[Biojava-l] Re: GO client API in biojava

[Michael L. Heuer]

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