[BioPython] OBO format parser and genome databasing
Sean Davis
sdavis2 at mail.nih.gov
Thu Jun 28 10:47:55 UTC 2007
Leighton Pritchard wrote:
> Hi Sean,
>
> On Thu, 2007-06-28 at 09:38 +0100, Peter wrote:
>> Sean Davis wrote:
>>> Does anyone know of an OBO format parser for python?
>> This is the replacement for the older GO flat file format, right?
>
> I have been using the BioPerl load_ontology.pl script to load .obo files
> into BioSQL. Unfortunately, there have been some issues with the
> GO .obo files and that script, and I've had to fall back on the flat
> files. The Sequence Ontology/SOFA .obo files seem to work with it OK,
> though.
>
>>> As a more general question, is anyone using the chado database schema
>>> with python?
>> I haven't.
>
> Nor me - still sticking with BioSQL for now.
Thanks, Leighton.
Sean
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