From 610d386ae711cc799186a06f1c506d361cd377d2 Mon Sep 17 00:00:00 2001 From: Alida Avola <81253886+AvolaAmg@users.noreply.github.com> Date: Thu, 4 Apr 2024 16:32:23 +0100 Subject: [PATCH] NTR-border-associated-macrophage (#2319) * NTR-border-associated-macrophage Fixes #2285 * Update cl-edit.owl * Update cl-edit.owl * Update cl-edit.owl * Update cl-edit.owl * Update cl-edit.owl * Update cl-edit.owl * Update cl-edit.owl --- src/ontology/cl-edit.owl | 78 +++++++++++++++++++++++++++++++++------- 1 file changed, 66 insertions(+), 12 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index c5f59fc24..ff8a14332 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3026,6 +3026,10 @@ Declaration(Class(obo:CL_4040005)) Declaration(Class(obo:CL_4040006)) Declaration(Class(obo:CL_4042001)) Declaration(Class(obo:CL_4042002)) +Declaration(Class(obo:CL_4042003)) +Declaration(Class(obo:CL_4042004)) +Declaration(Class(obo:CL_4042005)) +Declaration(Class(obo:CL_4042006)) Declaration(Class(obo:CP_0000000)) Declaration(Class(obo:CP_0000025)) Declaration(Class(obo:CP_0000027)) @@ -11263,26 +11267,31 @@ SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000878 obo:CL_0000864 # Class: obo:CL_0000879 (meningeal macrophage) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:ana") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:11591794") obo:IAO_0000115 obo:CL_0000879 "A central nervous system macrophage found in the meninges (the three membranes that surround the brain). This macrophage types is highly phagocytic and expresses scavenger receptors.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:ana") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:11591794") Annotation(oboInOwl:hasDbXref "PMID:24078900") Annotation(oboInOwl:hasDbXref "PMID:37232741") obo:IAO_0000115 obo:CL_0000879 "A border associated macrophage that is part of a meninx. This macrophage type is elongated and amoeboid spindle-shaped with limited mobility. This macrophage is highly phagocytic, expresses scavenger receptors, has dynamic protrusions and extends its processes during inflammation.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33556248") oboInOwl:hasExactSynonym obo:CL_0000879 "subdural leptomeningeal macrophage") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:28323268") oboInOwl:hasExactSynonym obo:CL_0000879 "subdural meningeal macrophage") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33556248") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0000879 "MM") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38347231") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0000879 "MnMΦ") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0000879 "sdΜΦ") AnnotationAssertion(rdfs:label obo:CL_0000879 "meningeal macrophage") -EquivalentClasses(obo:CL_0000879 ObjectIntersectionOf(obo:CL_0000878 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002360) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0005044))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000879 obo:CL_0000878) +EquivalentClasses(obo:CL_0000879 ObjectIntersectionOf(obo:CL_4042003 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002360) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0005044))) +SubClassOf(obo:CL_0000879 obo:CL_4042003) -# Class: obo:CL_0000880 (choroid-plexus macrophage) +# Class: obo:CL_0000880 (choroid plexus macrophage) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:ana") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:9550136") obo:IAO_0000115 obo:CL_0000880 "A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This cell expresses scavenger receptors.") -AnnotationAssertion(rdfs:label obo:CL_0000880 "choroid-plexus macrophage") -EquivalentClasses(obo:CL_0000880 ObjectIntersectionOf(obo:CL_0000878 ObjectSomeValuesFrom(obo:RO_0001025 obo:UBERON_0001886) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0005044))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000880 obo:CL_0000878) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:ana") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:37232741") Annotation(oboInOwl:hasDbXref "PMID:9550136") obo:IAO_0000115 obo:CL_0000880 "A border associated macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This central nervous system macrophage has a star-like shaped body and expresses scavenger receptors.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0000880 "cpMΦ") +AnnotationAssertion(rdfs:label obo:CL_0000880 "choroid plexus macrophage") +EquivalentClasses(obo:CL_0000880 ObjectIntersectionOf(obo:CL_4042003 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001886) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0005044))) # Class: obo:CL_0000881 (perivascular macrophage) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:16507898") obo:IAO_0000115 obo:CL_0000881 "A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+.") -AnnotationAssertion(rdfs:comment obo:CL_0000881 "Markers: Human/monkey, mice: CD163. Human: CD14+CD16+CD163+.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:16507898") Annotation(oboInOwl:hasDbXref "PMID:37232741") obo:IAO_0000115 obo:CL_0000881 "A border associated macrophage that is adjacent to a small blood vessel of a brain. A perivascular macrophage expresses the markers CD14, CD16 and CD163. In homeostatic conditions, this central nervous system macrophage has a non-motile cell body with extending and retracting projections through the blood vessel wall.