gray_ed at hotmail.com
Thu Aug 1 13:42:57 BST 2013
Thank you so so much!
From: Magali [mailto:mr6 at ebi.ac.uk]
Sent: Thursday, August 01, 2013 4:25 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] External_name
The name is known as the gene's display_xref, which is a DBEntry object.
The following call $gene->display_xref->display_id should display the name
like on the web page.
Hope that helps,
On 01/08/13 01:41, Ed wrote:
> 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 use?
> 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
>> Is this always the external_name of a Gene or are there cases where
>> it is not?
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