[ensembl-dev] Xenbase Xref in Ensembl

[Frederic Bastian]

Cool !

> Le 25 févr. 2014 à 16:19, Sébastien Moretti <sebastien.moretti at unil.ch> a écrit :
> 
> 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/
> 
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