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Adjust hierarchy of somatosensory neurons (sensu Teleostei)
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Fixes #2727
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@AvolaAmg
AvolaAmg committed Nov 13, 2024
1 parent e4cf2a3 commit a4640c1
Showing 1 changed file with 33 additions and 5 deletions.
38 changes: 33 additions & 5 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -3087,6 +3087,8 @@ Declaration(Class(obo:CL_4042033))
Declaration(Class(obo:CL_4042034))
Declaration(Class(obo:CL_4042035))
Declaration(Class(obo:CL_4042036))
Declaration(Class(obo:CL_4042037))
Declaration(Class(obo:CL_4042038))
Declaration(Class(obo:CL_4047006))
Declaration(Class(obo:CL_4047007))
Declaration(Class(obo:CL_4047011))
Expand Down Expand Up @@ -3366,7 +3368,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition")

AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to")

# Annotation Property: obo:IAO_0000700 (has ontology root term)
# Annotation Property: obo:IAO_0000700 (preferred_root)

AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root")

Expand Down Expand Up @@ -3456,11 +3458,11 @@ 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")

Expand Down Expand Up @@ -8013,6 +8015,7 @@ SubClassOf(obo:CL_0000529 obo:CL_0000710)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:1842357") Annotation(oboInOwl:hasDbXref "doi:10.1242/dev.108.1.121") obo:IAO_0000115 obo:CL_0000530 "A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed.")
AnnotationAssertion(rdfs:label obo:CL_0000530 "primary neuron (sensu Teleostei)")
SubClassOf(obo:CL_0000530 obo:CL_0000540)
SubClassOf(obo:CL_0000530 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002240))
SubClassOf(Annotation(obo:IAO_0000233 "https://github.com/obophenotype/cell-ontology/pull/1950") obo:CL_0000530 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_32443))

# Class: obo:CL_0000531 (primary sensory neuron (sensu Teleostei))
Expand All @@ -8023,6 +8026,10 @@ EquivalentClasses(obo:CL_0000531 ObjectIntersectionOf(obo:CL_0000101 obo:CL_0000

# Class: obo:CL_0000532 (CAP motoneuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:17971221") Annotation(oboInOwl:hasDbXref "PMID:35431796") obo:IAO_0000115 obo:CL_0000532 "A primary motor neuron with its soma in the caudal region of a spinal cord. The axon of this motoneuron exit the spinal cord from one single point and innervates muscles from its lateral region.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:3746410") oboInOwl:hasExactSynonym obo:CL_0000532 "CaP motorneuron")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:17971221") oboInOwl:hasRelatedSynonym obo:CL_0000532 "cap cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18077593") oboInOwl:hasRelatedSynonym obo:CL_0000532 "caudal primary motor neuron")
AnnotationAssertion(rdfs:label obo:CL_0000532 "CAP motoneuron")
SubClassOf(obo:CL_0000532 obo:CL_0000533)

Expand All @@ -8045,7 +8052,9 @@ SubClassOf(obo:CL_0000534 obo:CL_0000530)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:1842357") Annotation(oboInOwl:hasDbXref "doi:10.1242/dev.108.1.121") obo:IAO_0000115 obo:CL_0000535 "A neuron of teleosts that develops later than a primary neuron, typically during the larval stages.")
AnnotationAssertion(rdfs:label obo:CL_0000535 "secondary neuron (sensu Teleostei)")
SubClassOf(obo:CL_0000535 obo:CL_0000540)
SubClassOf(obo:CL_0000535 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002240))
SubClassOf(Annotation(obo:IAO_0000233 "https://github.com/obophenotype/cell-ontology/pull/1950") obo:CL_0000535 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_32443))
SubClassOf(obo:CL_0000535 ObjectSomeValuesFrom(obo:RO_0002202 obo:UBERON_0002342))

# Class: obo:CL_0000536 (secondary motor neuron (sensu Teleostei))

Expand Down Expand Up @@ -32735,6 +32744,25 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38020069") rdfs:comment
AnnotationAssertion(rdfs:label obo:CL_4042036 "melanin-concentrating hormone neuron"@en)
SubClassOf(obo:CL_4042036 obo:CL_2000029)

