From 303deaaf95a926ae7ef1df335c0797ed5b5ab9bd Mon Sep 17 00:00:00 2001 From: nicolevasilevsky Date: Fri, 22 Nov 2019 14:52:32 -0800 Subject: [PATCH 1/6] add subclassOf assertions addresses #557 --- 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 d266b98a1..cd5f29ab9 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -7965,6 +7965,7 @@ AnnotationAssertion(rdfs:comment obo:CL_0000583 "Markers: Mouse: F4/80mid, CD11b AnnotationAssertion(rdfs:label obo:CL_0000583 "alveolar macrophage"^^xsd:string) EquivalentClasses(obo:CL_0000583 ObjectIntersectionOf(obo:CL_0000864 ObjectSomeValuesFrom(obo:RO_0001025 obo:UBERON_0002299) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001013) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001807) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001813) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001931) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000002064) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000002972) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0019882) ObjectSomeValuesFrom( obo:PR_000001012) ObjectSomeValuesFrom( obo:PR_000001206))) SubClassOf(Annotation(oboInOwl:is_inferred "true"^^xsd:string) obo:CL_0000583 obo:CL_0000864) +SubClassOf(obo:CL_0000583 obo:CL_1001603) # Class: obo:CL_0000584 (enterocyte) @@ -8980,6 +8981,7 @@ SubClassOf(obo:CL_0000690 obo:CL_0000488) AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0000691 "cell"^^xsd:string) AnnotationAssertion(rdfs:label obo:CL_0000691 "stellate interneuron"^^xsd:string) SubClassOf(obo:CL_0000691 obo:CL_0000099) +SubClassOf(obo:CL_0000691 obo:CL_0000122) # Class: obo:CL_0000692 (terminal Schwann cell) @@ -21648,6 +21650,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0009005 "GOC:pr") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0009005 "http://en.wikipedia.org/wiki/Salivary_gland") AnnotationAssertion(rdfs:label obo:CL_0009005 "salivary gland cell") SubClassOf(obo:CL_0009005 obo:CL_0002371) +SubClassOf(obo:CL_0009005 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001044)) # Class: obo:CL_0010000 (keratinized cell of hair follicle) From 3036c110459e8dfcf8e3edb6bc552a21e0942e8d Mon Sep 17 00:00:00 2001 From: nicolevasilevsky Date: Fri, 22 Nov 2019 14:53:37 -0800 Subject: [PATCH 2/6] add synonym to CL:0000815 --- src/ontology/cl-edit.owl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index cd5f29ab9..509541db2 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -10278,6 +10278,7 @@ AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000815 "suppressor T-cell"^ AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000815 "suppressor T-lymphocyte"^^xsd:string) AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000815 "BTO:0004520"^^xsd:string) AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000815 "FMA:84070"^^xsd:string) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000815 "Treg") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000815 "regulatory T lymphocyte"^^xsd:string) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000815 "regulatory T-cell"^^xsd:string) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000815 "regulatory T-lymphocyte"^^xsd:string) From d735677145e3c09fb62980ff47072a49be222a43 Mon Sep 17 00:00:00 2001 From: nicolevasilevsky Date: Fri, 22 Nov 2019 14:56:50 -0800 Subject: [PATCH 3/6] fix typos --- src/ontology/cl-edit.owl | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 509541db2..69f4031d5 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -14993,14 +14993,15 @@ SubClassOf(obo:CL_0002142 obo:CL_0000318) SubClassOf(obo:CL_0002142 obo:CL_0000434) SubClassOf(obo:CL_0002142 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000423)) -# Class: obo:CL_0002143 (dark chief cell of parathyroid cell) +# Class: obo:CL_0002143 (dark chief cell of parathyroid gland cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm"^^xsd:string) Annotation(oboInOwl:hasDbXref "ISBN:0721662544"^^xsd:string) obo:IAO_0000115 obo:CL_0002143 "A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules."