[ensembl-dev] Xenbase Xref in Ensembl

[Sébastien Moretti]

I got it with the API

Thanks

> Hi Sébastien,
>
> The XenBase id is stored as well.
> If you look at the gene page, the description contains more information
> about the Xenbase id ( Source:Jamboree;Acc:XB-GENE-6076969 in this example).
>
> If you are using the API, it corresponds to the dbprimary_acc entry in
> the xref table.
>
> You are right, the name is not very convenient, probably for historical
> reasons.
>
> We will change this in the next release (76, not the one coming out this
> week).
>
>
> Regards,
> Magali
>
> On 25/02/2014 14:41, Sébastien Moretti wrote:
>> Thanks Magali I can see it now (not very convenient this name).
>>
>> Do you also store the XenBase id (e.g. XB-GENE-6076969 for your
>> example) as you do for Zebrafish with zfin_id ?
>>
>>> Hi Sébastien,
>>>
>>> External references from Xenbase are stored in Ensembl under the
>>> external_db name Xenopus_Jamboree and displayed under the name Jamboree.
>>>
>>> As you can see on the gene page
>>> http://www.ensembl.org/Xenopus_tropicalis/Gene/Matches?g=ENSXETG00000014526;r=GL172656.1:1913116-1927218;t=ENSXETT00000031783
>>>
>>>
>>> the Xenbase external references are also used as official gene names for
>>> Xenopus.
>>>
>>>
>>> Hope that helps,
>>> Magali
>>>
>>> On 25/02/2014 13:51, Sébastien Moretti wrote:
>>>> Hi
>>>>
>>>> I wonder why I cannot find external references to XenBase for Xenopus
>>>> genes in Ensembl.
>>>>
>>>> Did I miss them or is there a reason?
>>>>
>>>> Thanks

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/