Where To Obtain Metabolic Pathway Datasets

Question

[albin.aaron]

I've been looking through the files available at www.reactome.org 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.

[Pierre Lindenbaum]

http://www.reactome.org/download/index.html ?

[albin.aaron]

Yes, those are the files I've been looking through and haven't found the pathway data I described. For example, if I look at the Human protein-protein interaction pairs file, it gives reactions as a format like REACT_27257.1. If I look at the Events in their Biopax format for humans, there is an entry for that reaction that simply has a comment with a link to the reactome website to view the pathway diagram. However, what I'm looking for is the actual data used to create that diagram.

Answer 1

[IV]

Reactome can be downloaded in a multitude of formats:

You can check out more in the relevant web page: http://www.reactome.org/download/

KEGG offers free access to its REST-style API, where you can directly download or have access to the pathways that you're interested at: http://www.kegg.jp/kegg/rest/

Through this API you can get the KEGG XML pages (KGML).

You just cannot download the whole database dump, as in the case of Reactome. Nevertheless, the API is really convenient.

Cheers,

IV

[albin.aaron]

Well, I still couldn't understand where the pathway data is for reactome, but I believe I can get what I need from KEGG. Specifically, "In KGML the pathway element specifies one graph object with the entry elements as its nodes and the relation and reaction elements as its edges." The KGML files are retrieved using a get method, and so I'd just need to query and get all pathways for humans that they list here (http://rest.kegg.jp/list/pathway/hsa). Thanks for pointing me in this direction.