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juxtaglomerular complex cell merged with kidney granular cell #3109

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557e9ad
juxtaglomerular complex cell merged with kidney granular cell
JABelfiore May 2, 2025
50cb90e
Update kidney_upper_slim.owl
JABelfiore May 2, 2025
e9a3431
" issue amend
JABelfiore May 2, 2025
d2d8261
Update cl-edit.owl
JABelfiore May 2, 2025
c7de84a
deprecated true
JABelfiore May 2, 2025
0d5cdd0
Update kidney_upper_slim.owl
JABelfiore May 8, 2025
f0cb94c
Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge
JABelfiore May 8, 2025
d9172ce
Update kidney_upper_slim.tsv
JABelfiore May 8, 2025
51e8251
Revert "Update kidney_upper_slim.owl"
JABelfiore May 8, 2025
4e07d99
Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge
JABelfiore May 8, 2025
c340c06
Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge
JABelfiore May 12, 2025
8fd6c3a
Revert "Update kidney_upper_slim.tsv"
JABelfiore May 12, 2025
5e47f45
Update kidney_upper_slim.csv
JABelfiore May 12, 2025
bb0c612
update slims
JABelfiore May 12, 2025
dcb2009
Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge
JABelfiore May 15, 2025
0a182dc
Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge
aleixpuigb May 21, 2025
099f5bb
Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge
JABelfiore May 22, 2025
90bef01
glomerulus update and abbreviation fix
JABelfiore May 22, 2025
e17b36e
updated to related synonym
JABelfiore Jun 16, 2025
3bd0091
Merge branch 'master' into 2471-juxtaglomerular-complex-cells-merge
JABelfiore Jun 16, 2025
45a075b
Revert "Merge branch 'master' into 2471-juxtaglomerular-complex-cells…
JABelfiore Jun 16, 2025
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26 changes: 15 additions & 11 deletions src/ontology/cl-edit.owl
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Expand Up @@ -9277,14 +9277,18 @@ SubClassOf(obo:CL_0000647 ObjectSomeValuesFrom(obo:RO_0002353 obo:GO_0000768))
# Class: obo:CL_0000648 (kidney granular cell)

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(terms:contributor obo:CL_0000648 <https://orcid.org/0009-0005-7919-4905>)
AnnotationAssertion(terms:date obo:CL_0000648 "2025-05-02T12:33:27Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000648 "juxtaglomerular cell")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000648 "FMA:84138")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000648 "JG cell")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000648 "KUPO:0001028")
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")
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@aleixpuigb aleixpuigb May 22, 2025 •
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Please, add this term (JG cell) as related synonym, and add the AP has_synonym_type 'abbreviation' (entity IRI).

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)))
SubClassOf(obo:CL_0000648 obo:CL_0000192)
SubClassOf(obo:CL_0000648 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002303))

# Class: obo:CL_0000649 (prickle cell)

Expand Down Expand Up @@ -15704,9 +15708,9 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002173 "polar cushion cells
AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0002173 "lacis cell")
AnnotationAssertion(rdfs:label obo:CL_0002173 "extraglomerular mesangial cell")
EquivalentClasses(obo:CL_0002173 ObjectIntersectionOf(obo:CL_0002320 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002321)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002173 obo:CL_0000648)
SubClassOf(obo:CL_0002173 obo:CL_0000650)
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002173 obo:CL_0002320)
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002173 obo:CL_1000618)

# Class: obo:CL_0002174 (follicular cell of ovary)

Expand Down Expand Up @@ -27213,14 +27217,14 @@ EquivalentClasses(obo:CL_1000617 ObjectIntersectionOf(obo:CL_1000504 ObjectSomeV
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000617 obo:CL_1000504)
SubClassOf(obo:CL_1000617 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001294))

# Class: obo:CL_1000618 (juxtaglomerular complex cell)
# Class: obo:CL_1000618 (obsolete juxtaglomerular complex cell)

AnnotationAssertion(obo:IAO_0000233 obo:CL_1000618 "https://github.com/obophenotype/cell-ontology/issues/2471")
AnnotationAssertion(obo:IAO_0100001 obo:CL_1000618 obo:CL_0000648)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000618 "KUPO:0001028")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GO:0072052") oboInOwl:hasExactSynonym obo:CL_1000618 "juxtaglomerulus cell")
AnnotationAssertion(rdfs:label obo:CL_1000618 "juxtaglomerular complex cell")
EquivalentClasses(obo:CL_1000618 ObjectIntersectionOf(obo:CL_0002681 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002303)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000618 obo:CL_0002681)
SubClassOf(obo:CL_1000618 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002303))
AnnotationAssertion(rdfs:comment obo:CL_1000618 "merged with kidney granular cell")
AnnotationAssertion(rdfs:label obo:CL_1000618 "obsolete juxtaglomerular complex cell")
AnnotationAssertion(owl:deprecated obo:CL_1000618 "true"^^xsd:boolean)

