[Biojava-l] Re: Biojava-l digest, Vol 1 #597 - 2 msgs

[Chris Mungall]

On Tue, 19 Mar 2002 biojava-l-request@biojava.org wrote:

> Message: 2
> From: "Matthew Pocock" <matthew_pocock@yahoo.co.uk>
> To: "Tom Oinn" <tmo@ebi.ac.uk>, <biojava-l@biojava.org>
> Subject: Re: start using biojava Was: [Biojava-l] NetBlast for java?
> Date: Tue, 19 Mar 2002 12:12:12 -0000
> 
> > I'd be happy to put our GO browser and client API into biojava, what
> > would you need for this to work? I'm guessing that a standard schema
> > (probably the one used by the stanford people) and the appropriate ego
                                  ^^^^^^^^

ahem... Berkeley (and Colorado)

> > adapter for it, but then you have everything there already.
> >
> > See http://www.ebi.ac.uk/ego for more information.
> >
> > Tom
> 
> This would be great. I presume from the docs that the interfaces are
> de-coupled from the database schema? The only stumbling block currently is
> that ego seems to be GPL which would kill our lGPL licensing. I'm sure we
> can come to some arrangement about that, though.
> 
> Looking forward to it,
> 
> Matthew

You might also want to check out John Richter's DAG Edit code, see
geneontology.sf.net

AFAIK, Ego is wicked for handling the associations between the ontology
terms and gene products whilst John's code is more geared towards the
ontologies themselves. John's code is also moving in the direction of a
full DAML OIL model. John & Tom - don't suppose you've ever discussed
common interfaces etc?

When I get half an hour spare I'll write the sql transformations that load
the bioSQL database from the main GO db (by the way, we're berkeley and
colorado people, not stanford people!). The bioSQL ontology extension is
the schema I imagine you want to be targetting.
 
> 
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