Hi, I would like to extract all the metabolism pathways with their compounds for a organism (in my case the Sorghum - sgi , 139 metabolism pathways). Usually I use : http://rest.kegg.jp/link/cpd/map0xxxx for each metabolism pathway and convert the data with name and format that I need. So it's long and not sustainable to be updated regularly. Can you give me some tips to manipulate the Kegg database to extract full metabolisms including compounds and compounds name (and maybe same for genes).
Example: for 2 metabolisms patways, here map00010 and map00020 (I tried http://rest.kegg.jp/link/cpd/sgi00010 but dosen't work):
I do http://rest.kegg.jp/link/cpd/map00010 path:map00010 cpd:C00022 path:map00010 cpd:C00024 path:map00010 cpd:C00031 …..
and
http://rest.kegg.jp/link/cpd/map000020
path:map00020 cpd:C00022
path:map00020 cpd:C00024
path:map00020 cpd:C00026
….
After that, I manually merge these data and add the name of each of them …
But what I want it's directly something close of the final file that I need to generate: Full organism
map00010 Glycolysis / Gluconeogenesis Pyruvic acid; Acetyl-CoA; D-Glucose; Acetic acid ...
map00020 Citrate cycle (TCA cycle) Pyruvic acid; Acetyl-CoA; Oxoglutaric acid ...
...
Any help would be appreciated. Thanks for your time in advance.