[ensembl-dev] REPOST Retrieving VegaID XRefs

[Andy Yates]

Hi Trevor,

So to answer your questions:

1). The database types OTTG and OTTT are used to flag alternative genes/transcripts and so are linked only to genes and transcripts. It is these xrefs which are used to flag the alternatives in the web interface on gene and transcript summary pages.

2). The Vega_% databases are the import of data from Vega and are used to bring in alternative display symbols and xrefs to the vega database. These exist on the transcript and protein levels & not the gene level

So yes to capture the vega link from all object levels use both types. If you want to do the association from genes & transcripts then you're safe to use just the OTT external db names.

Hope this helps and sorry for the confusion & long wait for a reply

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 4 Jan 2013, at 13:21, PATERSON Trevor <trevor.paterson at roslin.ed.ac.uk> wrote:

> I’m posting this question again incase it got overlooked in the pre-xmas excitement
>  
> From: PATERSON Trevor 
> Sent: 19 December 2012 15:16
> To: 'dev at ensembl.org'
> Subject: Retrieving VegaID XRefs
>  
> I am looking for a bit of clarification on retrieving Vega Identifiers for Genes, Transcripts and Translations through the API or directly through MySql (using the  Xref, Object_Xref and external_db tables).
>  
> (I am using human Brca2 as an example, gene: ENSG00000139618, transcript: ENST00000380152, translation: ENSP00000369497, looking at Release 67 database here)
>  
> I can see that the database name I appear to need to use  for a Gene’s Vega ID  is OTTG and for a Transcript the database  is OTTT
>  
> [however, there are ‘possible’?  other databases available : Vega_gene, Vega_gene_like, Vega_transcript, Vega_mouse_transcript, Vega_transcript_like]
>  
> in the case of Translations, there are no xrefs for OTTP, but there are a couple of entries for the  ‘Vega_translation’  - one of which appears to have the correct Vega ID: OTTHUMP00000018803, whilst the other – which is given the same ‘priority’ - appears to be an internal database id: 153814
>  
> Am I missing some obvious trick to pull these out
>  
> In the PerlAPI I have gone down the route of using:
>  
> @xrefs = @{ $translation->get_all_object_xrefs('OTT%') };
> and
> @xrefs = @{ $translation->get_all_object_xrefs('Vega%') };
>  
> is there a better method?
>  
> I was hoping I would be consistently be able to use the database names ‘OTTG’, ‘OTTT’ and ‘OTTP’, but it looks like I also need ‘Vega%’ to be safe…
> Trevor Paterson PhD
> trevor.paterson at roslin.ed.ac.uk
> Bioinformatics 
> The Roslin Institute
> Royal (Dick) School of Veterinary Studies
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