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KEGG- map searching

I would like to ask how (with which method from Kegg api) i can get the genomes or the pathways participating in a specific map for example map00010.
Thank you

Re: KEGG- map searching

Reply #1
Hi,

just found this post, the easiest would be to go with the Bioconductor package KEGGSOAP.
http://www.bioconductor.org/packages/re ... GSOAP.html

You will have to search for the neutral mass, so any adduct formation has to be undone
prior to using KEGGSOAP.

Yours,
Steffen
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE

Re: KEGG- map searching

Reply #2
KEGG also propose a REST-Style API described in this page: http://www.genome.jp/kegg/rest/keggapi.html
You will have to got the response from the URL.
For instance following rest address:
Code: [Select]
http://rest.kegg.jp/link/cpd/map00010
will provide the list of metabolites belonging to this map :
Code: [Select]
path:map00010	cpd:C00022
path:map00010 cpd:C00024
path:map00010 cpd:C00031
path:map00010 cpd:C00033
path:map00010 cpd:C00036
path:map00010 cpd:C00068
path:map00010 cpd:C00074
path:map00010 cpd:C00084
path:map00010 cpd:C00103
path:map00010 cpd:C00111
path:map00010 cpd:C00118
path:map00010 cpd:C00186
path:map00010 cpd:C00197
path:map00010 cpd:C00221
path:map00010 cpd:C00236
path:map00010 cpd:C00267
path:map00010 cpd:C00469
path:map00010 cpd:C00631
path:map00010 cpd:C00668
path:map00010 cpd:C01159
path:map00010 cpd:C01172
path:map00010 cpd:C01451
path:map00010 cpd:C05125
path:map00010 cpd:C05345
path:map00010 cpd:C05378
path:map00010 cpd:C06186
path:map00010 cpd:C06187
path:map00010 cpd:C06188
path:map00010 cpd:C15972
path:map00010 cpd:C15973
path:map00010 cpd:C16255
Dr JOURDAN Fabien
INRA UMR1331 TOXALIM-MeX
180 Chemin de Tournefeuille
BP 93173 F31027 Toulouse Cedex 3
France