[BioC] KEGGgraph

Paul Shannon pshannon at fhcrc.org
Tue Oct 30 19:01:13 CET 2012

Hi Ricardo,

A few quick observations, and then an invitation to further discussion.

1) KEGG has played a central role in bioinformatics for years but now, it seems, it no longer can.  None of the publicly available data has been updated since KEGG 'went private' in the summer of 2011.

2) Here in Seattle, I -- and others elsewhere -- are exploring REACTOME, Nature/NCI and WikiPathways as ongoing sources of metabolic (and other) network graphs.

3) The RCytoscape package http://bioconductor.org/packages/2.11/bioc/html/RCytoscape.html is designed to make R/Cytoscape network visualization easy.  It comes with lots of documentation and a website:  http://rcytoscape.systemsbiology.net/versions/current/index.html

Which metabolic pathway are you working on?  Perhaps I can use it as a case study in my exploration of KEGG alternatives.


 - Paul

On Oct 30, 2012, at 10:47 AM, Ricardo Silva wrote:

> Hello all,
> I've been trying to create the most complete possible compound map for
> an organism, and KEGGgraph was the best approach until now.
> Someone already worked with graphs metabolites in R?
> I have a doubt if the KEGGgraph merging process can miss nodes, that's
> because,
> looking at the compounds in each reaction:
>    read.delim(paste("http://rest.kegg.jp/link/reaction/", orgId,
> sep=""),header=FALSE)
>    read.delim(paste("http://rest.kegg.jp/link/compound/", orgId,
> sep=""),header=FALSE)
> where orgId is the tree letter organism code, I have a set of compounds
> different than the one retrivied bellow:
> When I use the mergeGraphs function:
> for (i in 1:length(allPath)) {
>        retrieveKGML(allPath[i], organism=orgId, destfile=tmp,
> method="wget", quiet=TRUE)
>        lg[[i]]  <- parseKGML(tmp)
>        if(length(lg[[i]]@reactions))  lt[[i]] <-
> KEGGpathway2reactionGraph(lg[[i]])
>    }
>    lt <- lt[!unlist(lapply(lt, is.null))]
>    merged <- mergeGraphs(lt)
> where allPath represents all organism pathways in kegg.
> the nodes of obtained graph are different from those obtained asking
> compounds by reaction, m'I missing something?
> Additionally, someone know's an automated way to export the graph to
> cytoscape, or even to write a KGML?
> Thanks in advance
> Ricardo
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