[Open-bio-l] Re: GO client API in biojava

[Michael L. Heuer]

cross-posting to additional open-bio mailing lists I wasn't aware of until
now.  Apologies if you see this message several times.

   michael

---------- Forwarded message ----------
Date: Wed, 20 Mar 2002 17:29:50 -0500 (EST)
From: Michael L. Heuer <heuermh@acm.org>
To: biojava-l@biojava.org
Subject: Re: GO client API in biojava


I see moderation for attachments is now enforced on the open-bio lists,
so if the e-mail with the attachment never makes it through, the proposal
is also available from

> http://shore.net/~heuermh/vocabulary-PROPOSAL.tar.gz

   michael


On Wed, 20 Mar 2002, Michael L. Heuer wrote:

>
> said proposal attached,
>
>    michael
>
>
> > Message: 2
> > Date: Tue, 19 Mar 2002 15:06:45 -0500 (EST)
> > From: "Michael L. Heuer" <heuermh@acm.org>
> > To: <biojava-l@biojava.org>
> > Subject: [Biojava-l] Re: GO client API in biojava
> >
> >
> > Mattew Pocock wrote:
> >
> > > Tom Oinn wrote:
> > >
> > > > 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
> > > > adapter for it, but then you have everything there already.
> > >
> > > 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.
> >
> > I'm not sure if this is the best way to go.
> >
> > The ego api, although the basis for a very nice tool (thanks, Tom!), is
> > specific to the Gene Ontology, and is read-only.
> >
> > With structured vocabularies and ontologies becoming more prevalent in the
> > various bioinformatics projects (GO, biosql, DAS 2.0, etc), maybe we need
> > to aim a bit more general?
> >
> > I should be able to run the package of interfaces we use for a structured
> > vocabulary api through the lawyers this afternoon, to submit to biojava as
> > a proposal.
> >
> >    michael
> >
>
>