From da02263390d9530c169f4fc087d3b4caaa9c3438 Mon Sep 17 00:00:00 2001 From: Alida Avola <81253886+AvolaAmg@users.noreply.github.com> Date: Mon, 28 Oct 2024 12:18:43 +0000 Subject: [PATCH] Move terms under [peripheral nervous system neuron] (#2665) * Move terms under [peripheral nervous system neuron] Fixes #2656 * Move terms under [peripheral nervous system neuron] Fixes #2656 * Update cl-edit.owl * Update cl-edit.owl * Update cl-edit.owl * Update cl-edit.owl * Update cl-edit.owl --------- Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com> --- 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 e9e583c0c..b3cc10c7b 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3181,6 +3181,7 @@ Declaration(Class(obo:PR_000014419)) Declaration(Class(obo:PR_000014898)) Declaration(Class(obo:PR_000015325)) Declaration(Class(obo:PR_000015665)) +Declaration(Class(obo:PR_000016626)) Declaration(Class(obo:PR_000017299)) Declaration(Class(obo:PR_000032148)) Declaration(Class(obo:PR_000032533)) @@ -3342,7 +3343,7 @@ 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") @@ -3436,11 +3437,11 @@ 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") @@ -4556,7 +4557,7 @@ 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) @@ -4579,7 +4580,7 @@ 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) @@ -4587,7 +4588,7 @@ 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) @@ -5118,8 +5119,8 @@ AnnotationAssertion(owl:deprecated obo:CL_0000161 "true"^^xsd:boolean) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0517223651") Annotation(oboInOwl:hasDbXref "PMID:31613538") Annotation(oboInOwl:hasDbXref "PMID:31670611") obo:IAO_0000115 obo:CL_0000162 "An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by its pyramidal shape, abundant mitochondria, and a complex network of secretory canaliculi lined with microvilli. It secretes hydrochloric acid into the stomach lumen and produces intrinsic factor, essential for vitamin B12 absorption.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000162 "BTO:0001780") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000162 "FMA:62901") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Parietal_cell") oboInOwl:hasExactSynonym obo:CL_0000162 "oxyntic cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29263912") oboInOwl:hasExactSynonym obo:CL_0000162 "gastric parietal cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Parietal_cell") oboInOwl:hasExactSynonym obo:CL_0000162 "oxyntic cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29263912") Annotation(oboInOwl:hasDbXref "PMID:31613538") rdfs:comment obo:CL_0000162 "Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function.") AnnotationAssertion(rdfs:label obo:CL_0000162 "parietal cell") SubClassOf(obo:CL_0000162 obo:CL_0000151) @@ -5892,7 +5893,6 @@ 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) @@ -6834,7 +6834,7 @@ 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) @@ -9958,7 +9958,7 @@ 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_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)) @@ -24121,7 +24121,7 @@ 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) @@ -24501,7 +24501,7 @@ 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) @@ -28013,8 +28013,8 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "HPA:HPA") Annotation(oboInOwl AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1001591 "CALOHA:TS-1277") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "fallopian tube glandular cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "fallopian tube glandular cells") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "uterine tube glandular cell") AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_1001591 "oviduct glandular cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "uterine tube glandular cell") AnnotationAssertion(rdfs:label obo:CL_1001591 "oviduct secretory cell") EquivalentClasses(obo:CL_1001591 ObjectIntersectionOf(obo:CL_1100001 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000993))) SubClassOf(obo:CL_1001591 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004804)) @@ -30543,7 +30543,7 @@ 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)