[BioC] extracting interactions between members of the KEGG pathways

[Wolfgang Huber]

Hi Jane,

here's what Imre Vastrik from Reactome said regarding your question:

"We probably can't help with KEGG ;-). Reactome content is projected 
into pair-wise interaction space (see 
http://www.reactome.org/download/interactions.README.txt). The data 
(human only) is available at:
http://www.reactome.org/download/current/homo_sapiens.interactions.txt.gz

I imagine that another bit of useful information would be the 
association of sequence identifiers with pathways (not contained in the 
file above) so that one can go from a pathway to identifiers and for an 
indentifier to pathways."

----

There are a number of additional datasets in different file formats to 
download http://www.reactome.org/download/

Cheers
  Wolfgang



-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber
-------------------------------------


Jane Fridlyand wrote:
> Hello,
> 
> I was wondering whether there is an infrastructure in one of the BioC
> packages to extract connections between members of the KEGG pathways. As
> far as I can tell KEGG package allows to get the identifiers of the
> members very easily, however I do not see a way of going one step further
> so to be able to produce a graph (where presence of each edge indicates
> known interaction or same compound )
> 
> Thank you. Any help /suggestion is greatly appreciated.
> 
> Jane
> 
>