[Biopython-dev] [Biopython] Gene ontology parsing

Peter Cock p.j.a.cock at googlemail.com
Thu Jul 14 07:56:09 UTC 2011

Hi Kyle,

Last year you wrote this on the main Biopython mailing list,

On Fri, Jul 23, 2010 at 5:17 PM, Kyle <kellrott at gmail.com> wrote:
>> There are already several people working on GO stuff in branches on github,
>> e.g. Chris Lasher, Kyle Ellrott, Tamás Nepusz. I don't know if any of them are
>> doing OBO v1.2, but it would be sensible to check and try and combine efforts.
> The branch at http://github.com/kellrott/biopython/tree/gosupport
> should parse most of the information held in OBO v1.2.
> Chris's original version was targeted only for the GO OBO file, as
> there was a typecheck to make sure the node ID's started with 'GO:'.
> That's disable in my branch, and I've used the package to parse a few
> of the other ontologies found at www.obofoundry.org.
> The module is currently called Bio.GO, but maybe it should be
> re-factored to represent the fact that it covers general OBO files,
> and not just the GO file specifically.
> The main things things keeping it from merging into the main branch
> are proper documentation, complete unit tests, and making sure that it
> covers all of the standard usage practices.
> If you can try it out, and let me know which function are missing (and
> maybe contribute some code), we can push this thing forward.
> Kyle

Does your code still exist, perhaps on a different branch? I couldn't
find it at the URL http://github.com/kellrott/biopython/tree/gosupport

I'm at the CodeFest preceding BOSC 2011, and Herve (CC'd) is
interested in parsing OBO files in Biopython.



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