From a41d599fd8eb8cd87d5234f4c8d6e84aacff34ca Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Tue, 1 Oct 2024 12:08:45 +0100 Subject: [PATCH 1/3] Fixes #2486 Fixes #2484 Added 2 new terms ( a grouping term and a subclass) with textual and logical defs and references --- src/ontology/cl-edit.owl | 24 +++++++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 0b91d5306..2d6d3a408 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3091,6 +3091,8 @@ Declaration(Class(obo:CL_4052008)) Declaration(Class(obo:CL_4052009)) Declaration(Class(obo:CL_4052010)) Declaration(Class(obo:CL_4052011)) +Declaration(Class(obo:CL_4052015)) +Declaration(Class(obo:CL_4052016)) Declaration(Class(obo:CL_4052048)) Declaration(Class(obo:CL_4052049)) Declaration(Class(obo:CP_0000000)) @@ -32580,7 +32582,7 @@ EquivalentClasses(obo:CL_4047052 ObjectIntersectionOf(obo:CL_1000347 ObjectSomeV # Class: obo:CL_4047101 (liver-resident natural killer cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26330348") Annotation(oboInOwl:hasDbXref "PMID:26639736") Annotation(oboInOwl:hasDbXref "PMID:27798170") Annotation(oboInOwl:hasDbXref "PMID:32351704") Annotation(oboInOwl:hasDbXref "PMID:34230995") Annotation(oboInOwl:hasDbXref "PMID:35865550") Annotation(oboInOwl:hasDbXref "PMID:31114585") obo:IAO_0000115 obo:CL_4047101 "A natural killer cell resident to the liver, located in the hepatic sinusoids. In humans this cell type is distinguished from circulating natural killer cells by CD49a or CD69 gene expression. Liver-resident natural killer cells have also been shown to express CCR5, EOMES, KLRB1, GZMK, and CXCR6 in humans.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26330348") Annotation(oboInOwl:hasDbXref "PMID:26639736") Annotation(oboInOwl:hasDbXref "PMID:27798170") Annotation(oboInOwl:hasDbXref "PMID:31114585") Annotation(oboInOwl:hasDbXref "PMID:32351704") Annotation(oboInOwl:hasDbXref "PMID:34230995") Annotation(oboInOwl:hasDbXref "PMID:35865550") obo:IAO_0000115 obo:CL_4047101 "A natural killer cell resident to the liver, located in the hepatic sinusoids. In humans this cell type is distinguished from circulating natural killer cells by CD49a or CD69 gene expression. Liver-resident natural killer cells have also been shown to express CCR5, EOMES, KLRB1, GZMK, and CXCR6 in humans.") AnnotationAssertion(terms:contributor obo:CL_4047101 ) AnnotationAssertion(terms:contributor obo:CL_4047101 "https://orcid.org/0000-0001-8134-3037") AnnotationAssertion(terms:date obo:CL_4047101 "2024-07-29T13:43:11Z"^^xsd:dateTime) @@ -32727,6 +32729,26 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:7107724") oboInOwl:hasRe AnnotationAssertion(rdfs:label obo:CL_4052011 "follicle associated enterocyte") SubClassOf(obo:CL_4052011 obo:CL_0000584) +# Class: obo:CL_4052015 (endocrine gland capillary endothelial cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18480313") obo:IAO_0000115 obo:CL_4052015 "Any capillary endothelial cell that is part of the endocrine gland.") +AnnotationAssertion(terms:contributor obo:CL_4052015 ) +AnnotationAssertion(terms:date obo:CL_4052015 "2024-09-30T15:27:49Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:CL_4052015 "endocrine gland capillary endothelial cell") +SubClassOf(obo:CL_4052015 obo:CL_0002144) +SubClassOf(obo:CL_4052015 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002368)) + +# Class: obo:CL_4052016 (pituitary gland capillary endothelial cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10810312") Annotation(oboInOwl:hasDbXref "PMID:32910242") Annotation(oboInOwl:hasDbXref "PMID:4899902") obo:IAO_0000115 obo:CL_4052016 "A capillary endothelial cell that is part of the pituitary gland, particularly in the anterior pituitary. This cell is distinguished by its numerous fenestrations, which are covered by a single-layered diaphragm. The diaphragm features a dense ring-like structure, facilitating the passage of hormones and other substances essential for