[Biopython-dev] Pathway module

Tarjei S Mikkelsen tarjei at genome.wi.mit.edu
Fri Aug 3 21:59:38 EDT 2001

> > if you are not aware, look up BIND on the net. 
> >
> I found the text and my first impression is that its too ambitious for
> what we are doing.  We are not supporting kinetics or simulation.  Our
> mandate, as I understand it, is to provide tools that make it 
> easier to work with databses like BIND, to complement not duplicate 
> their functionality.

I totally agree on this point. What we need is something that is both
much more lightweight and more "processed" than the BIND data model.
Out "Pathway" should be a data structure that makes it simple to operate
on data selectively extracted from BIND or other databases.

Basically it's the difference between the Bio.GenBank.Record class and
the Bio.Seq class.

On the other hand, BIND appears to have matured and gained some 
momentum since last time I heard of it, and there is no doubt that 
a module for parsing and selecting BIND data would be very useful.
It would be something to look at after our WIT/EMP and KEGG 
modules. (After all, with 6 pathways stored the BIND database is 
currently much less useful than these two).

On a related note, The EcoCyc ontology paper 
(Karp P. (2000) Bioinformatics, v16, n3, p269-285) is also worth a
look for anyone interested in this topic.


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