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

[PATERSON Trevor]

Thanks both...

I think that resolves my problems 
- to get a total list of synonyms for an ensemblgenomes gene (by asking for xref synonyms)  
I need to add in the special case DisplayXRef to my query...

but this shouldn't be necessary for ensembl vertebrates..

cheers 
trevor



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-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Magali
Sent: 16 January 2013 17:00
To: dev at ensembl.org
Subject: Re: [ensembl-dev] DisplayXRefs IDs not listed in object_xref table

Hi Trevor,

As for Ensembl databases, this should not happen.
To assign a display xref, we chose from the list of object_xref attached to the object.
If you have seen cases where it does happen, please could you give us examples and we will investigate what could have gone wrong.


Regards,
Magali

On 16/01/13 16:34, Dan Staines wrote:
> 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.
>


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