[Biopython-dev] WIT database

Tarjei S Mikkelsen tarjei at genome.wi.mit.edu
Sat Jul 21 16:14:36 EDT 2001


 I'm new to this project, but I'm currently in the process of
writing a BioPython parser for the KEGG database, which is very
similar to WIT. I'll soon be posting a module for parsing the
KEGG/Ligand database here, which I hope you'll integrate into

 I've also been toying with the idea of writing a parser for the
pathway section of KEGG, but I think that to maximize the usefulness
of such a module there should first be a set of objects for representing
reactions and pathways (a Bio.Pathway module). This would make it
possible to manipulate information from databases like KEGG and WIT
in a uniform manner - just like all sequence information is parsed into
a Bio.Seq object.

 If there is interest I'd be happy to collaborate, or even take the
lead, in developing a Bio.Pathway module. As Cayte says below,
this is an interesting challenge because, as far as I know, this is
not a functionality that is currently present in any of the other bio*


 Tarjei Mikkelsen
 tarjei at genome.wi.mit.edu

> -----Original Message-----
> From: biopython-dev-admin at biopython.org
> [mailto:biopython-dev-admin at biopython.org]On Behalf Of Cayte
> Sent: Saturday, July 21, 2001 6:35 PM
> To: biopython-dev at biopython.org
> Subject: [Biopython-dev] WIT database
>    After some cleanup of old parsers, I plan to write a parser for the WIT
> database.  It should be interesting because it is a database of metabolic
> steps instead of sequences.
>                                            Cayte
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