skeletal tissue definition

[wdahdul]

Can we make the VSAO definition primary in Uberon?

VSAO: external_definition "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]"^^string

current: Connective tissue that functions in mechanical and structural support. Definition ref 1: VSAO:0000015

Note the def ref 1 in uberon references VSAO but it doesn't have the exact VSAO definition.

[cmungall]

The definition in Uberon:

Connective tissue that functions in mechanical and structural support.

Came from VSAO, and has been that way for all versions of VAO/VSAO here:

• http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/vocab/skeletal/obo/

However, as you say, we have an external definition, which is your preferred one:

property_value: external_definition "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" xsd:string {ontology="VSAO", external_class="VSAO:0000015", date_retrieved="2012-08-14", source="GO_REF:0000034", source="PSPUB:0000170"}

Where did this come from, if not the main vertebrate_skeletal_anatomy.obo file or its predecessors? This had me stumped.

In fact it came from the embedded VSAO inside teleost_anatomy_VSAO_edit.obo. I used this file to slurp the external_definition tags for TAO, and it ended up pulling the embedded VSAO ones, some of which were more up to date than anything in the main VSAO files. I should have added a check here. Or added another qualifier for the file from which it was retrieved.

Anyway, I will make the preferred one the main definition.

[cmungall]

Note I also added the developmental relations.

[wdahdul]

Hi Chris,

We updated the definition based on coauthor comments in the VSAO manuscript. I think the update was done to the version of VSAO in the vocab-releases folder, not the skeletal/obo folder. That's why you also see the def embedded in the TAO file.
We should be using the VSAO version in the vocab-releases folder for all referencing in uberon because it is the most up-to-date.
Thanks!

On Oct 15, 2012, at 4:58 PM, Chris Mungall wrote:

The definition in Uberon:

Connective tissue that functions in mechanical and structural support.
Came from VSAO, and has been that way for all versions of VAO/VSAO here:

http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/vocab/skeletal/obo/
However, as you say, we have an external definition, which is your preferred one:

property_value: external_definition "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" xsd:string {ontology="VSAO", external_class="VSAO:0000015", date_retrieved="2012-08-14", source="GO_REF:0000034", source="PSPUB:0000170"}
Where did this come from, if not the main vertebrate_skeletal_anatomy.obo file or its predecessors? This had me stumped.

In fact it came from the embedded VSAO inside teleost_anatomy_VSAO_edit.obo. I used this file to slurp the external_definition tags for TAO, and it ended up pulling the embedded VSAO ones, some of which were more up to date than anything in the main VSAO files. I should have added a check here. Or added another qualifier for the file from which it was retrieved.

Anyway, I will make the preferred one the main definition.

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