# Class: obo:CL_4042037 (middle primary motoneuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35431796") Annotation(oboInOwl:hasDbXref "PMID:3746410") obo:IAO_0000115 obo:CL_4042037 "A type of primary motor neuron located in the middle region of the spinal cord. This primary motor neuron type is characterized by their distinct axonal pathways that innervate the middle trunk muscles.")
AnnotationAssertion(terms:contributor obo:CL_4042037 <https://orcid.org/0000-0002-0098-8958>)
AnnotationAssertion(terms:date obo:CL_4042037 "2024-11-13T13:39:28Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_4042037 "ZFA:0005179")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:3746410") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042037 "MiP")
AnnotationAssertion(rdfs:label obo:CL_4042037 "middle primary motoneuron"@en)
SubClassOf(obo:CL_4042037 obo:CL_0000533)

# Class: obo:CL_4042038 (rostral primary motorneuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35431796") Annotation(oboInOwl:hasDbXref "PMID:3746410") obo:IAO_0000115 obo:CL_4042038 "A type of primary motor neuron situated in the rostral region of the spinal cord. RoP neurons extend their axons to innervate the dorsal trunk musculature.")
AnnotationAssertion(terms:contributor obo:CL_4042038 <https://orcid.org/0000-0002-0098-8958>)
AnnotationAssertion(terms:date obo:CL_4042038 "2024-11-13T13:42:01Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:3746410") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042038 "RoP")
AnnotationAssertion(rdfs:label obo:CL_4042038 "rostral primary motorneuron"@en)
SubClassOf(obo:CL_4042038 obo:CL_0000533)

# Class: obo:CL_4047006 (fetal artery endothelial cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047006 "An endothelial cell that lines an artery in the fetal circulatory system.")
Expand Down Expand Up @@ -33159,11 +33187,11 @@ EquivalentClasses(obo:CL_4052025 ObjectIntersectionOf(obo:GO_0005634 ObjectSomeV
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34727990") Annotation(oboInOwl:hasDbXref "PMID:35908794") Annotation(oboInOwl:hasDbXref "PMID:36361732") Annotation(oboInOwl:hasDbXref "doi:10.1101/2024.05.15.594276") obo:IAO_0000115 obo:CL_4052026 "A fast type II muscle cell that is part of the skeletal muscle tissue. This cell is characterized by its intermediate metabolic profile, utilizing both glycolytic and oxidative pathways for energy production. In humans, it is distinguished by the expression of myosin heavy chain 1 (MYH1).")
AnnotationAssertion(terms:contributor obo:CL_4052026 <https://orcid.org/0009-0000-8480-9277>)
AnnotationAssertion(terms:date obo:CL_4052026 "2024-11-04T10:26:29Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34727990") oboInOwl:hasExactSynonym obo:CL_4052026 "type 2x fiber")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34727990") oboInOwl:hasExactSynonym obo:CL_4052026 "type 2x muscle cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34727990") oboInOwl:hasExactSynonym obo:CL_4052026 "type 2x muscle fiber")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2024.05.15.594276") oboInOwl:hasExactSynonym obo:CL_4052026 "type IIx muscle fiber")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34727990") oboInOwl:hasExactSynonym obo:CL_4052026 "type 2x fiber")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34727990") Annotation(oboInOwl:hasDbXref "PMID:27199166") rdfs:comment obo:CL_4052026 "In humans, type IIx fiber contains high levels of MYLK2, enhancing contraction speed and force via myosin phosphorylation, especially under low calcium. This mechanism supports post-activation potentiation, increasing force output in fast-twitch muscles. Additionally, this fiber has abundant ACTN3 (α-actinin-3), linked to muscle power, and exhibits the highest shortening velocity among human muscle fiber types. Notably, type IIx fiber is selectively lost in aging-related sarcopenia, increases in proportion in type 2 diabetes and obesity, and is the first to degenerate in Duchenne Muscular Dystrophy, impacting muscle function across various conditions.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27199166") Annotation(oboInOwl:hasDbXref "PMID:34727990") rdfs:comment obo:CL_4052026 "In humans, type IIx fiber contains high levels of MYLK2, enhancing contraction speed and force via myosin phosphorylation, especially under low calcium. This mechanism supports post-activation potentiation, increasing force output in fast-twitch muscles. Additionally, this fiber has abundant ACTN3 (α-actinin-3), linked to muscle power, and exhibits the highest shortening velocity among human muscle fiber types. Notably, type IIx fiber is selectively lost in aging-related sarcopenia, increases in proportion in type 2 diabetes and obesity, and is the first to degenerate in Duchenne Muscular Dystrophy, impacting muscle function across various conditions.")
AnnotationAssertion(rdfs:label obo:CL_4052026 "type IIx muscle cell")
SubClassOf(obo:CL_4052026 obo:CL_0002212)
SubClassOf(obo:CL_4052026 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001134))
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