From 9e4c0077bccc8799f6587517cb6a7b26fabf00b0 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Wed, 16 Oct 2024 14:15:30 +0100 Subject: [PATCH 1/6] Move terms under [peripheral nervous system neuron] Fixes #2656 --- src/ontology/cl-edit.owl | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 588dbc3bf..10650f145 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3330,7 +3330,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition") AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to") -# Annotation Property: obo:IAO_0000700 (preferred_root) +# Annotation Property: obo:IAO_0000700 (has ontology root term) AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root") @@ -3424,11 +3424,11 @@ AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym") AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference") -# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym) +# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym") -# Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym) +# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym) AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") @@ -4544,7 +4544,7 @@ SubClassOf(obo:CL_0000101 obo:CL_0000526) # Class: obo:CL_0000102 (polymodal neuron) AnnotationAssertion(rdfs:label obo:CL_0000102 "polymodal neuron") -SubClassOf(obo:CL_0000102 obo:CL_0000540) +SubClassOf(obo:CL_0000102 obo:CL_2000032) # Class: obo:CL_0000103 (bipolar neuron) @@ -4567,7 +4567,7 @@ EquivalentClasses(obo:CL_0000104 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeV AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FMA:67305") Annotation(oboInOwl:hasDbXref "GOC:tfm") obo:IAO_0000115 obo:CL_0000105 "Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000105 "FMA:67305") AnnotationAssertion(rdfs:label obo:CL_0000105 "pseudounipolar neuron") -SubClassOf(obo:CL_0000105 obo:CL_0000540) +SubClassOf(obo:CL_0000105 obo:CL_2000032) # Class: obo:CL_0000106 (unipolar neuron) @@ -4575,7 +4575,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "FMA:67278") Annotation(oboInO AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000106 "FMA:67278") AnnotationAssertion(oboInOwl:inSubset obo:CL_0000106 cl:BDS_subset) AnnotationAssertion(rdfs:label obo:CL_0000106 "unipolar neuron") -SubClassOf(obo:CL_0000106 obo:CL_0000540) +SubClassOf(obo:CL_0000106 obo:CL_2000032) # Class: obo:CL_0000107 (autonomic neuron) @@ -5545,7 +5545,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000210 "CALOHA:TS-0868") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000210 "FMA:86740") AnnotationAssertion(rdfs:label obo:CL_0000210 "photoreceptor cell") AnnotationAssertion(foaf:depiction obo:CL_0000210 "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg"^^xsd:anyURI) -EquivalentClasses(obo:CL_0000210 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0050908))) +EquivalentClasses(obo:CL_0000210 ObjectIntersectionOf(obo:CL_2000032 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0050908))) SubClassOf(obo:CL_0000210 obo:CL_0008028) # Class: obo:CL_0000211 (electrically active cell) @@ -6821,7 +6821,7 @@ SubClassOf(obo:CL_0000378 obo:CL_0000630) # Class: obo:CL_0000379 (sensory processing neuron) AnnotationAssertion(rdfs:label obo:CL_0000379 "sensory processing neuron") -SubClassOf(obo:CL_0000379 obo:CL_0000540) +SubClassOf(obo:CL_0000379 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000010))) # Class: obo:CL_0000380 (thecogen cell) @@ -7939,14 +7939,14 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000526 "FMA:87653") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000526 "input neuron") AnnotationAssertion(rdfs:label obo:CL_0000526 "afferent neuron") -SubClassOf(obo:CL_0000526 obo:CL_0000540) +SubClassOf(obo:CL_0000526 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000010))) # Class: obo:CL_0000527 (efferent neuron) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D009476") obo:IAO_0000115 obo:CL_0000527 "A neuron which sends impulses peripherally to activate muscles or secretory cells.") