Skip to content

Commit

Permalink
Fixes#2395- Revise Epithelial Cell of Proximal Tubule and Subclasses (#…
Browse files Browse the repository at this point in the history 
…2401)

* Fixes#2395-STILL IN PROGRESS

THIS TICKET IS STILL IN PROGRESS - pending on uberon approval and release

Terms "proximal tubule segment 1," "proximal tubule segment 2," and "proximal tubule segment 3" will be added in uberon

These uberon terms have been asserted as equivalent classes for the corresponding CL terms (kidney epithelial proximal tubule segment 1, segment 2, and segment 3).

* Revert "Fixes#2395-STILL IN PROGRESS"

This reverts commit 8ac6c16.

* imported Uberon terms "proximal convoluted tubule segment 1" and "proximal convoluted tubule segment 2" into CL

imported Uberon terms "proximal convoluted tubule segment 1" and "proximal convoluted tubule segment 2" into CL

* Updated logical defs

- Added logical defs of "epithelial cell of proximal tubule segment 1"
"epithelial cell of proximal tubule segment 2"
"epithelial cell of proximal tubule segment 3"

Included uberon terms "proximal convoluted tubule segment 1" and "proximal convoluted tubule segment 2" into CL logical defs

Updated logical defs of "kidney proximal convoluted tubule epithelial cell" and "kidney proximal straight tubule epithelial cell"

* Update cl-edit.owl

* Update cl-edit.owl

* Updated the textual defintions

- Updated the textual definitions for "epithelial cell of proximal tubule segment 1", "epithelial cell of proximal tubule segment 2" and "epithelial cell of proximal tubule segment 3" to include primary functions
-Added more references to support the updated textual definitions

* Update cl-edit.owl

* Update cl-edit.owl

* Updated textual defintions

- Updated textual definition for "brush border cell of the proximal tubule" and added references
-Updated textual definitions for proximal tubule S1, S2 and S3 cells

* updated textual definitions

* Update cl-edit.owl
  • Loading branch information
@Caroline-99
Caroline-99 authored Jul 2, 2024
1 parent 42b85d6 commit 5e2931d
Show file tree
Hide file tree
Showing 7 changed files with 122 additions and 19 deletions.
2 changes: 1 addition & 1 deletion src/mappings/fbbt.sssom.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
#license: "https://creativecommons.org/licenses/by/4.0/"
#subject_source: "obo:fbbt.owl"
#object_source: "obo:cl.owl"
#mapping_date: "2024-04-24"
#mapping_date: "2024-05-31"
subject_id subject_label predicate_id object_id mapping_justification
FBbt:00000092 primordial germ cell semapv:crossSpeciesExactMatch CL:0000301 semapv:ManualMappingCuration
FBbt:00000124 epithelial cell semapv:crossSpeciesExactMatch CL:0000066 semapv:ManualMappingCuration
Expand Down
1 change: 1 addition & 0 deletions src/mappings/zfa.sssom.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
# ZFA: "http://purl.obolibrary.org/obo/ZFA_"
#mapping_set_id: "http://purl.obolibrary.org/obo/zfa/zfa.sssom.tsv"
#license: "https://creativecommons.org/licenses/by/3.0/"
#subject_source: "http://purl.obolibrary.org/obo/zfa.owl"
subject_id subject_label predicate_id object_id mapping_justification mapping_cardinality
ZFA:0000003 adaxial cell semapv:crossSpeciesExactMatch CL:0007016 semapv:UnspecifiedMatching 1:1
ZFA:0000084 yolk semapv:crossSpeciesExactMatch CL:0000428 semapv:UnspecifiedMatching 1:1
Expand Down
26 changes: 15 additions & 11 deletions src/ontology/cl-edit.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3137,6 +3137,8 @@ Declaration(Class(obo:UBERON_0003677))
Declaration(Class(obo:UBERON_0003718))
Declaration(Class(obo:UBERON_0004024))
Declaration(Class(obo:UBERON_0004026))
Declaration(Class(obo:UBERON_0004196))
Declaration(Class(obo:UBERON_0004197))
Declaration(Class(obo:UBERON_0005101))
Declaration(Class(obo:UBERON_0005102))
Declaration(Class(obo:UBERON_0005378))
Expand Down Expand Up @@ -3253,7 +3255,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition")

AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to")

# Annotation Property: obo:IAO_0000700 (has ontology root term)
# Annotation Property: obo:IAO_0000700 (preferred_root)

AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root")

Expand Down Expand Up @@ -3347,11 +3349,11 @@ AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym")

AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference")

# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym)
# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym)

AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym")

# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym)
# Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym)

AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym")

Expand Down Expand Up @@ -16897,13 +16899,13 @@ SubClassOf(obo:CL_0002306 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000413

# Class: obo:CL_0002307 (brush border cell of the proximal tubule)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:1-4160-2328-3") obo:IAO_0000115 obo:CL_0002307 "A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:1-4160-2328-3") Annotation(oboInOwl:hasDbXref "PMID:23799132") obo:IAO_0000115 obo:CL_0002307 "A brush border epithelial cell located in the proximal tubule of the kidney, essential for reabsorbing substances like glucose and amino acids from the glomerular filtrate. These cells also secrete organic ions, playing a crucial role in maintaining kidney homeostasis, including electrolyte and acid-base balance, and excreting metabolic waste.")
AnnotationAssertion(terms:contributor obo:CL_0002307 <https://orcid.org/0000-0003-1980-3228>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002307 "2010-09-14T11:29:20Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:comment obo:CL_0002307 "The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions.")
AnnotationAssertion(rdfs:label obo:CL_0002307 "brush border cell of the proximal tubule")
EquivalentClasses(obo:CL_0002307 ObjectIntersectionOf(obo:CL_0002306 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0005903)))
SubClassOf(obo:CL_0002307 obo:CL_0002306)
SubClassOf(obo:CL_0002307 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0005903))

