How to get the latest KEGG pathway

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Raymond ▴ 20

@raymond-14020

Last seen 5.5 years ago

Hi,

I want to draw KEGG pathways with my nodes colored correlated to p-value*log(foldchange).

From :

http://keggscape.readthedocs.io/en/latest/pythonscripting.html

I used "http://rest.kegg.jp/list/pathway/hsa" to get all human kegg pathways, and "http://rest.kegg.jp/get/' + pathwayid + '/kgml" to download the correspond pathway for cytoscape input.

However, when I checked the xml files, it showed that they were created in May 14, 2014 .

Anyone here knows how to get the latest version of KEGG pathways?

Also, my current strategy is to use "KEGGscape" and my own script to color all nodes according to my own p-values. Any other suggestions?

regards,

Raymond

KEGG kegg.db kegggraph • 2.9k views

ADD COMMENT • link 6.9 years ago Raymond ▴ 20

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This site is for questions about Bioconductor software, but you don't seem to be using any. If you are not using Bioconductor, please send you questions to another forum such as Biostars.

Anyway, what you get from http://rest.kegg.jp is, by definition, the latest KEGG information. KEGG licensing arrangements prevent anyone from downloading and redistributing KEGG information, so what is on rest.kegg.jp is by far the latest. All other sources are years out of date.