[Biopython-dev] Project ideas for GSoC (or other student projects)

Peter Cock p.j.a.cock at googlemail.com
Thu Mar 21 16:11:44 UTC 2013

On Fri, Mar 15, 2013 at 11:06 PM, Bartek Wilczynski
<bartek at rezolwenta.eu.org> wrote:
> Hi All,
> I would add one more (old) idea for a GSoC pool, i.e. adding support
> for different biological ontologies to biopython.
> This was already discussed some time ago
> (http://www.biopython.org/w/index.php?title=Gene_Ontology&redirect=no)
> mostly in the context of gene ontology, and to some extent this is
> addressed by the development of GOAtools
> (https://github.com/tanghaibao/goatools), but I think it would be
> worth to have a decent support for OBO-file-based ontologies (not only
> gene ontology, I'm also interested myself in anatomical ontologies,
> there are also other available at obofoundry.org) in biopython.
> I think it would need to include support for IO operations on both OBO
> and annotation files, as well as statistical enrichment measures and
> potentially some visualisation.
> Would anyone be interested in co-mentoring this project? There is one
> student in my department who would be interested in applying to GSoC
> for this project, but I think it would be great if other people joined
> the discussion on the functionality and having more people involved is
> always better...
> best
> Bartek Wilczynski

That's a good idea - I would have used this recently with some GO
stuff (e.g. given a GO term, is it a molecular function, biological
process, or cellular compartment - can solve this easily by traversing
up any branch of the DAG).

Right now we need to put this list of ideas on the wiki page (ready
for combining into the OBF page which will be shown to Google
to make our case for taking part in the GSoC 2013 program).

If any of you as a potential mentor want to put up an outline
proposal, even better.


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