endocrine signalling.") +AnnotationAssertion(terms:contributor obo:CL_4052016 ) +AnnotationAssertion(terms:date obo:CL_4052016 "2024-09-30T15:31:45Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:4899902") oboInOwl:hasNarrowSynonym obo:CL_4052016 "capillary endothelial cell of the anterior pituitary") +AnnotationAssertion(rdfs:label obo:CL_4052016 "pituitary gland capillary endothelial cell") +EquivalentClasses(obo:CL_4052016 ObjectIntersectionOf(obo:CL_0002144 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000007))) +SubClassOf(obo:CL_4052016 obo:CL_4052015) +SubClassOf(obo:CL_4052016 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000007)) + # Class: obo:CL_4052048 (intercalated cell of salivary gland) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30855909") Annotation(oboInOwl:hasDbXref "PMID:35799078") Annotation(oboInOwl:hasDbXref "PMID:36726292") Annotation(oboInOwl:hasDbXref "PMID:37724716") obo:IAO_0000115 obo:CL_4052048 "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption.") From d1e96d7087c5186ab1590c230c7520ce3866465c Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Thu, 10 Oct 2024 10:21:22 +0100 Subject: [PATCH 2/3] Update cl-edit.owl --- src/ontology/cl-edit.owl | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 8306872c8..623aba96f 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -32794,23 +32794,22 @@ SubClassOf(obo:CL_4052014 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002064)) # Class: obo:CL_4052015 (endocrine gland capillary endothelial cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18480313") obo:IAO_0000115 obo:CL_4052015 "Any capillary endothelial cell that is part of the endocrine gland.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18480313") obo:IAO_0000115 obo:CL_4052015 "Any capillary endothelial cell that is part of an endocrine gland.") AnnotationAssertion(terms:contributor obo:CL_4052015 ) AnnotationAssertion(terms:date obo:CL_4052015 "2024-09-30T15:27:49Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:CL_4052015 "endocrine gland capillary endothelial cell") -SubClassOf(obo:CL_4052015 obo:CL_0002144) -SubClassOf(obo:CL_4052015 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002368)) +EquivalentClasses(obo:CL_4052015 ObjectIntersectionOf(obo:CL_0002144 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002368))) # Class: obo:CL_4052016 (pituitary gland capillary endothelial cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10810312") Annotation(oboInOwl:hasDbXref "PMID:32910242") Annotation(oboInOwl:hasDbXref "PMID:4899902") obo:IAO_0000115 obo:CL_4052016 "A capillary endothelial cell that is part of the pituitary gland, particularly in the anterior pituitary. This cell is distinguished by its numerous fenestrations, which are covered by a single-layered diaphragm. The diaphragm features a dense ring-like structure, facilitating the passage of hormones and other substances essential for endocrine signalling.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10810312") Annotation(oboInOwl:hasDbXref "PMID:32910242") obo:IAO_0000115 obo:CL_4052016 "A capillary endothelial cell that is part of the pituitary gland. This cell is characterized by its fenestrated structure which facilitates the efficient transport of hormones and other signaling molecules, essential for endocrine signalling.") AnnotationAssertion(terms:contributor obo:CL_4052016 ) AnnotationAssertion(terms:date obo:CL_4052016 "2024-09-30T15:31:45Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:4899902") oboInOwl:hasNarrowSynonym obo:CL_4052016 "capillary endothelial cell of the anterior pituitary") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:4899902") rdfs:comment obo:CL_4052016 "In the anterior pituitary gland of rats, capillary endothelial cells are distinguished by numerous fenestrations, which are covered by a single-layered diaphragm. The diaphragm features a dense ring-like