From 2454a4fbc7f016d3700185eb8fe488f90b798cbd Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Thu, 26 Oct 2023 16:35:33 +0100 Subject: [PATCH 1/3] Fixes #1266 populate mononuclear phagocyte Fixes #1266 populate mononuclear phagocyte --- src/ontology/cl-edit.owl | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 9e2590a30..24b2d96b7 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -4300,6 +4300,7 @@ AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000092 "chondroclast") AnnotationAssertion(rdfs:comment obo:CL_0000092 "Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid.") AnnotationAssertion(rdfs:label obo:CL_0000092 "osteoclast") EquivalentClasses(obo:CL_0000092 ObjectIntersectionOf(obo:CL_0000766 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001474) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000001850) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000001937) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000001944) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000007597) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000011178) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001954) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000002062) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0045453))) +SubClassOf(obo:CL_0000092 obo:CL_0000113) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000092 obo:CL_0000766) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000092 obo:CL_0001035) SubClassOf(obo:CL_0000092 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000576)) @@ -4500,6 +4501,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000113 "BTO:0001433") AnnotationAssertion(rdfs:label obo:CL_0000113 "mononuclear phagocyte") EquivalentClasses(obo:CL_0000113 ObjectIntersectionOf(obo:CL_0000518 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001407))) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000113 obo:CL_0000518) +SubClassOf(obo:CL_0000113 obo:CL_0000842) # Class: obo:CL_0000114 (surface ectodermal cell) @@ -5643,6 +5645,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000235 "histiocyte") AnnotationAssertion(rdfs:comment obo:CL_0000235 "Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid.") AnnotationAssertion(rdfs:label obo:CL_0000235 "macrophage") EquivalentClasses(obo:CL_0000235 ObjectIntersectionOf(obo:CL_0000766 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0002504) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0006909) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0031268))) +SubClassOf(obo:CL_0000235 obo:CL_0000113) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000235 obo:CL_0000766) SubClassOf(obo:CL_0000235 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000576)) From 8d369b276b04b682af5219339c1ce3eb01c3cad2 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Fri, 27 Oct 2023 09:05:06 +0100 Subject: [PATCH 2/3] Fix hierarchy --- 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 24b2d96b7..da861f61b 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -4300,7 +4300,7 @@ AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000092 "chondroclast") AnnotationAssertion(rdfs:comment obo:CL_0000092 "Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid.") AnnotationAssertion(rdfs:label obo:CL_0000092 "osteoclast") EquivalentClasses(obo:CL_0000092 ObjectIntersectionOf(obo:CL_0000766 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001474) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000001850) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000001937) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000001944) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000007597) ObjectSomeValuesFrom(obo:BFO_0000051 obo:PR_000011178) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001954) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000002062) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0045453))) -SubClassOf(obo:CL_0000092 obo:CL_0000113) +SubClassOf(obo:CL_0000092 obo:CL_0000518) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000092 obo:CL_0000766) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000092 obo:CL_0001035) SubClassOf(obo:CL_0000092 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000576)) From 7e6e5faee7ff0a048cdd1c3f564d040913eb5a51 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 13 Nov 2023 11:40:37 +0000 Subject: [PATCH 3/3] Add dendritic cell and monocyte --- src/ontology/cl-edit.owl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 871a4eea8..449a8b131 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -7209,6 +7209,7 @@ AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000451 "interdigitating c AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000451 "veiled cell") AnnotationAssertion(rdfs:label obo:CL_0000451 "dendritic cell") EquivalentClasses(obo:CL_0000451 ObjectIntersectionOf(obo:CL_0000738 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0042613) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001002) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001003) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001020) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001024) ObjectSomeValuesFrom(obo:CL_4030046 obo:PR_000001289) ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001407) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0001816) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0002504) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0019882) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0045580))) +SubClassOf(obo:CL_0000451 obo:CL_0000113) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000451 obo:CL_0000738) DisjointClasses(obo:CL_0000451 obo:CL_0000542) @@ -8297,6 +8298,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000576 "FMA:62864") AnnotationAssertion(rdfs:comment obo:CL_0000576 "Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid.") AnnotationAssertion(rdfs:label obo:CL_0000576 "monocyte") EquivalentClasses(obo:CL_0000576 ObjectIntersectionOf(obo:CL_0000766 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0001407) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0030225) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0030316) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0043011))) +SubClassOf(obo:CL_0000576 obo:CL_0000113) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000576 obo:CL_0000766) SubClassOf(obo:CL_0000576 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000559))