[ensembl-dev] Gene Synonyms through REST or Biomart

[Premanand Achuthan]

Hi Beat Wolf,

The synonyms is not always empty. If the external source has synonyms, 
then it should be available, for example look at HGNC

{"display_id": "BRCA2","primary_id": "HGNC:1101","version": 
"0","description": "BRCA2, DNA repair associated","dbname": 
"HGNC","synonyms": 
["BRCC2","FACD","FAD","FAD1","FANCD","FANCD1","XRCC11"],"info_text": 
"Generated via ensembl_manual","info_type": "DIRECT","db_display_name": 
"HGNC Symbol"}

I am afraid that at the moment you can do it only gene by gene via the 
REST endpoint or via the core API.

Thanks
Prem


On 22/05/2018 10:23, Wolf Beat wrote:
> Thank you for the quick answer.
>
>
> I did not know about this approach, but i have two issues with it:
>
> 1) The synonyms attribute seems to be always empty, so something seems wrong.
>
> 2) Sadly i need all synonyms for all genes for a specific species. Downloading it through that endpoint would be too slow. Thats why i initially looked at biomart, because all i need is a list of Ensembl gene id + all synonyms.
>
>
> Kind regards
>
>
> Beat Wolf
>
> ________________________________
> From: Dev <dev-bounces at ensembl.org> on behalf of Premanand Achuthan <prem at ebi.ac.uk>
> Sent: Tuesday, May 22, 2018 11:20:09 AM
> To: dev at ensembl.org
> Subject: Re: [ensembl-dev] Gene Synonyms through REST or Biomart
>
> Hi Beat Wolf,
>
> Please have a look at the /xrefs endpoint under "Cross References" and
> look for "synonyms" in the attribute list.
>
> http://rest.ensembl.org/xrefs/name/human/BRCA2?content-type=application/json
>
> http://rest.ensembl.org/xrefs/id/ENSG00000157764?content-type=application/json
>
> Hope it helps,
>
> Best Regards
> Prem
>
> On 22/05/2018 10:09, Wolf Beat wrote:
>> Hello,
>>
>>
>> I'm looking for a complete list of all synonyms of a gene or a set of genes. I can not find a way to get this information through biomart or the REST interface. Is there a way to do it?
>>
>>
>> Kind regards
>>
>>
>> Beat Wolf
>> _______________________________________________
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