[Biopython-dev] [Biopython] Gene ontology parsing

Kyle kellrott at gmail.com
Thu Jul 14 09:19:48 UTC 2011

(Hitting Reply-All this time)

I think I let the work being done by Chris Lasher and Tamas supersedes my work.

My patches got pulled into Chris's branch:

I'll be at BOSC starting tomorrow. (About to get on a plane to Vienna)


On Thu, Jul 14, 2011 at 12:56 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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.
> Thanks,
> Peter

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