[ensembl-dev] retrieving refseq gene build has no external name?

Magali mr6 at ebi.ac.uk
Mon Jul 29 14:41:07 BST 2013


Hi Stef,

In the otherfeatures database, we import directly the refseq annotation
as a full gene set.
These are identified by their stable_id, which is the refseq accession.

In the core database, we have our own ensembl gene annotation.
We then assign external references to these genes, for example to link
out to refseq accessions or HGNC names.

What you refer to as gene name (BRCA2 etc) is usually assigned using the
HGNC accessions.
We do not run such an external reference mapping for the externally
imported gene set from refseq, which is why you will not be able to find
a display name for those.


Hope that helps,
Magali

On 29/07/13 13:46, Stef van Lieshout wrote:
> Nobody knows a way to do this? (retrieving refseq gene models by
> gene-name)
>
> Stef
>
>
> ----- Original message -----
> From: Stef van Lieshout <mailsvl at fastmail.fm>
> To: dev at ensembl.org
> Subject: [ensembl-dev] retrieving refseq gene build has no external
> name?
> Date: Wed, 10 Jul 2013 13:45:01 +0200
>
> Hi all,
>
> It seems the refseq_human_imort gene models do not contain an external
> name, is that correct?
>
> Goal:
> What I try to do (with the API) is to get all refseq transcripts (NM_*)
> instead of ensembl transcripts (ENST*) for a certain gene name (eg
> BRCA2).
>
> You can do this with the "core" set by:
> my $ga = $registry->get_adaptor( 'human', 'core', 'gene' );
> my @genes = @{$ga->fetch_all_by_external_name( 'BRCA2' )};
>
> And I hoped to be able to do this for refseq models with:
> my $ga = $registry->get_adaptor( 'human', 'otherfeatures', 'gene' );
> my @genes = @{$ga->fetch_all_by_external_name( 'BRCA2' )};
>
> But that seems to fail because there are no external names defined (the
> key is there, but set to undef) for these genes.
>
> Is there another way to do this?
>
> Btw, I know you can get the transcripts by using the NM_ id as input,
> but this is not what I want: 
> my $gene = $ga->fetch_by_transcript_stable_id( 'NM_000059.3' );
>
> /Stef
>
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