# Class: obo:CL_1000681 (kidney cortex interstitial cell)

Expand Down Expand Up @@ -27490,8 +27494,8 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000850 "KUPO:0001057")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33491562") oboInOwl:hasExactSynonym obo:CL_1000850 "macula densa cell")
AnnotationAssertion(rdfs:label obo:CL_1000850 "macula densa epithelial cell")
EquivalentClasses(obo:CL_1000850 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002335)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000850 obo:CL_0000648)
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000850 obo:CL_0002584)
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000850 obo:CL_1000618)
SubClassOf(obo:CL_1000850 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0097730))
SubClassOf(obo:CL_1000850 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0003093))
SubClassOf(obo:CL_1000850 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_1900133))
Expand Down
39 changes: 19 additions & 20 deletions src/ontology/components/kidney_upper_slim.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -29,86 +29,85 @@ Declaration(Class(<http://purl.obolibrary.org/obo/CL_1000892>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_1000893>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_1001016>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_1001021>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0100001>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#inSubset>))


############################
# Classes
############################

# Class: <http://purl.obolibrary.org/obo/CL_0002188> (<http://purl.obolibrary.org/obo/CL_0002188>)
# Class: <http://purl.obolibrary.org/obo/CL_0002188> (glomerular endothelial cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_0002188> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_0002305> (<http://purl.obolibrary.org/obo/CL_0002305>)
# Class: <http://purl.obolibrary.org/obo/CL_0002305> (epithelial cell of distal tubule)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_0002305> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_0002306> (<http://purl.obolibrary.org/obo/CL_0002306>)
# Class: <http://purl.obolibrary.org/obo/CL_0002306> (epithelial cell of proximal tubule)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_0002306> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000450> (<http://purl.obolibrary.org/obo/CL_1000450>)
# Class: <http://purl.obolibrary.org/obo/CL_1000450> (epithelial cell of glomerular capsule)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000450> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000454> (<http://purl.obolibrary.org/obo/CL_1000454>)
# Class: <http://purl.obolibrary.org/obo/CL_1000454> (kidney collecting duct epithelial cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000454> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000500> (<http://purl.obolibrary.org/obo/CL_1000500>)
# Class: <http://purl.obolibrary.org/obo/CL_1000500> (kidney interstitial cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000500> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000505> (<http://purl.obolibrary.org/obo/CL_1000505>)
# Class: <http://purl.obolibrary.org/obo/CL_1000505> (kidney pelvis cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000505> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000507> (<http://purl.obolibrary.org/obo/CL_1000507>)
# Class: <http://purl.obolibrary.org/obo/CL_1000507> (kidney tubule cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000507> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000546> (<http://purl.obolibrary.org/obo/CL_1000546>)
# Class: <http://purl.obolibrary.org/obo/CL_1000546> (kidney medulla collecting duct epithelial cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000546> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000550> (<http://purl.obolibrary.org/obo/CL_1000550>)
# Class: <http://purl.obolibrary.org/obo/CL_1000550> (kidney papillary duct principal epithelial cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000550> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000612> (<http://purl.obolibrary.org/obo/CL_1000612>)
# Class: <http://purl.obolibrary.org/obo/CL_1000612> (kidney corpuscule cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000612> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000618> (<http://purl.obolibrary.org/obo/CL_1000618>)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000618> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000768> (<http://purl.obolibrary.org/obo/CL_1000768>)
# Class: <http://purl.obolibrary.org/obo/CL_1000768> (kidney connecting tubule epithelial cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000768> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000849> (<http://purl.obolibrary.org/obo/CL_1000849>)
# Class: <http://purl.obolibrary.org/obo/CL_1000849> (kidney distal convoluted tubule epithelial cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000849> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000891> (<http://purl.obolibrary.org/obo/CL_1000891>)
# Class: <http://purl.obolibrary.org/obo/CL_1000891> (kidney arterial blood vessel cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000891> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000892> (<http://purl.obolibrary.org/obo/CL_1000892>)
# Class: <http://purl.obolibrary.org/obo/CL_1000892> (kidney capillary endothelial cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000892> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1000893> (<http://purl.obolibrary.org/obo/CL_1000893>)
# Class: <http://purl.obolibrary.org/obo/CL_1000893> (kidney venous blood vessel cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1000893> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1001016> (<http://purl.obolibrary.org/obo/CL_1001016>)
# Class: <http://purl.obolibrary.org/obo/CL_1001016> (kidney loop of Henle ascending limb epithelial cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1001016> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

# Class: <http://purl.obolibrary.org/obo/CL_1001021> (<http://purl.obolibrary.org/obo/CL_1001021>)
# Class: <http://purl.obolibrary.org/obo/CL_1001021> (kidney loop of Henle descending limb epithelial cell)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/CL_1001021> <http://purl.obolibrary.org/obo/cl#kidney_upper_slim>)

Expand Down
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