structure.") AnnotationAssertion(rdfs:label obo:CL_4052016 "pituitary gland capillary endothelial cell") EquivalentClasses(obo:CL_4052016 ObjectIntersectionOf(obo:CL_0002144 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000007))) -SubClassOf(obo:CL_4052016 obo:CL_4052015) -SubClassOf(obo:CL_4052016 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000007)) +SubClassOf(obo:CL_4052016 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002064)) # Class: obo:CL_4052048 (intercalated cell of salivary gland) From 5ef0900652acf7eb34fd95cb1cfb18a816a88c8b Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Thu, 10 Oct 2024 12:15:12 +0100 Subject: [PATCH 3/3] Update cl-edit.owl --- src/ontology/cl-edit.owl | 53 +++++++++++++++------------------------- 1 file changed, 20 insertions(+), 33 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index f3f20134f..54edf906d 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3094,11 +3094,10 @@ Declaration(Class(obo:CL_4052011)) Declaration(Class(obo:CL_4052012)) Declaration(Class(obo:CL_4052013)) Declaration(Class(obo:CL_4052014)) -Declaration(Class(obo:CL_4052018)) -Declaration(Class(obo:CL_4052019)) -Declaration(Class(obo:CL_4052014)) Declaration(Class(obo:CL_4052015)) Declaration(Class(obo:CL_4052016)) +Declaration(Class(obo:CL_4052018)) +Declaration(Class(obo:CL_4052019)) Declaration(Class(obo:CL_4052048)) Declaration(Class(obo:CL_4052049)) Declaration(Class(obo:CP_0000000)) @@ -32773,6 +32772,24 @@ AnnotationAssertion(rdfs:label obo:CL_4052014 "pancreatic islet capillary endoth EquivalentClasses(obo:CL_4052014 ObjectIntersectionOf(obo:CL_0002144 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000006))) SubClassOf(obo:CL_4052014 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002064)) +# Class: obo:CL_4052015 (endocrine gland capillary endothelial cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18480313") obo:IAO_0000115 obo:CL_4052015 "Any capillary endothelial cell that is part of an endocrine gland.") +AnnotationAssertion(terms:contributor obo:CL_4052015 ) +AnnotationAssertion(terms:date obo:CL_4052015 "2024-09-30T15:27:49Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label obo:CL_4052015 "endocrine gland capillary endothelial cell") +EquivalentClasses(obo:CL_4052015 ObjectIntersectionOf(obo:CL_0002144 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002368))) + +# Class: obo:CL_4052016 (pituitary gland capillary endothelial cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10810312") Annotation(oboInOwl:hasDbXref "PMID:32910242") obo:IAO_0000115 obo:CL_4052016 "A capillary endothelial cell that is part of the pituitary gland. This cell is characterized by its fenestrated structure which facilitates the efficient transport of hormones and other signaling molecules, essential for endocrine signalling.") +AnnotationAssertion(terms:contributor obo:CL_4052016 ) +AnnotationAssertion(terms:date obo:CL_4052016 "2024-09-30T15:31:45Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:4899902") rdfs:comment obo:CL_4052016 "In the anterior pituitary gland of rats, capillary endothelial cells are distinguished by numerous fenestrations, which are covered by a single-layered diaphragm. The diaphragm features a dense ring-like structure.") +AnnotationAssertion(rdfs:label obo:CL_4052016 "pituitary gland capillary endothelial cell") +EquivalentClasses(obo:CL_4052016 ObjectIntersectionOf(obo:CL_0002144 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000007))) +SubClassOf(obo:CL_4052016 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002064)) + # Class: obo:CL_4052018 (fallopian tube epithelial cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Fallopian_tube") obo:IAO_0000115 obo:CL_4052018 "Any epithelial cell that is part of the fallopian tube.") @@ -32793,36 +32810,6 @@ SubClassOf(obo:CL_4052019 obo:CL_0000066) SubClassOf(obo:CL_4052019 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003889)) SubClassOf(obo:CL_4052019 