Question: Retrieving data from Kegg
0
gravatar for Paul
2.8 years ago by
Paul80
India
Paul80 wrote:

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?

ADD COMMENTlink modified 2.8 years ago by EagleEye6.6k • written 2.8 years ago by Paul80
0
gravatar for EagleEye
2.8 years ago by
EagleEye6.6k
Sweden
EagleEye6.6k wrote:

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

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by EagleEye6.6k
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