[Biopython-dev] Building Gene Ontology support into Biopython

[Brad Chapman]

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