Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. Join them; it only takes a minute:

Sign up
Here's how it works:
  1. Anybody can ask a question
  2. Anybody can answer
  3. The best answers are voted up and rise to the top

I've been looking through the files available at along with some others but I only find images/pdfs of metabolic pathway diagrams. Where is the actual data these pathways are drawn from? I imagine there should be some kind of directed graph representation. I'm limited to freely available datasets, so unfortunately I'm not able to check out those such as KEGG.

share|improve this question
KEGG should be open for anyone, if I am not completely wrong. – Chris Jan 22 '14 at 19:10
According to their download page, access to the ftp files for KEGG require a paid academic subscription (through I suppose the tools on their website are free, but I haven't found the pathway data I'm looking for (that is, I see where I'm only able to browse pathway diagrams). – Aaron Jan 22 '14 at 19:21
Well, now I see that KEGG has a XML markup of their pathways, but it is only available from querying their API ( I wonder if there is an easy way to grab all pathway files. – Aaron Jan 22 '14 at 19:34
up vote 2 down vote accepted

KEGG is definitely your choice!

It is possible to get the whole list(s) of pathways: (reference pathways) or (for human).

Then you can use these IDs to retrieve information about individual pathways: (GeneBank-like format), (image), (KEGG xml). It will take a while, of course, and I'd recommend not to overload their server and make delays between queries. With the GeneBank-like format batch querying is also possible:

This should likely be a one-time or at least rare operation, because of the load on their server (and I don't think they make big changes very often). You can retrieve info for new pathways, once they appear in

share|improve this answer
Yes, this is actually precisely what I ended up doing. I wrote a python script which iterated through the human pathway file, sent a get request to their API and just saved each kgml file to hard disk. For the GeneBank-like format, those don't indicate any relationship among gene or compounds involved right? It looks like it is simply a list. – Aaron Jan 23 '14 at 16:15
@Aaron: as far as I know, they are just listed. It's a pity, the API has no batching for the xml output, but KEGG is great any case! – har-wradim Jan 23 '14 at 18:57

Your Answer


By posting your answer, you agree to the privacy policy and terms of service.

Not the answer you're looking for? Browse other questions tagged or ask your own question.