vertebral centrum: review request

[cmungall]

Following on from #382, I have renamed and axiomatized UBERON:0001075 from "vertebral centrum" to "bony vertebral centrum", and added a new generic parent UBERON:0016491 ! vertebral centrum element

All this follows the standard pattern we put down (this is a consequence: making distinctions is infectious. You end up paralleling entire graphs...)

It's not clear where all synonyms should go. See below for how it looks.

Naming conventions: does it look OK? ie. with the "bomy" prefix.

Definitions: we never quite settled on the def for centrum. VSAO had "Skeletal element that surrounds the notochord" but this is not valid the the centrum does not surround the notocohord in most adult vertebrates. See below for my modification.

Note I didn't add develops_from as it seems some centra are not endochondral.

I think we also need to examine all subtypes and parts to ensure whether o use the bony subclass or the generic parent.

@alex-dececchi @wdahdul comments welcone

[Term]
id: UBERON:0016491 ! vertebral centrum element
name: vertebral centrum element
def: "Skeletal element that functionally replaces the notochord[VSAP,modified]." [VSAO:0000183, VSAO:curator, UBERON:cjm]
comment: The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.
synonym: "centrum" BROAD  [VSAO:0000183]
synonym: "centrum of vertebra" EXACT []
property_value: external_definition "Skeletal element that surrounds the notochord.[VSAO]" xsd:string {ontology="VSAO", external_class="VSAO:0000183", date_retrieved="2012-08-14", source="VSAO:curator"}
synonym: "centre vertébral@fr" EXACT [TAO:0000126]
synonym: "périchorde@fr" EXACT [TAO:0000126]
is_a: UBERON:0004765 {source="VSAO"} ! skeletal element
relationship: part_of UBERON:0010913 {source="VSAO"} ! vertebral element
xref: VSAO:0000183 ! vertebral centrum

[Term]
id: UBERON:0001075
name: bony vertebral centrum
xref: Wikipedia:Body_of_vertebra
comment: AO notes: VSAO definition states it surrounds notochord but not applicable to post-natal.
subset: uberon_slim
subset: vertebrate_core
synonym: "vertebral centrum" RELATED  [MA:0001457]
synonym: "corpus vertebrae" RELATED PLURAL [Wikipedia:Body_of_vertebra]
synonym: "centra" RELATED PLURAL [PHENOSCAPE:ad]
synonym: "vertebral centra" RELATED PLURAL [PHENOSCAPE:ad]
synonym: "corpus vertebrae (vertebrale)" EXACT  [FMA:11945]
synonym: "vertebral body" EXACT  [FMA:11945]
synonym: "body of vertebra" EXACT [FMA:11945]
synonym: "corpus vertebra" EXACT LATIN []
synonym: "arcocentrum" NARROW INCONSISTENT [PMID:11746457]
synonym: "holocentrum" NARROW [PMID:11746457]
synonym: "autocentrum" NARROW [PMID:11746457, ZFA:0000126]
intersection_of: UBERON:0016491 ! vertebral centrum element
intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue
relationship: part_of UBERON:0002412 ! vertebra
xref: FMA:11945 ! body of vertebra
xref: MA:0001457 ! vertebral body
xref: AAO:0000697 ! centrum
xref: ZFA:0000126 ! centrum
xref: OpenCyc:Mx4rvXU4VpwpEbGdrcN5Y29ycA
xref: ncithesaurus:Vertebral_Body ! Vertebral Body
xref: OpenCyc:Mx4rvXU4VpwpEbGdrcN5Y29ycA ! vertebral body
property_value: foaf-depicted_by http://upload.wikimedia.org/wikipedia/commons/thumb/6/63/Corpusvertebrae.png/200px-Corpusvertebrae.png
xref: SCTID:361745008 ! Entire body of vertebra
xref: SCTID:362867001 ! Entire centrum of vertebra
xref: TAO:0000126 ! centrum
property_value: foaf-depicted_by http://upload.wikimedia.org/wikipedia/commons/6/63/Corpusvertebrae.png
property_value: external_definition "Cylindrical body of bone, round or oval in cross section, which functionally replaces the notochord.[AAO]" xsd:string {ontology="AAO", external_class="AAO:0000697", date_retrieved="2012-06-20", source="AAO:Duellman_and_Trueb_2008"}
property_value: external_definition "Centra are represented by mineralized, calcified, or ossified portions that surround the notochord. The autocentrum, present in Danio and all other living teleosts, is formed by direct ossification outside the elastica externa of the notochord (Arratia, 1999).[TAO]" xsd:string {ontology="TAO", external_class="TAO:0000126", date_retrieved="2012-08-14", source="ZFIN:curator"}
property_value: external_comment "The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.[VSAO]" xsd:string {ontology="VSAO", external_class="VSAO:0000183", date_retrieved="2012-09-06", source="Curator"}
relationship: evolved_multiple_times_in NCBITaxon:7742 {source="PMID:11746457", notes="The formation of centra, which is not homologous among vertebrate groups, is acquired independently in some lineages of placoderms, most advanced actinopterygians, and some dipnoans and rhipidistians"} ! Vertebrata
property_value: external_definition "The body is the largest part of a vertebra, and is more or less cylindrical in shape. Its upper and lower surfaces are flattened and rough, and give attachment to the intervertebral fibrocartilages, and each presents a rim around its circumference. In front, the body is convex from side to side and concave from above downward. Behind, it is flat from above downward and slightly concave from side to side. Its anterior surface presents a few small apertures, for the passage of nutrient vessels. On the posterior surface is a single large, irregular aperture, or occasionally more than one, for the exit of the basi-vertebral veins from the body of the vertebra. [WP,unvetted][Wikipedia:Body_of_vertebra]." xsd:string {source="Wikipedia:Body_of_vertebra"}
xref: UMLS:C0223084 {source="ncithesaurus:Vertebral_Body"}

[Term]
id: UBERON:0009291
name: cartilaginous vertebral centrum
synonym: "cartilaginous centrum of vertebra" EXACT []
synonym: "postcaudal cartilaginous centrum" NARROW [PMID:11746457]
comment: cartilaginous centrum of vertebra[PMID:11746457]
intersection_of: UBERON:0016491 ! vertebral centrum element
intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue
relationship: part_of UBERON:0011094 ! vertebra cartilage element
xref: SCTID:317278007 ! cartilaginous centrum of vertebra

[gouttegd]

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.