[BioPython] OBO format parser and genome databasing

Leighton Pritchard lpritc at scri.ac.uk
Thu Jun 28 09:33:46 UTC 2007


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
Errol Road, Invergowrie, Perth and Kinross, Scotland DD2 5DA
e:lpritc at scri.ac.uk            w:http://bioinf.scri.ac.uk/lp
gpg/pgp: 0xFEFC205C
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views 
expressed by the sender are not necessarily the views of SCRI and its 
subsidiaries.  This email and any files transmitted with it are confidential 
to the intended recipient at the e-mail address to which it has been 
addressed.  It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this 
confidentiality and you must not use, disclose, copy, print or rely on this 
e-mail in any way. Please notify postmaster at scri.ac.uk quoting the 
name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are 
present in this email, neither the Institute nor the sender accepts any 
responsibility for any viruses, and it is your responsibility to scan the email 
and the attachments (if any).




More information about the Biopython mailing list