[ensembl-dev] BioMart Variation

Ma, Man Chun John manchunjohn-ma at uiowa.edu
Thu Feb 17 19:22:20 GMT 2011


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...?


John MC Ma
Graduate Assistant
Kwitek Lab
Department of Internal Medicine
3125E MERF
375 Newton Road
Iowa City IA 52242

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