[ensembl-dev] BioMart Variation

[Rhoda Kinsella]

Hi John
Apologies. Please disregard my previous e-mail. I mistakenly assumed  
you required Ensembl gene IDs when you are looking for Ensembl SNP  
ID's. My mistake. Yes you are correct and we will try to rectify this  
for release 62.
Regards
Rhoda

On 18 Feb 2011, at 10:38, Rhoda Kinsella wrote:

> 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.
> Regards
> Rhoda
>
> <figure_1.tiff>
>
> <figure_2.pptx>
>
>
>
> 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,
> Hinxton
> Cambridge CB10 1SD,
> UK.
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.