[Biopython-dev] KEGG API Wrapper

[Zachary Charlop-Powers]

Kevin,
Michiel,


I just tested Kevin's code for a few simple queries and it worked great. I have always liked KEGG's organization of data and really appreciate this RESTful interface to their data; in some ways I think it easier to use the web interfaces for KEGG than it is for NCBI. Plus the KEGG coverage of metabolic networks is awesome.  I found the examples in Kevin's test script to be fairly self-explanatory but a simple-spelled out example in the Tutorial would be nice.

One thought, though, is that you can retrieve MANY different types of data from the KEGG Rest API - which means that the user will probably have to parse the data his/herself. Data retrieved with "list" can return lists of genes or compounds or organism and after a  cursory look  these are each formatted differently. Also true with the 'find' command. So I think you were right to leave out parsers because i think they will be a moving target highly dependent on the query.

Thank You Kevin,
zach cp





On Oct 13, 2012, at 7:38 AM, Michiel de Hoon <mjldehoon at yahoo.com<mailto:mjldehoon at yahoo.com>> wrote:

Hi Kevin,

It would be great to have better KEGG support in Biopython, so I think that this is useful and could in principle be merged into Biopython. But before we do so, is there some documentation for your code (or even better, for the Bio.KEGG module as a whole)? Then it's easier to see how this module can be used, and to discuss any modifications.

Thanks for your contribution!
-Michiel.

--- On Wed, 10/10/12, Kevin Wu <kjwu at ucsd.edu<mailto:kjwu at ucsd.edu>> wrote:

From: Kevin Wu <kjwu at ucsd.edu<mailto:kjwu at ucsd.edu>>
Subject: [Biopython-dev] KEGG API Wrapper
To: Biopython-dev at lists.open-bio.org<mailto:Biopython-dev at lists.open-bio.org>
Date: Wednesday, October 10, 2012, 5:27 PM
Hi,

I've written a simple wrapper on top of KEGG's new REST API
(
http://www.kegg.jp/kegg/docs/keggapi.html). The main
functionality of this
module is that can detect some invalid queries based on
kegg's defined
rules. I've implemented each of the examples given on the
api docs as tests
as well. Here's a quick example of its usage.

The api call to http://rest.kegg.jp/get/hsa:10458+ece:Z5100/aaseq can
be
done using the wrapper as:
KEGG.query("get", ["hsa:10458", "ece:Z5100"], "aaseq")

Querying the api works well with the current parsers written
for KEGG
formats. Let me know if there are issues or if it's useful
enough to be
merged into Biopython!

https://github.com/kevinwuhoo/biopython

Thanks!
Kevin
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Zach Charlop-Powers
Post-Doctoral Fellow
Laboratory of Genetically Encoded Small Molecules
Rockefeller University

zcharlop at rockefeller.edu<mailto:zcharlop at rockefeller.edu>