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Add sensory corpuscle #3295

Merged
merged 11 commits into from
Sep 3, 2024
24 changes: 18 additions & 6 deletions src/ontology/uberon-edit.obo
Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@ synonymtypedef: PENDING_REVIEW "expert consultation and attribution required"
synonymtypedef: SENSU "taxonomic disambiguation"
synonymtypedef: SYSTEMATIC "a systematic synonym used as the base name for design patterns"
default-namespace: uberon
idspace: NIF_Subcellular http://www.neurolex.org/wiki/
treat-xrefs-as-equivalent: AEO
treat-xrefs-as-equivalent: BILA
treat-xrefs-as-equivalent: BSPO
Expand Down Expand Up @@ -72993,8 +72994,8 @@ id: UBERON:0003532
name: hindlimb skin
def: "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic]
synonym: "hind limb skin" EXACT [OBOL:automatic]
synonym: "lower limb skin" EXACT [FMA:23102]
synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473]
synonym: "lower limb skin" EXACT [FMA:23102]
synonym: "skin of hind limb" EXACT [OBOL:automatic]
synonym: "skin of hindlimb" EXACT [OBOL:automatic]
synonym: "skin of lower extremity" EXACT [OBOL:automatic]
Expand Down Expand Up @@ -76936,7 +76937,7 @@ xref: NIF_Subcellular:FMA_83604
xref: SCTID:37419002
xref: Wikipedia:File\:Gray935.png
xref: Wikipedia:Lamellar_corpuscle
is_a: UBERON:0012449 {source="Wikipedia"} ! mechanoreceptor
is_a: UBERON:8900000 {source="Wikipedia"} ! sensory corpuscle
relationship: part_of UBERON:0002067 {notes="may also be located in organs - check"} ! dermis
property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray935.png" xsd:anyURI
property_value: external_ontology_notes "FMA treats pacinia and G-M as distinct" xsd:string {external_ontology="FMA"}
Expand Down Expand Up @@ -152842,7 +152843,7 @@ def: "The Corpuscles of Herbst or Herbst corpuscles are a nerve-ending similar t
synonym: "corpuscles of Herbst" RELATED [Wikipedia:Corpuscles_of_Herbst]
synonym: "Herbst corpuscle" RELATED [Wikipedia:Corpuscles_of_Herbst]
xref: Wikipedia:Corpuscles_of_Herbst
is_a: UBERON:0012449 {source="Wikipedia"} ! mechanoreceptor
is_a: UBERON:8900000 {source="Wikipedia"} ! sensory corpuscle
relationship: only_in_taxon NCBITaxon:8782 ! Aves

[Term]
Expand Down Expand Up @@ -152877,7 +152878,7 @@ xref: NCIT:C13171
xref: SCTID:41421000
xref: UMLS:C0205831 {source="ncithesaurus:Meissner_Corpuscle"}
xref: Wikipedia:Meissner%27s_corpuscle
is_a: UBERON:0012449 {source="Wikipedia"} ! mechanoreceptor
is_a: UBERON:8900000 {source="Wikipedia"} ! sensory corpuscle
relationship: part_of UBERON:0002199 ! integument

[Term]
Expand Down Expand Up @@ -152945,7 +152946,7 @@ xref: NCIT:C13175
xref: SCTID:53140000
xref: UMLS:C0035943 {source="ncithesaurus:Ruffinis_Corpuscle"}
xref: Wikipedia:Bulbous_corpuscle
is_a: UBERON:0012449 {source="FMA"} ! mechanoreceptor
is_a: UBERON:8900000 {source="FMA"} ! sensory corpuscle
relationship: part_of UBERON:0002199 ! integument
property_value: curator_notes "there is some debate as to its existence[ISBN:9780849388118]" xsd:string
property_value: external_ontology_notes "MP says subcutaneous tissue of digits; NCITA says hypodermis" xsd:string {external_ontology="MP"}
Expand Down Expand Up @@ -177321,7 +177322,7 @@ alt_id: UBERON:0025487
synonym: "regional part of gustatory epithelium" EXACT HUMAN_PREFERRED [BIRNLEX:4100]
is_obsolete: true
consider: BIRNLEX:4100
consider: http://uri.neuinfo.org/nif/nifstd/nifext_13
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consider: nifext:13

[Term]
id: UBERON:0025236
Expand Down Expand Up @@ -224513,6 +224514,17 @@ relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 ! Aleix Puig-
relationship: located_in UBERON:8600025 ! intervillous space
property_value: dcterms-date "2024-04-15T10:05:35Z" xsd:dateTime

[Term]
id: UBERON:8900000
name: sensory corpuscle
def: "A mechanosensory complex in the terminal end of some nerves that forms a corpuscle. It consists of one or more neuronal terminations and associated non-neuronal cells." [PMID:35356056]
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synonym: "COEC" RELATED OMO:0003000 [PMID:35356056]
synonym: "cutaneous end-organ complex" EXACT [PMID:35356056]
xref: http://www.wikidata.org/entity/Q126363978
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The definition of multi cell part structure is:

A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.

In sensory corpuscles there are some complete cells. I'm not aware if there is a term that comprises parts of cells and complete cells, but I will have a look.

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The definition of multi cell part structure is:

A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.

In sensory corpuscles there are some complete cells. I'm not aware if there is a term that comprises parts of cells and complete cells, but I will have a look.

Oh, curious. I had not seen the definition, I interpreted quite the oposite from the label!!

So apparently the capsule of the Pacinian corpuscle is being excluded altogether from the Pacinian corpuscle itself.

I'll copy that in the issue.

is_a: UBERON:0012449 ! mechanoreceptor
property_value: dcterms-date "2024-06-12T13:51:05Z" xsd:string
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created_by: https://orcid.org/0000-0003-2473-2313

[Typedef]
id: aboral_to
name: aboral to
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