[ensembl-dev] Retrieving VegaID XRefs

PATERSON Trevor trevor.paterson at roslin.ed.ac.uk
Wed Dec 19 15:16:17 GMT 2012


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 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<mailto:trevor.paterson at roslin.ed.ac.uk>
Bioinformatics
The Roslin Institute
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Easter Bush
Midlothian
EH25 9RG
Scotland UK

phone +44 (0)131 651 9157

http://bioinformatics.roslin.ed.ac.uk/

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