[BiO BB] Ensembl and Gene Ontology terms

Paco B C mleczny at gmail.com
Thu Feb 14 03:00:52 EST 2008


Ey, DAS protocol looks very interesting for what I want to do.
Thanks a lot to all of you!
Paco

2008/2/12 Charles Danko <dankoc at gmail.com>:

> 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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