[BioPython] OBO format parser and genome databasing

[Leighton Pritchard]

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.

L.

-- 
Dr Leighton Pritchard B.Sc.(Hons) MRSC
D131, Plant Pathology Programme, SCRI
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