[DAS] retrieve genes by name

[Andreas Kahari]

On Tue, Jul 13, 2004 at 01:38:46PM +0200, Maximilian Haeussler wrote:
> >First of all, you need a DAS server that understands the IDs
> >you're trying to use.  I'm a bit unsure wheather DAS is the
> >right tool here though.  Try something like EnsMart instead
> >(http://www.ensembl.org/Multi/martview).
>
> OK, so I won't use DAS, that's nice to know. I couldn't really figure that 
> out from the documentation.

What documentation would this be?

> >For bulk queries, or more complicated stuff, you might want to
> >look into using the BioMart or Ensembl APIs.  DAS could be, I
> >think, a bit too simple.  BioMart is discussed on the mart-dev
> >(http://www.ebi.ac.uk/biomart/contact.html) list, and Ensembl on
> >the ensembl-dev list (http://www.ensembl.org/Docs/).
> 
> Hum...I'm not sure, but when I use the ensembl apis, won't I miss a couple 
> of model organisms? Arabidopsis, for instance? OK, there is 
> http://atensembl.arabidopsis.info/ which might also be useable with the 
> ensembl apis. So ensembl seems to be the most comprehensive way to go if I 
> want to bulk-download genes of as many organisms as possible...

You mentioned HUGO IDs, so I thought you were interested in
human genes only.  You never mentioned what sources of data you
had available, so I picked the solution I had closest at hand.

AFAIK, there is no place which has all data for all species in
one single format.  Ensembl gets close, but we don't do plants.

Regards,
Andreas


-- 
|=)(=| Andreas Kähäri      EMBL, European Bioinformatics Institute
|(==)|                     Wellcome Trust Genome Campus
|=)(=| Ensembl Developer   Hinxton, Cambridgeshire, CB10 1SD
|(==)| DAS Team Leader	    United Kingdom