KGML pathway download

Question

[guillaume.rbt]

Hi all,

I would like to download the KGML files from all pathway of Arabidopsis Thaliana. It may be achieved using KEGG API (http://www.kegg.jp/kegg/rest/keggapi.html), but if it is I haven’t figured out how.

If anyone have an idea...

Thanks,

[guillaume.rbt]

Thank you very much Pierre, it works perfectly !

Answer 1

[Pierre Lindenbaum]

something like:

$ curl -s  "http://rest.kegg.jp/list/organism" | grep "Arabidopsis thaliana"
T00041  ath Arabidopsis thaliana (thale cress)  Eukaryotes;Plants;Eudicots;Mustard family


$ curl "http://rest.kegg.jp/list/pathway/T00041" | cut -f 1 | while read A; do  curl -o "${A}.xml" "http://rest.kegg.jp/get/${A}/kgml" ; done

[efosa15]

please what language is this?

[Pierre Lindenbaum]

bash https://en.wikipedia.org/wiki/Bash_(Unix_shell)