[ensembl-dev] External_name

Ed gray_ed at hotmail.com
Thu Aug 1 01:41:20 BST 2013

Hi Magali,

Thank you for responding, you are very helpful.  I appreciate it and I
understand.  But I remain confused about the specific algorithm, field or
function call to make to get the 'name' displayed to the left of the ensembl
stable id on the web page.

When using the Ensembl API to reconstruct the 'name' displayed to the left
of the ensembl stable id on the web page for a gene, what algorithm should I

Is it simply gene->external_name or something a bit more complicated?


-----Original Message-----
From: Magali [mailto:mr6 at ebi.ac.uk] 
Sent: Wednesday, July 31, 2013 4:23 AM
To: Ensembl developers list
Cc: Ed
Subject: Re: [ensembl-dev] External_name

Hi Ed,

For ensembl objects (Gene, Transcript, Translation), we have external
references which are mappings from our models to external sources like
Uniprot or HGNC.
These can be seen under the 'External references' tab on the gene and
transcript pages.

For each object, if we have a trusted external reference, we also use this
as a display name.
Trusted sources are HGNC, MGI, RGD, ZFIN_ID, Uniprot gene name, EntrezGene,
RFAM and miRBase.
This is the name which you will see on the left of the ensembl stable id.

For our major species, there should always be a display name, but for some
species with less data, we can not always assign a name.
In those cases, you will only see the stable id.

Hope that helps,

On 30/07/13 20:41, Ed wrote:
> Hi Developers!
> I am trying to get the text that is often used to the left of the 
> ENSEMBL name of a gene in a Gene Pane of the application.
> For instance, for ENSSSCG00000030483 the characters CTDSPL2 are displayed.
> Is this always the external_name of a Gene or are there cases where it 
> is not?
> Ed
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