[ensembl-dev] BioMart Variation

Rhoda Kinsella rhoda at ebi.ac.uk
Fri Feb 18 10:38:28 GMT 2011

Hi John,
If you select the Ensembl variation mart and use the "GENE ASSOCIATED  
VARIATION FILTERS" you can upload your list of Ensembl ID's and use  
these to filter your query (see figure 1). You can also select the  
Ensembl gene mart as a second dataset and use the ID list limit filter  
to filter on Ensembl gene IDs. To do this select the Rat variation  
mart dataset and select any filters and attributes that you wish to  
get from there. Then select the second dataset on the the left panel  
(see figure 2) and select the Rat ensembl gene mart dataset and any  
filters and attributes that you would like before hitting the result  
button. It is not possible to add a gene filter in the "Limit to  
variants with these IDs" filter for the variation mart as this is a  
SNP centric mart. I can, however add a filter for all Ensembl gene IDs  
in the Ensembl gene mart under Filter->GENE->Limit to genes for  
release 62. You will then be able to filter on Ensembl Genes via the  
second dataset as described above. Please contact me if you require  
further assistance with your query.

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On 17 Feb 2011, at 19:22, Ma, Man Chun John 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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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Cambridge CB10 1SD,

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