Fixes #2627 Revise logical definition of 'inflammatory macrophage' (#…

…2633)

* Fixes #2627 Revise logical definition of 'inflammatory macrophage'

Fixes #2627 Revise logical definition of 'inflammatory macrophage'

* Replace GO term

src/ontology/cl-edit.owl

@@ -3093,9 +3093,9 @@ Declaration(Class(obo:CL_4052010))
 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_4052048))
 Declaration(Class(obo:CL_4052049))
 Declaration(Class(obo:CP_0000000))
@@ -11264,7 +11264,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000863 "classically activat
 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:28923980") oboInOwl:hasRelatedSynonym obo:CL_0000863 "M1 macrophage")
 AnnotationAssertion(rdfs:comment obo:CL_0000863 "Markers: Express: TNFa, IL1b, IL6, iNOS, NADPH-oxidase; produce: reactive oxygen species, nitric oxide; role or process: immune, inflammation (inflammatory response).")
 AnnotationAssertion(rdfs:label obo:CL_0000863 "inflammatory macrophage")
-EquivalentClasses(obo:CL_0000863 ObjectIntersectionOf(obo:CL_0000861 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0032611) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0032635) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0032640) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0042554) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0042742) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0051767)))
+EquivalentClasses(obo:CL_0000863 ObjectIntersectionOf(obo:CL_0000861 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0032611) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0032635) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0032640) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0042554) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0042742) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0045428)))
 SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000863 obo:CL_0000861)
 
 # Class: obo:CL_0000864 (tissue-resident macrophage)
@@ -32759,6 +32759,17 @@ AnnotationAssertion(rdfs:label obo:CL_4052013 "externa theca cell")
 EquivalentClasses(obo:CL_4052013 ObjectIntersectionOf(obo:CL_0000503 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000156)))
 SubClassOf(obo:CL_4052013 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_4052010))
 
+# 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 <https://orcid.org/0009-0000-8480-9277>)
+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_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.")
@@ -32779,17 +32790,6 @@ 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 <https://orcid.org/0009-0000-8480-9277>)
-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_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.")

src/ontology/imports/go_terms.txt

@@ -12,3 +12,4 @@ GO:0000279
 GO:0036053
 GO:0036376
 GO:1990573
+GO:0045428