Hi, There is actually a Biomart available for COSMIC now:
http://www.sanger.ac.uk/genetics/CGP/cosmic/biomart/martview/ and www.biomart.org Hope this helps. Best wishes, Jon --------------------------------------------------------- Jon Teague Senior Scientific Manager, Informatics Cancer Genome Project Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SA, UK Tel: +44 (0)1223 494823 Fax: +44 (0)1223 494809 Web: http://www.sanger.ac.uk/genetics/CGP/ --------------------------------------------------------- -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Richard Holland Sent: 17 May 2010 19:53 To: Kan, Zhengyan Cc: [email protected] Subject: Re: [mart-dev] dataset not suitable for biomart? Technically it can transform anything - as long as the data can be transformed into reverse star, then the original data format is irrelevant. However MartBuilder versions up to 0.7 have trouble with CHADO and similar schemas where all tables refer back to a single central ID table. But in these cases you can still do your own transformations by hand without using MartBuilder - once you have something in reverse-star form then MartEditor can understand it and you can build a mart out of it. There may well be fixes for CHADO-like schemas in the forthcoming 0.8 version of MartBuilder. Arek and co. will let you know I'm sure. cheers, Richard On 15 May 2010, at 01:47, Kan, Zhengyan wrote: > Hi, Bio-mart team: > > I wonder if there are some data sets not suitable for transformation > into Biomart. In my experience, I had difficulties transforming the > COSMIC database into Biomart as the data is very decentralized. It may > just be my lack of knowledge about the Biomart system though. > > My understanding is that Biomart uses a 'top-down', reverse-star schema. > Should this type of schema applicable to all genomic data sets or just a > limited spectrum? > > Many thanks! > > Zhengyan (George) Kan > Computational Biology > Pfizer, La Jolla > > -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: [email protected] http://www.eaglegenomics.com/ -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
