[BiO BB] Ensembl and Gene Ontology terms

Charles Danko dankoc at gmail.com
Tue Feb 12 11:15:10 EST 2008


Hi, Paco,

If you want to do it all programmically from Java, I would suggest
Googling a protocol called DAS.  ENSEMBL has a DAS server from which
you should be able to pull GO annotations for ENSEMBL IDs quite
easily.

You can find java-based libraries to access a DAS connection, and
parse the resulting information here:
http://www.spice-3d.org/dasobert/.

Good luck!
Charles

2008/2/12 ocean <oceanhu at 126.com>:
>  Hey,Paco
>
> i think you can try BIOMART(www.biomart.org).  this database had done such thing already.
> you can  contract them for some help.
>
> good luck!
>
> Huhaiyang
>
>
>
>
> 在2008-02-12,"Paco B C" <mleczny at gmail.com> 写道:
>
>
> Hi!
> this is my first message in this list. My name is Paco and I'm doing my PhD.
> on Bioinformatics in University of Leuven, Belgium.
> I would like to build a java module that, given a list of Ensembl Gene
> Identifiers, it would give back their related Gene Ontology terms. I've
> accessed the GO database, but I can't find ENSG terms and I've read in the
> Ensembl website that they give the link to external databases for
> translation and transcript objects but not for genes (maybe in the future,
> but not now).
> My question is, do you know which database could I query in order to get
> this relation within Ensembl and GO terms?
> Thanks!
> Paco
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