[BioC] KEGGgraph question

Sim, Fraser Fraser_Sim at URMC.Rochester.edu
Mon Mar 16 14:24:30 CET 2009

Hi David,

Here's the result:

> library(KEGGgraph)
> library(Rgraphviz)
> KeggID = "04310"
> KEGGpathway = parseKGML(getKGMLurl(KeggID, organism = "hsa"))
> keggG = KEGGpathway2Graph(KEGGpathway, genesOnly = FALSE, expandGenes = TRUE)
> getDisplayName(keggGnodedata[["cpd:C00076"]])
[1] "C00076"

I think it should be Calcium;Ca2+


> sessionInfo()
R version 2.8.1 (2008-12-22) 

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] Rgraphviz_1.21.7 RBGL_1.18.0      KEGGgraph_0.8.15 graph_1.20.0    
[5] XML_1.99-0       rcom_2.0-4       rscproxy_1.0-12 

loaded via a namespace (and not attached):
[1] cluster_1.11.12 tools_2.8.1    

From: Jitao David Zhang [mailto:davidvonpku at gmail.com] 
Sent: Monday, March 16, 2009 2:23 AM
To: Sim, Fraser
Subject: Re: KEGGgraph question

Hi Fraser,

  Sorry for the late reply, have you tried getDisplayName?

Best wishes,
2009/3/3 Sim, Fraser <Fraser_Sim at urmc.rochester.edu>
Hi David,
I have been using the KEGGgraph package to plot Kegg pathways. I am working on the glioma pathway "05214". The compounds that are present in this library are not displaying their names as indicated from the KEGG website for example:
Here is the result of a "getKEGGnodeData" on node cpd:C00076.
KEGG Node (Entry 'cpd:C00076'):
[ displayName ]: C00076
[ Name ]: cpd:C00076
[ Type ]: compound
[ Link ]: http://www.genome.jp/dbget-bin/www_bget?compound+C00076
The link shows the name Calcium;Ca2+ on the website. Is there any way of retrieving this from the Kegg XML using your package?


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