618

Removed

Added

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OMO_0003000 `http://purl.obolibrary.org/obo/OMO_0003000`

extraglomerular mesangial cell `http://purl.obolibrary.org/obo/CL_0002173`

kidney granular cell `http://purl.obolibrary.org/obo/CL_0000648`

macula densa epithelial cell `http://purl.obolibrary.org/obo/CL_1000850`

obsolete juxtaglomerular complex cell `http://purl.obolibrary.org/obo/CL_1000618`

extraglomerular mesangial cell `http://purl.obolibrary.org/obo/CL_0002173`

kidney granular cell `http://purl.obolibrary.org/obo/CL_0000648`

macula densa epithelial cell `http://purl.obolibrary.org/obo/CL_1000850`

obsolete juxtaglomerular complex cell `http://purl.obolibrary.org/obo/CL_1000618`

aleixpuigb May 22, 2025 •

edited

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