[Biopython-dev] Building Gene Ontology support into Biopython

[Chris Lasher]

On Sun, Oct 18, 2009 at 12:34 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>
> Hi Chris;
>
> > I'd like to make GO support in Biopython a reality now.
>
> Awesome. Great to have you working on this.
>
> > Bioperl has solid GO support. I don't find their code straightforward
> > at all; I haven't picked out what component is responsible for what
> > task. Nonetheless, it could provide starting points to build support
> > for Biopython.
>
> Agreed. I worked on a tiny bit of Gene Ontology stuff a while ago
> and Chris Mungall was very helpful in explaining some of the high
> level decisions.
>
> > 1) First off, does anyone have any gene ontology Python code laying around?
>
> I have a couple of things here:
>
> http://bioinformatics.org/cgi-bin/cvsweb.cgi/biopy-pgml/Bio/PGML/GO/
>
> CVS says they haven't been touched in 7 years. Feel free to use it
> if it's helpful. I took the approach of working directly off an
> installed database as opposed to flat files.
>
> > 2) What is the Biopython stance on introducing third-party
> > dependencies?
>
> I think Michiel and Peter tackled this, but generally the approach
> has been to keep Biopython as a base library that doesn't require a
> lot of installs to get going.
>
> As far as graph libraries go, networkx is good and Eric did some
> work with it for the PhyloXML library this summer.
>
> Thanks again for taking this on,
> Brad

Right, well, first off, thanks for your input so far, guys. I don't
have time tonight to reply to individual points but I went ahead and
started a wiki page to coordinate this.

http://biopython.org/wiki/Gene_Ontology

It's a wiki, so you know what to do if you have an idea or a question.

I'm going to go ahead and make the executive decision to use NetworkX.
I think BioPerl's Ontology framework has both third-party
dependency-based (Graph.pm) and non-dependency-based solutions. Maybe
we can figure out something similar, but NetworkX is such an easy
dependency to satisfy that I'm going with it.

Looks like this is going to be a busy week.

Chris