^^xsd:string) AnnotationAssertion(oboInOwl:created_by obo:CL_0002143 "tmeehan"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:CL_0002143 "2010-08-24T02:18:36Z"^^xsd:string) AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002143 "FMA:69080"^^xsd:string) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002143 "dark chief cell of parathyroid cell"^^xsd:string) AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0002143 "cell"^^xsd:string) -AnnotationAssertion(rdfs:label obo:CL_0002143 "dark chief cell of parathyroid cell"^^xsd:string) +AnnotationAssertion(rdfs:label obo:CL_0002143 "dark chief cell of parathyroid gland cell") SubClassOf(obo:CL_0002143 obo:CL_0000446) # Class: obo:CL_0002144 (capillary endothelial cell) @@ -15040,14 +15041,15 @@ SubClassOf(obo:CL_0002146 obo:CL_0000318) SubClassOf(obo:CL_0002146 obo:CL_0000434) SubClassOf(obo:CL_0002146 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000423)) -# Class: obo:CL_0002147 (clear chief cell of parathyroid cell) +# Class: obo:CL_0002147 (clear chief cell of parathyroid gland cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm"^^xsd:string) Annotation(oboInOwl:hasDbXref "ISBN:0618947256"^^xsd:string) obo:IAO_0000115 obo:CL_0002147 "A chief cell of parathyroid glands that does not stain with hematoxylin or eosin. This cell is larger, has a larger nucleus and fewer secretory granules than dark chief cells."^^xsd:string) AnnotationAssertion(oboInOwl:created_by obo:CL_0002147 "tmeehan"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:CL_0002147 "2010-08-24T10:39:42Z"^^xsd:string) AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002147 "FMA:69081"^^xsd:string) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002147 "clear chief cell of parathyroid cell") AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0002147 "cell"^^xsd:string) -AnnotationAssertion(rdfs:label obo:CL_0002147 "clear chief cell of parathyroid cell"^^xsd:string) +AnnotationAssertion(rdfs:label obo:CL_0002147 "clear chief cell of parathyroid gland cell"^^xsd:string) SubClassOf(obo:CL_0002147 obo:CL_0000446) # Class: obo:CL_0002148 (dental pulp cell) @@ -15641,7 +15643,7 @@ AnnotationAssertion(rdfs:label obo:CL_0002202 "epithelial cell of tracheobronchi EquivalentClasses(obo:CL_0002202 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0007196))) SubClassOf(obo:CL_0002202 obo:CL_0002632) -# Class: obo:CL_0002203 (Brush cell of epithelium proper of large intestine) +# Class: obo:CL_0002203 (brush cell of epithelium proper of large intestine) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm"^^xsd:string) obo:IAO_0000115 obo:CL_0002203 "Brush cell found in the epithelial layer of the colon."^^xsd:string) AnnotationAssertion(oboInOwl:created_by obo:CL_0002203 "tmeehan"^^xsd:string) @@ -15650,7 +15652,7 @@ AnnotationAssertion(oboInOwl:hasAlternativeId obo:CL_0002203 "CL:1000387"^^xsd:s AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002203 "FMA:263222"^^xsd:string) AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0002203 "cell"^^xsd:string) AnnotationAssertion(rdfs:comment obo:CL_0002203 "Brush cells are a distinct cell type from brush border cell-types."^^xsd:string) -AnnotationAssertion(rdfs:label obo:CL_0002203 "Brush cell of epithelium proper of large intestine"^^xsd:string) +AnnotationAssertion(rdfs:label obo:CL_0002203 "brush cell of epithelium proper of large intestine"^^xsd:string) EquivalentClasses(obo:CL_0002203 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000059))) SubClassOf(obo:CL_0002203 obo:CL_0002204) SubClassOf(obo:CL_0002203 obo:CL_0002253) @@ -16395,7 +16397,7 @@ AnnotationAssertion(oboInOwl:created_by obo:CL_0002265 "tmeehan"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:CL_0002265 "2010-09-10T11:37:35Z"^^xsd:string) AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002265 "FMA:268744"^^xsd:string) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002265 "colon D-cell") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002265 "colonc delta cell") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002265 "colonic delta cell") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002265 "delta cell of colon") AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0002265 "cell"^^xsd:string) AnnotationAssertion(rdfs:label obo:CL_0002265 "type D cell of colon"^^xsd:string) From 1b0cc0a2667cda300bc9f7758a3274a44b59dbbd Mon Sep 17 00:00:00 2001 From: nicolevasilevsky Date: Fri, 22 Nov 2019 14:58:30 -0800 Subject: [PATCH 4/6] fix typos --- src/ontology/cl-edit.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 69f4031d5..e5d911467 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -13861,7 +13861,7 @@ SubClassOf(obo:CL_0002050 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0002049)) # Class: obo:CL_0002051 (CD38-high pre-BCR positive cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:18432934"^^xsd:string) obo:IAO_0000115 obo:CL_0002051 "A pre-BCR positive T cell that is CD38-high."^^xsd:string) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:18432934"^^xsd:string) obo:IAO_0000115 obo:CL_0002051 "A pre-BCR positive B cell that is CD38-high."^^xsd:string) AnnotationAssertion(oboInOwl:created_by obo:CL_0002051 "tmeehan"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:CL_0002051 "2010-04-28T02:27:47Z"^^xsd:string) AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0002051 "cell"^^xsd:string) @@ -22621,13 +22621,13 @@ EquivalentClasses(obo:CL_1000322 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeV SubClassOf(obo:CL_1000322 obo:CL_0000069) SubClassOf(obo:CL_1000322 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0009970)) -# Class: obo:CL_1000323 (pylroric gastric gland goblet cell) +# Class: obo:CL_1000323 (pyloric gastric gland goblet cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm"^^xsd:string) obo:IAO_0000115 obo:CL_1000323 "A goblet cell that is part of the epithelium of pyloric gland."^^xsd:string) AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000323 "FMA:263061"^^xsd:string) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_1000323 "goblet cell of epithelium of pyloric gland") AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_1000323 "cell"^^xsd:string) -AnnotationAssertion(rdfs:label obo:CL_1000323 "pylroric gastric gland goblet cell"^^xsd:string) +AnnotationAssertion(rdfs:label obo:CL_1000323 "pyloric gastric gland goblet cell"^^xsd:string) EquivalentClasses(obo:CL_1000323 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008861))) SubClassOf(obo:CL_1000323 ObjectSomeValuesFrom(obo:BFO_0000050 ObjectIntersectionOf(obo:UBERON_0000483 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008861)))) From 52c051186794deb264142ca480364f23a5dfdb87 Mon Sep 17 00:00:00 2001 From: nicolevasilevsky Date: Fri, 22 Nov 2019 14:59:33 -0800 Subject: [PATCH 5/6] fix typos --- src/ontology/cl-edit.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index e5d911467..42ac09a46 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -4408,7 +4408,7 @@ EquivalentClasses(obo:CL_0000170 ObjectIntersectionOf(obo:CL_0000151 ObjectSomeV AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm"^^xsd:string) Annotation(oboInOwl:hasDbXref "ISBN:0721662544"^^xsd:string) obo:IAO_0000115 obo:CL_0000171 "A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon."^^xsd:string) AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000171 "BTO:0000990"^^xsd:string) AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000171 "FMA:70585"^^xsd:string) -AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000171 "alpha cell of iselt of Langerhans"^^xsd:string) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000171 "alpha cell of islet of Langerhans"^^xsd:string) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000171 "pancreatic alpha cell"^^xsd:string) AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0000171 "cell"^^xsd:string) AnnotationAssertion(rdfs:label obo:CL_0000171 "pancreatic A cell"^^xsd:string) @@ -21056,7 +21056,7 @@ EquivalentClasses(obo:CL_0005018 ObjectIntersectionOf(obo:CL_0000151 ObjectSomeV # Class: obo:CL_0005019 (pancreatic epsilon cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:14970313"^^xsd:string) obo:IAO_0000115 obo:CL_0005019 "Ghrelin secreting cells found in the found in the exocrine pancreas."