[ensembl-dev] BioMart Variation

Fiona Cunningham fiona at ebi.ac.uk
Fri Feb 18 10:37:52 GMT 2011

 Dear John,

Thank you for reporting this inconsistency. I have just tried
searching the rat variation Biomart with this identifier
"ENSRNOSNP2900811", and it does in fact work despite, as you say, the
interface requesting that you use dbSNP identifiers. Can you try your
query and just ignore that the interface requests dbSNP identifiers?

Does this solve your problem?sorry about the misleading interface. We
will try and rectify it.
Best regards,


Fiona Cunningham
Ensembl Variation Project Leader, EBI
t: 01223 494612 || e: fiona at ebi.ac.uk

On 17 February 2011 19:22, Ma, Man Chun John <manchunjohn-ma at uiowa.edu> wrote:
> Hi,
> I was trying to use BioMart's web interface to obtain information on some rat SNPs and found something I'd say of an inconvenience: I tried to search the SNPs by their Ensembl ID, but the Biomart web interface appeared to only allow rs# in "Limit to variants with these IDs" filter, which means I can't use an Ensembl ID to search a web service hosted by Ensembl.
> What's worse is, due to Ensembl's retreation of Ensembl:STAR-gtype dataset from dbSNP and that NCBI hasn't yet incorporated the re-submitted SNPs to dbSNP (there's no dbSNP 131 for rat yet), our lab has decided not to use rs# in the short term.
> Does that mean the only way I can do batch queries on the Variation database with Ensembl IDs is through the API...?
> Cheers,
> John MC Ma
> Graduate Assistant
> Kwitek Lab
> Department of Internal Medicine
> 3125E MERF
> 375 Newton Road
> Iowa City IA 52242
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