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Retrieving data from Kegg

My aim is to find all the genes and their pathways associated with the organism (Mycobacterium smegmatis, msm) from a pathway database (such as Kegg), with their name and description.

I could retrieve all the pathways and the gene IDs associated "msm" using the link

http://rest.kegg.jp/link/msm/pathway

path:msm00010   msm:MSMEG_0127
path:msm00010   msm:MSMEG_0154
path:msm00010   msm:MSMEG_0217
path:msm00010   msm:MSMEG_0255
path:msm00010   msm:MSMEG_0455
path:msm00010   msm:MSMEG_0502
path:msm00010   msm:MSMEG_0718
path:msm00010   msm:MSMEG_0752
....................

But now I need the name and description and of each pathway associated with the Gene IDs. for e.g.

GeneID PathwayID Name Description

What I have the link http://rest.kegg.jp/get/msm00010 to get details of each and every gene ID. But is there any way where I could get name and description of all the pathways at one go?

kegg pathway database genes genome
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updated by EagleEye EagleEye • written by Paul Paul

1 answer

GeneSCF is perfect for your task. Check this post for some example. Also check this post for general usage.

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written by EagleEye EagleEye

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