From 93421d9406c5ef9531ea778754af079817b5dd36 Mon Sep 17 00:00:00 2001 From: bvarner-ebi <95643797+bvarner-ebi@users.noreply.github.com> Date: Wed, 27 Sep 2023 11:20:10 +0100 Subject: [PATCH 1/3] Addresses #2158 Refine subclasses of 'kidney cell' --- src/ontology/cl-edit.owl | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index bd4a03f3a..8255526ac 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -26527,6 +26527,7 @@ SubClassOf(obo:CL_1000495 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000190 # Class: obo:CL_1000497 (kidney cell) +AnnotationAssertion(obo:IAO_0000115 obo:CL_1000497 "A cell that is part of a kidney.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000497 "KUPO:0001010") AnnotationAssertion(rdfs:label obo:CL_1000497 "kidney cell") EquivalentClasses(obo:CL_1000497 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002113))) @@ -26573,36 +26574,33 @@ SubClassOf(obo:CL_1000510 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000418 # Class: obo:CL_1000546 (kidney medulla collecting duct epithelial cell) +AnnotationAssertion(obo:IAO_0000115 obo:CL_1000546 "An epithelial cell that is part of a renal medulla collecting duct.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000546 "KUPO:0001060") AnnotationAssertion(rdfs:label obo:CL_1000546 "kidney medulla collecting duct epithelial cell") -EquivalentClasses(obo:CL_1000546 ObjectIntersectionOf(obo:CL_1000497 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005185))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000546 obo:CL_1000497) -SubClassOf(obo:CL_1000546 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005185)) +EquivalentClasses(obo:CL_1000546 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005185))) # Class: obo:CL_1000547 (kidney inner medulla collecting duct epithelial cell) AnnotationAssertion(obo:IAO_0000115 obo:CL_1000547 "An epithelial cell that is part of some inner medullary collecting duct.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000547 "KUPO:0001061") AnnotationAssertion(rdfs:label obo:CL_1000547 "kidney inner medulla collecting duct epithelial cell") -EquivalentClasses(obo:CL_1000547 ObjectIntersectionOf(obo:CL_1000497 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004205))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000547 obo:CL_1000497) -SubClassOf(obo:CL_1000547 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004205)) +EquivalentClasses(obo:CL_1000547 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004205))) +SubClassOf(obo:CL_1000547 obo:CL_1000546) # Class: obo:CL_1000548 (kidney outer medulla collecting duct epithelial cell) +AnnotationAssertion(obo:IAO_0000115 obo:CL_1000548 "An epithelial cell that is part of an outer medullary collecting duct.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000548 "KUPO:0001062") AnnotationAssertion(rdfs:label obo:CL_1000548 "kidney outer medulla collecting duct epithelial cell") -EquivalentClasses(obo:CL_1000548 ObjectIntersectionOf(obo:CL_1000497 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004204))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000548 obo:CL_1000497) -SubClassOf(obo:CL_1000548 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004204)) +EquivalentClasses(obo:CL_1000548 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004204))) +SubClassOf(obo:CL_1000548 obo:CL_1000546) # Class: obo:CL_1000549 (kidney cortex collecting duct epithelial cell) +AnnotationAssertion(obo:IAO_0000115 obo:CL_1000549 "An epithelial cell that is part of a cortical collecting duct.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000549 "KUPO:0001063") AnnotationAssertion(rdfs:label obo:CL_1000549 "kidney cortex collecting duct epithelial cell") -EquivalentClasses(obo:CL_1000549 ObjectIntersectionOf(obo:CL_1000497 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004203))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000549 obo:CL_1000497) -SubClassOf(obo:CL_1000549 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004203)) +EquivalentClasses(obo:CL_1000549 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004203))) # Class: obo:CL_1000550 (kidney papillary duct principal epithelial cell) @@ -27381,11 +27379,11 @@ SubClassOf(obo:CL_1001224 obo:CL_1001145) # Class: obo:CL_1001225 (kidney collecting duct cell) +AnnotationAssertion(obo:IAO_0000115 obo:CL_1001225 "A cell that is part of a collecting duct of renal tubule.