[Biopython-dev] KEGG support

[Renato Alves]

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Hi everyone,

KEGG support in Biopython has been mostly untouched for the past 8 years
with only a few changes and test additions. There is code in the tree to
work with the Enzyme and Compound databases but not for others such as
GENES, ORTHOLOGY, DRUG, ...

Considering the fact that I will need to write some code to work with
other formats I was planning to contribute and integrate it with the
SeqIO interface. This will require some additional homework on my part.

KEGG also has a SOAP based API [1]. It's functionality could be in some
aspects compared to NCBI eutils. Using the python SOAP library suds [2]
I had no problem interacting with it.

So just in case someone was already working on this secretly :) I would
like to know to make my life easier. If not I would also like to know if
you would be interested in the addition and finally what's your thought
about the SOAP interface and the suds (optional) dependency.

Just a word on suds. Even though the project has been around for a few
years now, it's still not available in most Linux distros. On my
personal experience with it it's probably the simplest and easy to use
SOAP library for python out there.

Cheers,
Renato

[1] - http://www.genome.jp/kegg/soap/doc/keggapi_manual.html
[2] - https://fedorahosted.org/suds/
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