[ensembl-dev] External_name

[Ed]

Dear Magali,

Thank you so so much!

Ed

-----Original Message-----
From: Magali [mailto:mr6 at ebi.ac.uk] 
Sent: Thursday, August 01, 2013 4:25 AM
To: Ensembl developers list
Cc: Ed
Subject: Re: [ensembl-dev] External_name

Hi Ed,

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,
Magali

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?
>
> Ed
>
>
> -----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,
> Magali
>
> 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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>
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