[Biodevelopers] Regarding microarray database development

[Dan Bolser]

This is an extract from an email a friend sent me in response to this
question...

To the best of my knowledge both SMD and EBI give them through their
web interface. It's not straight foreward how to batch download them.
I've got a great deal of data that I am using from:
http://cmgm.stanford.edu/~kimlab/multispecies/Data/index.html
                                                                                
They are from Stuart and Segal's paper which is essentially everything SMD
contains for human, worm, fly and yeast.

Panos

On Wed, 31 Mar 2004, Wiepert, Mathieu wrote:

> Hi,
> 
> Did you take a look at MAGE object model http://www.mged.org/Workgroups/MAGE/mage.html?  That should take you a far ways down the path...
> 
> See www.mged.org for more information.  Good luck,
> 
> 
> -mat
> 
> > -----Original Message-----
> > From: biodevelopers-admin at bioinformatics.org
> > [mailto:biodevelopers-admin at bioinformatics.org]On Behalf Of kaustubh
> > shinde
> > Sent: Monday, March 29, 2004 9:46 AM
> > To: biodevelopers at bioinformatics.org
> > Subject: [Biodevelopers] Regarding microarray database development
> > 
> > 
> > Hi,
> > I am computer science masters graduate and new to the field of 
> > bioinformatics. My objective is to set up a system that will download 
> > microarray data from public databases like NCBI, EBI etc 
> > which in turn I 
> > want to use for data mining. I would like to develop a 
> > relational database 
> > in mysql on linux.
> > 
> > I have spent last 2-3 weeks reading about the NCBI toolkit, 
> > Arrayexpress, 
> > and Miamexpress tools and also about Biojava.
> > While NCBI toolkit is specific to the NCBI, Arrayexpress and 
> > Miamexpress are 
> > data submission tools and would not allow me to download data 
> > directly from 
> > the servers. Biojava seems pretty useful but I am not sure if 
> > and how I 
> > could save the data in MAGE-ML format.
> > 
> > Keeping the objective - to make a system to download and 
> > analyse microarray 
> > data from VARIOUS public databases - in mind, what steps 
> > should I take? I 
> > understand that this question might sound utterly stupid to 
> > you. But I hope 
> > you understand the difficulties of a computer guy having very little 
> > background in biology or bioinformatics. Having said that, I 
> > have done quite 
> > a lot of reading on biology, microarrays and DNA, chromosomes related 
> > matter.
> > 
> > If you could show me the right direction that will be a great 
> > help. Right 
> > now I am lost and don't know how exactly I should proceed.
> > 
> > Thanks for you time. I am hoping for a positive reply.
> > Thank you,
> > Kaustubh
> > 
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