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0000881 "pvMΦ") AnnotationAssertion(rdfs:label obo:CL_0000881 "perivascular macrophage") -EquivalentClasses(obo:CL_0000881 ObjectIntersectionOf(obo:CL_0000878 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001981) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001483) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001889) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001925))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000881 obo:CL_0000878) +EquivalentClasses(obo:CL_0000881 ObjectIntersectionOf(obo:CL_4042003 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001981) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001483) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001889) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001925))) SubClassOf(obo:CL_0000881 obo:CL_4033054) +SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000881 obo:CL_4042003) # Class: obo:CL_0000882 (thymic medullary macrophage) @@ -31965,6 +31974,51 @@ AnnotationAssertion(rdfs:label obo:CL_4042002 "TAC3-positive medium spiny neuron SubClassOf(obo:CL_4042002 obo:CL_4030051) SubClassOf(obo:CL_4042002 ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000016004)) +# Class: obo:CL_4042003 (border associated macrophage) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") Annotation(oboInOwl:hasDbXref "PMID:37626977") obo:IAO_0000115 obo:CL_4042003 "A central nervous system macrophage that is part of a choroid plexus, a meninx and a perivascular space. A border associated macrophage interacts with various components of the CNS vasculature and meninges, it participates in immune surveillance and in the regulation of the blood brain barrier.") +AnnotationAssertion( obo:CL_4042003 ) +AnnotationAssertion( obo:CL_4042003 "2024-03-26T16:39:56Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36945367") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042003 "BAM") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33556248") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042003 "CAM") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") oboInOwl:hasRelatedSynonym obo:CL_4042003 "CNS-associated macrophage") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29426702") Annotation(oboInOwl:hasDbXref "PMID:37232741") rdfs:comment obo:CL_4042003 "In humans, a border associate macrophage expresses CD45 and CD11B. This cell is also known to have the following molecular signature: CD206, CD38, LYVE1, CD163, CD169.") +AnnotationAssertion(rdfs:label obo:CL_4042003 "border associated macrophage"@en) +SubClassOf(obo:CL_4042003 obo:CL_0000878) + +# Class: obo:CL_4042004 (choroid epiplexus macrophage) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31061494") Annotation(oboInOwl:hasDbXref "PMID:37232741") obo:IAO_0000115 obo:CL_4042004 "A choroid plexus macrophage that is part of the apical surface of some choroid plexus epithelium. This macrophage has a star-like shaped body.") +AnnotationAssertion( obo:CL_4042004 ) +AnnotationAssertion( obo:CL_4042004 "2024-03-26T19:14:58Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31433571") oboInOwl:hasExactSynonym obo:CL_4042004 "Kolmer’s cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38347231") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042004 "cpepiMΦ") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38347231") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042004 "epiplexus cpMΦ") +AnnotationAssertion(rdfs:label obo:CL_4042004 "choroid epiplexus macrophage"@en) +SubClassOf(obo:CL_4042004 obo:CL_0000880) +SubClassOf(obo:CL_4042004 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003911)) + +# Class: obo:CL_4042005 (stromal choroid plexus macrophage) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38347231") obo:IAO_0000115 obo:CL_4042005 "A choroid plexus macrophage that is part of a choroid plexus stroma.") +AnnotationAssertion( obo:CL_4042005 ) +AnnotationAssertion( obo:CL_4042005 "2024-03-26T19:21:51Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37626977") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042005 "cpstMΦ") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") Annotation(oboInOwl:hasDbXref "PMID:38347231") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042005 "stromal cpMΦ") +AnnotationAssertion(rdfs:label obo:CL_4042005 "stromal choroid plexus macrophage"@en) +SubClassOf(obo:CL_4042005 obo:CL_0000880) +SubClassOf(obo:CL_4042005 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005206)) + +# Class: obo:CL_4042006 (dural macrophage) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31061494") obo:IAO_0000115 obo:CL_4042006 "A border associated macrophage which is part of a dura matter. This macrophage phagocytoses intruding pathogens and foreign molecules detected in the bloodstream or in the cerebrospinal fluid. This cell has an amoeboid body with dynamic protrusions in homeostasis.") +AnnotationAssertion( obo:CL_4042006 ) +AnnotationAssertion( obo:CL_4042006 "2024-03-26T19:27:03Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042006 "dmMΦ") +AnnotationAssertion(rdfs:label obo:CL_4042006 "dural macrophage"@en) +SubClassOf(obo:CL_4042006 obo:CL_4042003) +SubClassOf(obo:CL_4042006 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002092)) + # Class: obo:CP_0000000 (obsolete CP:0000000) AnnotationAssertion(obo:IAO_0100001 obo:CP_0000000 obo:CL_0017500)