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000527 "output neuron") AnnotationAssertion(rdfs:label obo:CL_0000527 "efferent neuron") -SubClassOf(obo:CL_0000527 obo:CL_0000540) +SubClassOf(obo:CL_0000527 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000010))) # Class: obo:CL_0000528 (nitrergic neuron) @@ -9943,7 +9943,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41598-020-66092- AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41598-020-66092-9") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) Annotation(oboInOwl:hasSynonymType obo:OMO_0003004) oboInOwl:hasRelatedSynonym obo:CL_0000748 "BCs") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GSE137537") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) Annotation(oboInOwl:hasSynonymType obo:OMO_0003004) oboInOwl:hasRelatedSynonym obo:CL_0000748 "BPs") AnnotationAssertion(rdfs:label obo:CL_0000748 "retinal bipolar neuron") -EquivalentClasses(obo:CL_0000748 ObjectIntersectionOf(obo:CL_0000103 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001791))) +EquivalentClasses(obo:CL_0000748 ObjectIntersectionOf(obo:CL_2000032 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001791))) SubClassOf(obo:CL_0000748 obo:CL_0009004) SubClassOf(obo:CL_0000748 ObjectSomeValuesFrom(obo:RO_0002215 ObjectIntersectionOf(obo:GO_0061535 ObjectSomeValuesFrom(obo:BFO_0000050 obo:GO_0098976)))) SubClassOf(obo:CL_0000748 ObjectSomeValuesFrom(obo:RO_0002216 obo:GO_0007601)) @@ -24109,7 +24109,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:12486170") Annotation(ob AnnotationAssertion(rdfs:comment obo:CL_0010022 "This term is used in 3 GO terms that were created as part of the heart development focus project.") AnnotationAssertion(rdfs:label obo:CL_0010022 "cardiac neuron") AnnotationAssertion(rdfs:seeAlso obo:CL_0010022 "https://github.com/obophenotype/cell-ontology/pull/1488") -EquivalentClasses(obo:CL_0010022 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000948))) +EquivalentClasses(obo:CL_0010022 ObjectIntersectionOf(obo:CL_2000032 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000948))) # Class: obo:CL_0011000 (dorsal horn interneuron) @@ -24489,7 +24489,7 @@ AnnotationAssertion(owl:deprecated obo:CL_0011112 "true"^^xsd:boolean) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:NV") obo:IAO_0000115 obo:CL_0011113 "Neuron found in the spiral ganglion.") AnnotationAssertion(rdfs:label obo:CL_0011113 "spiral ganglion neuron") -EquivalentClasses(obo:CL_0011113 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000395))) +EquivalentClasses(obo:CL_0011113 ObjectIntersectionOf(obo:CL_2000032 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000395))) SubClassOf(obo:CL_0011113 obo:CL_0000540) # Class: obo:CL_0011114 (segmented neutrophil of bone marrow) @@ -30522,7 +30522,7 @@ SubClassOf(obo:CL_4023164 obo:CL_4023162) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22865660") obo:IAO_0000115 obo:CL_4023168 "A neuron that is part of the somatic sensory system. Somatosensory neurons innervate the skin or integument to detect different types of thermal, chemical, and mechanical touch stimuli.") AnnotationAssertion(terms:contributor obo:CL_4023168 ) AnnotationAssertion(rdfs:label obo:CL_4023168 "somatosensory neuron") -EquivalentClasses(obo:CL_4023168 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003942))) +EquivalentClasses(obo:CL_4023168 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003942) ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000010))) # Class: obo:CL_4023169 (trigeminal neuron) From b826fb12ccaf0b7f95f6394d56c3613c23924aac Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Wed, 16 Oct 2024 14:45:25 +0100 Subject: [PATCH 2/6] Move terms under [peripheral nervous system neuron] Fixes #2656 --- 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 10650f145..e7cfa9266 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -7939,7 +7939,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000526 "FMA:87653") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000526 "input neuron") AnnotationAssertion(rdfs:label obo:CL_0000526 "afferent neuron") -SubClassOf(obo:CL_0000526 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000010))) +SubClassOf(obo:CL_0000526 obo:CL_0000540) # Class: obo:CL_0000527 (efferent neuron) From fc5a8460137585eb71948592fc984bb10668972c Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Fri, 18 Oct 2024 12:10:25 +0100 Subject: [PATCH 3/6] Update cl-edit.owl --- 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 e7db81522..c0defd531 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3791,6 +3791,7 @@ SubClassOf(obo:CL_0000028 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000338)) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000029 "neuron neural crest derived") AnnotationAssertion(rdfs:label obo:CL_0000029 "neural crest derived neuron") EquivalentClasses(obo:CL_0000029 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000333))) +EquivalentClasses(obo:CL_0000029 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000010)) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000029 obo:CL_0000540) SubClassOf(obo:CL_0000029 