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Add sensory corpuscle #3295

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merged 11 commits into from
Sep 3, 2024
Merged

Add sensory corpuscle #3295

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e29800c
Add sensory corpuscle
lubianat Jun 12, 2024
db50cb7
Change date relation to dcterms-date
lubianat Jun 12, 2024
575cbb4
Change synonym type and remove superclass
lubianat Jun 12, 2024
439cf54
Merge branch 'master' into issue-3290
aleixpuigb Jun 25, 2024
3947dfe
define idspace for NIF_Subcellular
anitacaron Jun 25, 2024
bf9f4ae
declare idspace `NIFEXT` that is not OBO URI
anitacaron Jul 2, 2024
225bbc6
Merge branch 'master' into issue-3290
anitacaron Aug 14, 2024
81dcf6c
use `terms:contributor` instead of `created_by`
anitacaron Aug 14, 2024
9c9d960
Merge branch 'master' into issue-3290
anitacaron Aug 14, 2024
de943a0
Merge branch 'master' into issue-3290
Sep 2, 2024
4a3dee3
Merge branch 'master' into issue-3290
aleixpuigb Sep 3, 2024
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42 changes: 27 additions & 15 deletions src/ontology/uberon-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -7007,8 +7007,8 @@ consider: FBbt:00007012
consider: FMA:86454
consider: GO:0044464
consider: HAO:0000014
consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao-1337158144
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consider: NCIT:C34070
consider: NIF_Subcellular:sao-1337158144
consider: OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA
consider: TGMA:0001834
consider: UMLS:C1178969 {source="ncithesaurus:Cell_Part"}
Expand Down Expand Up @@ -11048,7 +11048,7 @@ is_obsolete: true
consider: FBbt:00005107
consider: FMA:67301
consider: GO:0043025
consider: NIF_Subcellular:sao1044911821
consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1044911821

[Term]
id: UBERON:0001023
Expand All @@ -11063,9 +11063,9 @@ consider: FBbt:00005110
consider: FMA:67314
consider: GAID:749
consider: GO:0030425
consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1211023249
consider: MESH:A08.663.256
consider: NCIT:C32447
consider: NIF_Subcellular:sao1211023249
consider: OpenCyc:Mx4rviIdspwpEbGdrcN5Y29ycA
consider: TGMA:0001373
consider: UMLS:C0011305
Expand All @@ -11082,8 +11082,8 @@ consider: FBbt:00005113
consider: FMA:61814
consider: GAID:751
consider: GO:0043005
consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao-867568886
consider: MESH:A08.663.256.500
consider: NIF_Subcellular:sao-867568886

[Term]
id: UBERON:0001025
Expand All @@ -11099,9 +11099,9 @@ consider: FBbt:00005114
consider: FMA:67408
consider: GAID:766
consider: GO:0045202
consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao914572699
consider: MESH:A08.850
consider: NCIT:C13281
consider: NIF_Subcellular:sao914572699
consider: SCTID:362298009
consider: UMLS:C0039062

Expand Down Expand Up @@ -11161,8 +11161,8 @@ replaced_by: GO:0031594
consider: FBbt:00005142
consider: FMA:61803
consider: GAID:809
consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1124888485
consider: MESH:D009469
consider: NIF_Subcellular:sao1124888485

[Term]
id: UBERON:0001030
Expand All @@ -11172,7 +11172,7 @@ is_obsolete: true
consider: FBbt:00005143
consider: FMA:67107
consider: GO:0048788
consider: NIF_Subcellular:sao1884931180
consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1884931180

[Term]
id: UBERON:0001031
Expand Down Expand Up @@ -63902,8 +63902,8 @@ is_obsolete: true
replaced_by: GO:0005883
consider: BIRNLEX:846
consider: FMA:63859
consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1316272517
consider: NCIT:C13263
consider: NIF_Subcellular:sao1316272517
consider: UMLS:C0027834

[Term]
Expand Down Expand Up @@ -64187,9 +64187,9 @@ replaced_by: GO:0005882
consider: BIRNLEX:879
consider: FMA:63851
consider: GAID:1079
consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao952483289
consider: MESH:A11.284.195.190.750.410
consider: NCIT:C13248
consider: NIF_Subcellular:sao952483289
consider: UMLS:C0021770

[Term]
Expand Down Expand Up @@ -64241,9 +64241,9 @@ is_obsolete: true
consider: FMA:63850
consider: GAID:1080
consider: GO:0005884
consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao2006047981
consider: MESH:A11.284.195.190.750.510
consider: NCIT:C13255
consider: NIF_Subcellular:sao2006047981
consider: UMLS:C0025979 {source="ncithesaurus:Actin_Filament"}

[Term]
Expand Down Expand Up @@ -76936,7 +76936,7 @@ 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 +152842,7 @@ 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 +152877,7 @@ 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 +152945,7 @@ 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 +177321,7 @@ 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 +224513,18 @@ 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]
synonym: "COEC" EXACT [PMID:35356056]
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synonym: "cutaneous end-organ complex" EXACT [PMID:35356056]
xref: http://www.wikidata.org/entity/Q126363978
is_a: UBERON:0005162 ! multi cell part structure
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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: http://purl.org/dc/elements/1.1/date "2024-06-12T13:51:05Z" xsd:dateTime
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created_by: https://orcid.org/0000-0003-2473-2313

[Typedef]
id: aboral_to
name: aboral to
Expand Down
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