[ensembl-dev] REST service

Sébastien MORETTI sebastien.moretti at unil.ch
Mon Nov 12 14:01:26 GMT 2012

Hi Rhoda

I think it could be very useful to have synonyms also in Biomart.
Both resources must return the same set of information in my opinion.


 > Hi Sébastien,
 > Apologies, after further investigation with my colleagues from the
 > core team, it seems that REST is also querying the external_synonym
 > table to also include the synonyms whereas we don't currently provide
 > these in BioMart. Do you think that this would be a useful addition
 > for you? If so, we can add this information for a future release.
 > Regards
 > Rhoda

> Here is an example:
>  From
> http://beta.rest.ensembl.org/xrefs/id/ENSG00000157764?content-type=application/xml
> I can see several synonyms for BRAF in EntrezGene and HGNC Symbol
> sections. E.g. BRAF1
>  From Biomart 7 or 8, BRAF1 is never there.
>> Hi Sébastien
>> The External attribute section of Biomart contains all the cross
>> references that you can get via REST. These can be classed as synonyms
>> or external references. You should be able to obtain the same
>> information from both resources. I hope that is clear, but if you have
>> an example query, I am happy to illustrate this.
>> Regards
>> Rhoda

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

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