^^xsd:string) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:14970313"^^xsd:string) obo:IAO_0000115 obo:CL_0005019 "Ghrelin secreting cells found in the exocrine pancreas."^^xsd:string) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0005019 "pancreatic E cell") AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0005019 "cell"^^xsd:string) AnnotationAssertion(rdfs:comment obo:CL_0005019 "In mammals the endocrine pancreas is called the Islets of Langerhans."^^xsd:string) From 525b58e8cdd873a132beef200d654f6ac6a47700 Mon Sep 17 00:00:00 2001 From: dosumis Date: Fri, 3 Jan 2020 11:30:18 +0000 Subject: [PATCH 6/6] chief cell of parathyroid gland cell->... chief cell of parathyroid gland --- src/ontology/cl-edit.owl | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 42ac09a46..53f42de7b 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -14993,15 +14993,14 @@ SubClassOf(obo:CL_0002142 obo:CL_0000318) SubClassOf(obo:CL_0002142 obo:CL_0000434) SubClassOf(obo:CL_0002142 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000423)) -# Class: obo:CL_0002143 (dark chief cell of parathyroid gland cell) +# Class: obo:CL_0002143 (dark chief cell of parathyroid gland) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm"^^xsd:string) Annotation(oboInOwl:hasDbXref "ISBN:0721662544"^^xsd:string) obo:IAO_0000115 obo:CL_0002143 "A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules."^^xsd:string) AnnotationAssertion(oboInOwl:created_by obo:CL_0002143 "tmeehan"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:CL_0002143 "2010-08-24T02:18:36Z"^^xsd:string) AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002143 "FMA:69080"^^xsd:string) -AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002143 "dark chief cell of parathyroid cell"^^xsd:string) AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0002143 "cell"^^xsd:string) -AnnotationAssertion(rdfs:label obo:CL_0002143 "dark chief cell of parathyroid gland cell") +AnnotationAssertion(rdfs:label obo:CL_0002143 "dark chief cell of parathyroid gland") SubClassOf(obo:CL_0002143 obo:CL_0000446) # Class: obo:CL_0002144 (capillary endothelial cell) @@ -15041,7 +15040,7 @@ SubClassOf(obo:CL_0002146 obo:CL_0000318) SubClassOf(obo:CL_0002146 obo:CL_0000434) SubClassOf(obo:CL_0002146 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000423)) -# Class: obo:CL_0002147 (clear chief cell of parathyroid gland cell) +# Class: obo:CL_0002147 (clear chief cell of parathyroid gland) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm"^^xsd:string) Annotation(oboInOwl:hasDbXref "ISBN:0618947256"^^xsd:string) obo:IAO_0000115 obo:CL_0002147 "A chief cell of parathyroid glands that does not stain with hematoxylin or eosin. This cell is larger, has a larger nucleus and fewer secretory granules than dark chief cells."^^xsd:string) AnnotationAssertion(oboInOwl:created_by obo:CL_0002147 "tmeehan"^^xsd:string) @@ -15049,7 +15048,7 @@ AnnotationAssertion(oboInOwl:creation_date obo:CL_0002147 "2010-08-24T10:39:42Z" AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002147 "FMA:69081"^^xsd:string) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002147 "clear chief cell of parathyroid cell") AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0002147 "cell"^^xsd:string) -AnnotationAssertion(rdfs:label obo:CL_0002147 "clear chief cell of parathyroid gland cell"^^xsd:string) +AnnotationAssertion(rdfs:label obo:CL_0002147 "clear chief cell of parathyroid gland"^^xsd:string) SubClassOf(obo:CL_0002147 obo:CL_0000446) # Class: obo:CL_0002148 (dental pulp cell)