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0002676)) @@ -7946,6 +7947,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000526 "FMA:87653") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000526 "input neuron") AnnotationAssertion(rdfs:label obo:CL_0000526 "afferent neuron") SubClassOf(obo:CL_0000526 obo:CL_0000540) +SubClassOf(obo:CL_0000526 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000010)) # Class: obo:CL_0000527 (efferent neuron) From 0a8951cd9fd049b33ecec1f9ac4a9e70285182a0 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Fri, 18 Oct 2024 12:16:06 +0100 Subject: [PATCH 4/6] Update cl-edit.owl --- src/ontology/cl-edit.owl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index c0defd531..c3f252d98 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -7947,7 +7947,6 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000526 "FMA:87653") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000526 "input neuron") AnnotationAssertion(rdfs:label obo:CL_0000526 "afferent neuron") SubClassOf(obo:CL_0000526 obo:CL_0000540) -SubClassOf(obo:CL_0000526 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000010)) # Class: obo:CL_0000527 (efferent neuron) From 49c37047770f88928d43e71c2b4acf5d6a9da634 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Fri, 18 Oct 2024 12:18:08 +0100 Subject: [PATCH 5/6] Update cl-edit.owl --- src/ontology/cl-edit.owl | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index c3f252d98..39644b695 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3791,7 +3791,6 @@ SubClassOf(obo:CL_0000028 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000338)) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000029 "neuron neural crest derived") AnnotationAssertion(rdfs:label obo:CL_0000029 "neural crest derived neuron") EquivalentClasses(obo:CL_0000029 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000333))) -EquivalentClasses(obo:CL_0000029 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000010)) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000029 obo:CL_0000540) SubClassOf(obo:CL_0000029 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0002676)) @@ -7953,7 +7952,7 @@ SubClassOf(obo:CL_0000526 obo:CL_0000540) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D009476") obo:IAO_0000115 obo:CL_0000527 "A neuron which sends impulses peripherally to activate muscles or secretory cells.") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000527 "output neuron") AnnotationAssertion(rdfs:label obo:CL_0000527 "efferent neuron") -SubClassOf(obo:CL_0000527 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000010))) +SubClassOf(obo:CL_0000527 obo:CL_0000540) # Class: obo:CL_0000528 (nitrergic neuron) From 91a75904c112aba227329478ff8ab6ebf2a2f383 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Fri, 18 Oct 2024 17:35:07 +0100 Subject: [PATCH 6/6] Update cl-edit.owl --- src/ontology/cl-edit.owl | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 39644b695..d027104cd 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -5881,7 +5881,6 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000247 "Rohon-Beard cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "VHOG:0001484") oboInOwl:hasRelatedSynonym obo:CL_0000247 "RB neuron") AnnotationAssertion(rdfs:label obo:CL_0000247 "Rohon-Beard neuron") SubClassOf(obo:CL_0000247 obo:CL_0000531) -SubClassOf(obo:CL_0000247 obo:CL_4023168) # Class: obo:CL_0000248 (obsolete microsporocyte) @@ -9947,7 +9946,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41598-020-66092- AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1038/s41598-020-66092-9") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) Annotation(oboInOwl:hasSynonymType obo:OMO_0003004) oboInOwl:hasRelatedSynonym obo:CL_0000748 "BCs") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GSE137537") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) Annotation(oboInOwl:hasSynonymType obo:OMO_0003004) oboInOwl:hasRelatedSynonym obo:CL_0000748 "BPs") AnnotationAssertion(rdfs:label obo:CL_0000748 "retinal bipolar neuron") -EquivalentClasses(obo:CL_0000748 ObjectIntersectionOf(obo:CL_2000032 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001791))) +EquivalentClasses(obo:CL_0000748 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001791))) SubClassOf(obo:CL_0000748 obo:CL_0009004) SubClassOf(obo:CL_0000748 ObjectSomeValuesFrom(obo:RO_0002215 ObjectIntersectionOf(obo:GO_0061535 ObjectSomeValuesFrom(obo:BFO_0000050 obo:GO_0098976)))) SubClassOf(obo:CL_0000748 ObjectSomeValuesFrom(obo:RO_0002216 obo:GO_0007601))