[Biojava-l] Gene Ontology

[Thomas Down]

On Mon, Dec 02, 2002 at 11:56:58AM -0500, Dudgeon, Tim wrote:
> There has been mention of a Gene Ontology API and/or browser within BioJava
> in the past.
> I've also started off down that route, but before I go too far I thought it
> made sense to check whether there was any consensus here.
> I don't want to reinvent the wheel yet again and will be happy to help get
> something into BioJava.
> 
> What I'd like to see is an API to the GO database (probably with adaptors to
> its various forms), plus some gui browser that can form a component of a
> bigger tool.
> Browser would probably initially use a JTree type appraach, but eventually
> something that better reflected the fact that a GO term can have multiple
> parents.

I've only ever used GO mysql by talking directly to the database.
But if you want an API (especially one which helps you build a nice
viewer) you might want to look at GOET:

    http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gmod/goet/

[sorry, I can't find a proper website at the moment.  Although
it uses the org.goet namespace, www.goet.org appears to be owned
by the Global Organization for Ethical Time Travel]

     Thomas.