[ensembl-dev] DisplayXRefs IDs not listed in object_xref table

[Dan Staines]

Hi Trevor,

On 01/16/2013 04:25 PM, PATERSON Trevor wrote:
> There appears to be some inconsistency as to whether the xref_id of a
> DisplayXRef
>
> (for a gene etc.) is added to the object_xref table.
>
> This seems to vary across version and between ‘ensembl’ and
> ‘ensemblgenomes’ databases.
>
> I am guessing that DisplayXRefs IDs are held to be ‘special’ and
> generally not added to the object_xref table,
>
> because they are held directly in the Gene and Transcript tables.
>
> Does anyone know if this is meant to be the rule?

Speaking for Ensembl Genomes, we frequently use the gene name from a 
UniProt record as the display_xref, but since they are not meaningful 
xrefs in the normal sense (as opposed to the UniProt accession), we 
remove them from the object_xref table so the xref only exists as a link 
from display_xref_id and are not displayed in the external references list.

Hope this explains things,

Dan.

-- 
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/