[BioC] extracting interactions between members of the KEGG pathways

[Peter (BioConductor List)]

Peter (BioConductor List) 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
> 
> 
> Have you looked at the Rgraphviz package?
> 
> "HowTo layout a pathway", focuses on drawing genetic networks using a 
> KEGG pathway as an example:
> 
> http://www.bioconductor.org/repository/devel/vignette/layingOutPathways.pdf

Having said that, re-reading this document (Jeff Gentry, May 17, 2005) 
it probably won't help you very much:

> At this time, there is no automated way to extract the appropriate information
> from KEGG (or other sites) and construct a graph. If one wishes to layout their
> own pathways, it requires manual construction of a graph, creating each node
> and then recording the edges. Likewise, for any basic attributes ..., they too
 > must be collected by hand.

:(