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Re-done-Alpha1,2 Beta1,2 tanycyte,NTR (#2506)
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* Re-done-t-type-GABAergic-VIP-cortical-interneuron-definition

fixes #2256

To follow changes in this PR, read @AmgAvola comments in the ticket #2256

Alpha1,2 Beta1,2 tanycyte added with definition, references, synonyms and logical definition.

* Update cl-edit.owl

add logical SubClass

* Remove unwanted parent term in imported PR term

* Update cl-edit.owl

---------

Co-authored-by: aleixpuig <[email protected]>
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@AvolaAmg @aleixpuigb
AvolaAmg and aleixpuigb authored Aug 21, 2024
1 parent b135731 commit b2f8c1c
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Showing 5 changed files with 916 additions and 11 deletions.
66 changes: 61 additions & 5 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -3058,6 +3058,10 @@ Declaration(Class(obo:CL_4042013))
Declaration(Class(obo:CL_4042014))
Declaration(Class(obo:CL_4042015))
Declaration(Class(obo:CL_4042016))
Declaration(Class(obo:CL_4042017))
Declaration(Class(obo:CL_4042018))
Declaration(Class(obo:CL_4042019))
Declaration(Class(obo:CL_4042020))
Declaration(Class(obo:CL_4052001))
Declaration(Class(obo:CL_4052002))
Declaration(Class(obo:CP_0000000))
Expand Down Expand Up @@ -3111,9 +3115,12 @@ Declaration(Class(obo:PR_000004919))
Declaration(Class(obo:PR_000005444))
Declaration(Class(obo:PR_000005460))
Declaration(Class(obo:PR_000007204))
Declaration(Class(obo:PR_000007479))
Declaration(Class(obo:PR_000007489))
Declaration(Class(obo:PR_000007785))
Declaration(Class(obo:PR_000009981))
Declaration(Class(obo:PR_000013502))
Declaration(Class(obo:PR_000014419))
Declaration(Class(obo:PR_000015325))
Declaration(Class(obo:PR_000015665))
Declaration(Class(obo:PR_000017299))
Expand Down Expand Up @@ -3269,7 +3276,7 @@ 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")

Expand Down Expand Up @@ -3363,11 +3370,11 @@ 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 @@ -14508,12 +14515,12 @@ SubClassOf(obo:CL_0002084 obo:CL_0002315)

# Class: obo:CL_0002085 (tanycyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "http://neurolex.org/wiki/Category:Tanycyte") obo:IAO_0000115 obo:CL_0002085 "Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "http://neurolex.org/wiki/Category:Tanycyte") obo:IAO_0000115 obo:CL_0002085 "A specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. A tanycyte is found in the adult brain, specifically in the third ventricle, cerebral aqueduct, spinal canal, and floor of the fourth ventricle. This cell type is involved in hormonal regulation, gatekeeping molecules between the bloodstream and cerebrospinal fluid, metabolic sensing, and regulating food intake.")
AnnotationAssertion(terms:contributor obo:CL_0002085 <https://orcid.org/0000-0003-1980-3228>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002085 "2010-07-15T11:21:11Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002085 "BTO:0001953")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002085 "FMA:54560")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002085 "stretch cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29351662") oboInOwl:hasExactSynonym obo:CL_0002085 "stretch cell")
AnnotationAssertion(rdfs:label obo:CL_0002085 "tanycyte")
SubClassOf(obo:CL_0002085 obo:CL_0000683)

Expand Down Expand Up @@ -32250,6 +32257,55 @@ SubClassOf(obo:CL_4042016 obo:CL_0000313)
SubClassOf(obo:CL_4042016 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005385))
SubClassOf(obo:CL_4042016 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011148))

# Class: obo:CL_4042017 (alpha1-tanycyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16344112") Annotation(oboInOwl:hasDbXref "PMID:26578855") Annotation(oboInOwl:hasDbXref "wikipedia:Tanycyte") obo:IAO_0000115 obo:CL_4042017 "A tanycyte cell found in the ventromedial and dorsomedial nuclei of the hypothalamus. This type of tanycyte extends its protrusions close to parenchymal neurons without contacting blood vessels. It expresses the glial marker S-100β.")
AnnotationAssertion(terms:contributor obo:CL_4042017 <https://orcid.org/0000-0002-0098-8958>)
AnnotationAssertion(terms:date obo:CL_4042017 "2024-08-19T13:06:16Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29351662") oboInOwl:hasRelatedSynonym obo:CL_4042017 "DMH tanycyte")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29351662") oboInOwl:hasRelatedSynonym obo:CL_4042017 "VMH tanycyte")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26578855") rdfs:comment obo:CL_4042017 "In rodents, a1 tanycytes are known to express DARPP-32, GPR50, NA Vimentin, Connexin 43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018).")
AnnotationAssertion(rdfs:label obo:CL_4042017 "alpha1-tanycyte"@en)
SubClassOf(obo:CL_4042017 obo:CL_0002085)
SubClassOf(obo:CL_4042017 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004642))
SubClassOf(obo:CL_4042017 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000014419))

