[Gmod-help] managing "omics" datasets with CHADO

[Yury Bukhman]

Dear GMOD Help Desk,

I'm interested in building an in-house database of "omics" data, such as microarray, RNA-seq and ChIP-seq, and associated bioinformatics analyzes, linked to gene annotations in several organisms.  I'm thinking that CHADO/GMOD could be a good starting point for me (is it?).  As the first prototype, I would like to load an Affymetrix microarray study of A.thaliana cell cultures into CHADO.  So far, we have installed CHADO locally and uploaded an A.thaliana GFF file.  I have several questions now.

How do we upload an Affymetrix array dataset?  I've seen a brief explanation on the Wiki page for the mage module.  Is there a more detailed worked example somewhere?  Also, what is the proper way to associate Affymetrix probe sets with genes?

If I decide to use CHADO for RNA-seq and ChIP-seq, would it require creating new modules?

Thanks.

Yury


-- 
Yury V. Bukhman, Ph.D.
Associate Scientist, Bioinformatics
Great Lakes Bioenergy Research Center
University of Wisconsin - Madison
445 Henry Mall, Rm. 513
Madison, WI 53706, USA
Phone: 608-890-2680  Fax: 608-890-2427
Email: ybukhman at glbrc.wisc.edu