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1001225 "KUPO:0001012") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1001225 "Wikipedia:Kidney_collecting_duct_cell") AnnotationAssertion(rdfs:label obo:CL_1001225 "kidney collecting duct cell") EquivalentClasses(obo:CL_1001225 ObjectIntersectionOf(obo:CL_1000497 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001232))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1001225 obo:CL_1000497) # Class: obo:CL_1001285 (vasa recta descending limb cell) @@ -30631,6 +30629,7 @@ AnnotationAssertion( obo:CL_4030018 obo:CL_4030018 "2022-06-27T15:25:10Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:CL_4030018 "kidney connecting tubule principal cell") EquivalentClasses(obo:CL_4030018 ObjectIntersectionOf(obo:CL_0005009 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005097))) +SubClassOf(obo:CL_4030018 obo:CL_1000768) # Class: obo:CL_4030019 (kidney connecting tubule intercalated cell) From 9e2e4e813ae29cb998324f6c9fb97a278c4aa39e Mon Sep 17 00:00:00 2001 From: bvarner-ebi <95643797+bvarner-ebi@users.noreply.github.com> Date: Wed, 27 Sep 2023 11:41:44 +0100 Subject: [PATCH 2/3] Update cl-edit.owl Edit 'kidney cortical cell' --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 8255526ac..3a891600c 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -20458,11 +20458,11 @@ SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002680 obo:CL_0000696 # Class: obo:CL_0002681 (kidney cortical cell) +AnnotationAssertion(obo:IAO_0000115 obo:CL_0002681 "A cell that is part of a cortex of kidney.") AnnotationAssertion( obo:CL_0002681 ) AnnotationAssertion(oboInOwl:creation_date obo:CL_0002681 "2011-10-25T03:49:41Z") AnnotationAssertion(rdfs:label obo:CL_0002681 "kidney cortical cell") EquivalentClasses(obo:CL_0002681 ObjectIntersectionOf(obo:CL_1000497 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001225))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002681 obo:CL_1000497) # Class: obo:CL_0003001 (bistratified retinal ganglion cell) From 59d57d9b32149807c318a73fac30c1f63f6cd903 Mon Sep 17 00:00:00 2001 From: bvarner-ebi <95643797+bvarner-ebi@users.noreply.github.com> Date: Wed, 27 Sep 2023 11:50:25 +0100 Subject: [PATCH 3/3] Update cl-edit.owl Add more text defs; remove more redundant subclasses --- src/ontology/cl-edit.owl | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 3a891600c..c803307b2 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -26534,35 +26534,31 @@ EquivalentClasses(obo:CL_1000497 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeV # Class: obo:CL_1000500 (kidney interstitial cell) +AnnotationAssertion(obo:IAO_0000115 obo:CL_1000500 "A cell that is part of kidney interstitium.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000500 "KUPO:0001013") AnnotationAssertion(rdfs:label obo:CL_1000500 "kidney interstitial cell") EquivalentClasses(obo:CL_1000500 ObjectIntersectionOf(obo:CL_1000497 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005215))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000500 obo:CL_1000497) -SubClassOf(obo:CL_1000500 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005215)) # Class: obo:CL_1000504 (kidney medulla cell) +AnnotationAssertion(obo:IAO_0000115 obo:CL_1000504 "A cell that is part of a renal medulla.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000504 "KUPO:0001017") AnnotationAssertion(rdfs:label obo:CL_1000504 "kidney medulla cell") EquivalentClasses(obo:CL_1000504 ObjectIntersectionOf(obo:CL_1000497 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000362))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000504 obo:CL_1000497) -SubClassOf(obo:CL_1000504 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000362)) # Class: obo:CL_1000505 (kidney pelvis cell) +AnnotationAssertion(obo:IAO_0000115 obo:CL_1000505 "A cell that is part of a renal pelvis.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000505 "KUPO:0001018") AnnotationAssertion(rdfs:label obo:CL_1000505 "kidney pelvis cell") EquivalentClasses(obo:CL_1000505 ObjectIntersectionOf(obo:CL_1000497 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001224))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000505 obo:CL_1000497) -SubClassOf(obo:CL_1000505 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001224)) # Class: obo:CL_1000507 (kidney tubule cell) +AnnotationAssertion(obo:IAO_0000115 obo:CL_1000507 "A cell that is part of a nephron tubule.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000507 "KUPO:0001020") AnnotationAssertion(rdfs:label obo:CL_1000507 "kidney tubule cell") EquivalentClasses(obo:CL_1000507 ObjectIntersectionOf(obo:CL_1000497 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001231))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000507 obo:CL_1000497) -SubClassOf(obo:CL_1000507 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001231)) # Class: obo:CL_1000510 (kidney glomerular epithelial cell)