# Class: obo:CL_0002308 (epithelial cell of skin gland)

Expand Down Expand Up @@ -27034,10 +27036,9 @@ SubClassOf(obo:CL_1000804 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000521

AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000838 "KUPO:0001045")
AnnotationAssertion(rdfs:label obo:CL_1000838 "kidney proximal convoluted tubule epithelial cell")
EquivalentClasses(obo:CL_1000838 ObjectIntersectionOf(obo:CL_0002306 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001287)))
EquivalentClasses(obo:CL_1000838 ObjectIntersectionOf(obo:CL_0002306 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001287) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0005903)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000838 obo:CL_0002306)
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000838 obo:CL_1000615)
SubClassOf(obo:CL_1000838 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001287))

# Class: obo:CL_1000839 (kidney proximal straight tubule epithelial cell)

Expand All @@ -27047,7 +27048,6 @@ EquivalentClasses(obo:CL_1000839 ObjectIntersectionOf(obo:CL_0002306 ObjectSomeV
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000839 obo:CL_0002306)
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000839 obo:CL_1000615)
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000839 obo:CL_1000616)
SubClassOf(obo:CL_1000839 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001290))

# Class: obo:CL_1000849 (kidney distal convoluted tubule epithelial cell)

Expand Down Expand Up @@ -30679,26 +30679,30 @@ SubClassOf(obo:CL_4030008 obo:CL_0000653)

# Class: obo:CL_4030009 (epithelial cell of proximal tubule segment 1)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31249312") obo:IAO_0000115 obo:CL_4030009 "A brush border cell that is part of segment 1 (S1) of the proximal tubule epithelium.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23799132") Annotation(oboInOwl:hasDbXref "PMID:23897681") Annotation(oboInOwl:hasDbXref "PMID:31249312") obo:IAO_0000115 obo:CL_4030009 "A brush border cell that is part of segment 1 (S1) of the proximal tubule epithelium, located in the renal cortex.")
AnnotationAssertion(terms:date obo:CL_4030009 "2022-05-10T13:14:00Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030009 "epithelial cell of segment 1 of proximal tubule")
AnnotationAssertion(rdfs:label obo:CL_4030009 "epithelial cell of proximal tubule segment 1")
EquivalentClasses(obo:CL_4030009 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004196) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0005903)))
SubClassOf(obo:CL_4030009 obo:CL_0002307)

# Class: obo:CL_4030010 (epithelial cell of proximal tubule segment 2)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31249312") obo:IAO_0000115 obo:CL_4030010 "A brush border cell that is part of segment 2 (S2) of the proximal tubule epithelium.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23799132") Annotation(oboInOwl:hasDbXref "PMID:23897681") Annotation(oboInOwl:hasDbXref "PMID:31249312") Annotation(oboInOwl:hasDbXref "PMID:31253652") obo:IAO_0000115 obo:CL_4030010 "A brush border cell that is part of segment 2 (S2) of the proximal tubule epithelium, located in the renal cortex. In addition to its reabsorptive functions, it is also specialized in the secretion of organic anions and cations, including para-aminohippurate.")
AnnotationAssertion(terms:date obo:CL_4030010 "2022-05-10T13:26:13Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030010 "epithelial cell of segment 2 of proximal tubule")
AnnotationAssertion(rdfs:label obo:CL_4030010 "epithelial cell of proximal tubule segment 2")
EquivalentClasses(obo:CL_4030010 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004197) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0005903)))
SubClassOf(obo:CL_4030010 obo:CL_0002307)

# Class: obo:CL_4030011 (epithelial cell of proximal tubule segment 3)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31249312") obo:IAO_0000115 obo:CL_4030011 "A brush border cell that is part of segment 3 (S3) of the proximal tubule epithelium.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23799132") Annotation(oboInOwl:hasDbXref "PMID:31249312") obo:IAO_0000115 obo:CL_4030011 "A brush border cell that is part of segment 3 (S3) of the proximal tubule epithelium, which extends from the medullary rays of the renal cortex into the outer medulla.")
AnnotationAssertion(terms:date obo:CL_4030011 "2022-05-10T13:31:06Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030011 "epithelial cell of segment 3 of proximal tubule")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31249312") rdfs:comment obo:CL_4030011 "The epithelial cell of proximal tubule segment 3 operates under relatively hypoxic conditions and is particularly susceptible to ischemic injury.")
AnnotationAssertion(rdfs:label obo:CL_4030011 "epithelial cell of proximal tubule segment 3")
EquivalentClasses(obo:CL_4030011 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001290) ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0005903)))
SubClassOf(obo:CL_4030011 obo:CL_0002307)

# Class: obo:CL_4030012 (kidney loop of Henle short descending thin limb epithelial cell)
Expand Down
4 changes: 2 additions & 2 deletions src/ontology/components/cellxgene_subset.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/cl/components/cellxgene_subset.owl>
<http://purl.obolibrary.org/obo/cl/releases/2024-05-15/components/cellxgene_subset.owl>
Annotation(owl:versionInfo "2024-05-15")
<http://purl.obolibrary.org/obo/cl/releases/2024-06-13/components/cellxgene_subset.owl>
Annotation(owl:versionInfo "2024-06-13")

Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000000>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000001>))
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/components/mappings.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4572,5 +4572,5 @@



<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->

Loading

0 comments on commit 5e2931d

Please sign in to comment.