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

[Scott Cain]

Hi Yury,

For microarray data, I don't think there is a publicly available
loader.  The people in the Nelson lab at UCLA wrote a loader, but I
don't think they ever published it.

For RNA-seq and Chip-seq data, I don't think you'd want to put the raw
data in Chado--generally, Chado is used for storing annotation results
(of course, that is potentially contradicted by what I wrote about the
Nelson's labs storing over a TB of array data in their Chado instance
:-)

Scott


On Sun, Apr 25, 2010 at 9:33 PM, Yury Bukhman <ybukhman at glbrc.wisc.edu> wrote:
> 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
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research