# Class: obo:CL_4042018 (alpha2-tanycyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16344112") Annotation(oboInOwl:hasDbXref "PMID:26578855") Annotation(oboInOwl:hasDbXref "PMID:29351662") Annotation(oboInOwl:hasDbXref "wikipedia:Tanycyte") obo:IAO_0000115 obo:CL_4042018 "A type of tanycyte found in the dorsomedial arcuate nucleus of the hypothalamus. This mono-ciliated tanycyte extends its protrusion to the arcuate nucleus and expresses the glial marker S-100β.")
AnnotationAssertion(terms:contributor obo:CL_4042018 <https://orcid.org/0000-0002-0098-8958>)
AnnotationAssertion(terms:date obo:CL_4042018 "2024-08-19T13:13:20Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29351662") oboInOwl:hasRelatedSynonym obo:CL_4042018 "dmARH tanycyte")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26578855") rdfs:comment obo:CL_4042018 "In rodents, this type of tanycyte is more developmentally advanced than alpha1 tanycytes, shows a high neurogenic competence and expresses the following markers DARPP-32, Vimentin, GPR50, Connexin-43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018)")
AnnotationAssertion(rdfs:label obo:CL_4042018 "alpha2-tanycyte"@en)
SubClassOf(obo:CL_4042018 obo:CL_0002085)
SubClassOf(obo:CL_4042018 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001932))
SubClassOf(obo:CL_4042018 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000014419))

# Class: obo:CL_4042019 (beta1-tanycyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16344112") Annotation(oboInOwl:hasDbXref "PMID:26578855") Annotation(oboInOwl:hasDbXref "PMID:29351662") Annotation(oboInOwl:hasDbXref "Wikipedia:Tanycyte") obo:IAO_0000115 obo:CL_4042019 "A type of tanycyte found in the lateral infundibular recess of the brain. This tanycyte has an elongated morphology with multiple microvilli extending to the third ventricle in the lateral zones of the median eminence. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH).")
AnnotationAssertion(terms:contributor obo:CL_4042019 <https://orcid.org/0000-0002-0098-8958>)
AnnotationAssertion(terms:date obo:CL_4042019 "2024-08-19T13:17:32Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29351662") oboInOwl:hasRelatedSynonym obo:CL_4042019 "vmARH tanycyte")
AnnotationAssertion(rdfs:label obo:CL_4042019 "beta1-tanycyte"@en)
SubClassOf(obo:CL_4042019 obo:CL_0002085)
SubClassOf(obo:CL_4042019 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0006250))
SubClassOf(obo:CL_4042019 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000007479))
SubClassOf(obo:CL_4042019 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000007489))

# Class: obo:CL_4042020 (beta2-tanycyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16344112") Annotation(oboInOwl:hasDbXref "PMID:26578855") Annotation(oboInOwl:hasDbXref "PMID:29351662") Annotation(oboInOwl:hasDbXref "wikipedia:Tanycyte") obo:IAO_0000115 obo:CL_4042020 "A type of tanycyte found in the floor of the infundibular recess in the brain. This tanycyte has an elongated morphology with multiple microvilli extending medially and ventrally to the median eminence, contacting the pial surface and blood vessels. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH).")
AnnotationAssertion(terms:contributor obo:CL_4042020 <https://orcid.org/0000-0002-0098-8958>)
AnnotationAssertion(terms:date obo:CL_4042020 "2024-08-19T13:21:39Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29351662") oboInOwl:hasRelatedSynonym obo:CL_4042020 "ME tanycyte")
AnnotationAssertion(rdfs:label obo:CL_4042020 "beta2-tanycyte"@en)
SubClassOf(obo:CL_4042020 obo:CL_0002085)
SubClassOf(obo:CL_4042020 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0006250))
SubClassOf(obo:CL_4042020 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000007479))
SubClassOf(obo:CL_4042020 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000007489))

# Class: obo:CL_4052001 (multiciliated ependymal cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25045600") Annotation(oboInOwl:hasDbXref "PMID:28067220") Annotation(oboInOwl:hasDbXref "PMID:37008045") obo:IAO_0000115 obo:CL_4052001 "An ependymal cell that lines the lateral, third, and fourth ventricles of the brain. The cell is characterized by multiple motile cilia on its apical surface, which beats in a coordinated manner to facilitate the movement of cerebrospinal fluid (CSF), contributing to brain homeostasis.")
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