ObjectSomeValuesFrom(obo:CL_4030045 obo:GO_0005929)) -# Class: obo:CL_4052014 (pancreatic islet capillary endothelial cell) - -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16607697") Annotation(oboInOwl:hasDbXref "PMID:27124642") Annotation(oboInOwl:hasDbXref "PMID:28396983") Annotation(oboInOwl:hasDbXref "PMID:33200981") obo:IAO_0000115 obo:CL_4052014 "A capillary endothelial cell that is part of islet of Langerhans, characterized by a high density of fenestrations —approximately ten times greater than those in exocrine pancreatic capillaries. These fenestrations facilitate efficient hormone exchange, which is essential for maintaining glucose homeostasis. The cell's structure and function are regulated by the local production of vascular endothelial growth factor-A (VEGF-A), which maintains its fenestrated architecture.") -AnnotationAssertion(terms:contributor obo:CL_4052014 ) -AnnotationAssertion(terms:date obo:CL_4052014 "2024-09-30T14:36:12Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16607697") Annotation(oboInOwl:hasDbXref "PMID:28396983") oboInOwl:hasBroadSynonym obo:CL_4052014 "islet endothelial cell") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16607697") oboInOwl:hasBroadSynonym obo:CL_4052014 "pancreatic islet endothelial cell") -AnnotationAssertion(rdfs:label obo:CL_4052014 "pancreatic islet capillary endothelial cell") -EquivalentClasses(obo:CL_4052014 ObjectIntersectionOf(obo:CL_0002144 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000006))) -SubClassOf(obo:CL_4052014 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002064)) - -# Class: obo:CL_4052015 (endocrine gland capillary endothelial cell) - -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18480313") obo:IAO_0000115 obo:CL_4052015 "Any capillary endothelial cell that is part of an endocrine gland.") -AnnotationAssertion(terms:contributor obo:CL_4052015 ) -AnnotationAssertion(terms:date obo:CL_4052015 "2024-09-30T15:27:49Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label obo:CL_4052015 "endocrine gland capillary endothelial cell") -EquivalentClasses(obo:CL_4052015 ObjectIntersectionOf(obo:CL_0002144 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002368))) - -# Class: obo:CL_4052016 (pituitary gland capillary endothelial cell) - -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10810312") Annotation(oboInOwl:hasDbXref "PMID:32910242") obo:IAO_0000115 obo:CL_4052016 "A capillary endothelial cell that is part of the pituitary gland. This cell is characterized by its fenestrated structure which facilitates the efficient transport of hormones and other signaling molecules, essential for endocrine signalling.") -AnnotationAssertion(terms:contributor obo:CL_4052016 ) -AnnotationAssertion(terms:date obo:CL_4052016 "2024-09-30T15:31:45Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:4899902") oboInOwl:hasNarrowSynonym obo:CL_4052016 "capillary endothelial cell of the anterior pituitary") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:4899902") rdfs:comment obo:CL_4052016 "In the anterior pituitary gland of rats, capillary endothelial cells are distinguished by numerous fenestrations, which are covered by a single-layered diaphragm. The diaphragm features a dense ring-like structure.") -AnnotationAssertion(rdfs:label obo:CL_4052016 "pituitary gland capillary endothelial cell") -EquivalentClasses(obo:CL_4052016 ObjectIntersectionOf(obo:CL_0002144 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000007))) -SubClassOf(obo:CL_4052016 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0002064)) - # Class: obo:CL_4052048 (intercalated cell of salivary gland) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30855909") Annotation(oboInOwl:hasDbXref "PMID:35799078") Annotation(oboInOwl:hasDbXref "PMID:36726292") Annotation(oboInOwl:hasDbXref "PMID:37724716") obo:IAO_0000115 obo:CL_4052048 "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption.")