Damian Smedley wrote:
Hi Ellen,
Another option is to use taverna (there is a link from the main biomart.org page I think). Tom who is the main developer on Taverna showed me a nice pipeline he constructed to do just such a query using BioMart queries as part of the workflow and I'm sure he could share this with you.
Of course :) We're doing a release of Taverna (1.4) on Monday hopefully which has much better biomart support and as Damian says I wrote a workflow using this version which does exactly what you were asking (I was curious and needed a test case!), so if running from an application or java code is your thing that would work just fine.
Cheers, Tom
