I have found a problem with how 'getKGMLurl' constructs the URL for retrieving the KGML files. It looks like the '_' should be '-' in non_metabolic portion of the generated url. I am using the current release versions, R2.10.0 and KEGGgraph 1.2.0. Thanks, Fraser > library(KEGGgraph) Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object(s) are masked from package:XML : addNode Loading required package: Rgraphviz Loading required package: grid > url <- getKGMLurl('04330', organism = "hsa") > url [1] "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa 04330. xml" > parseKGML(url) failed to load external entity "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa 04330. xml" Error: 1: failed to load external entity "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa 04330. xml" > parseKGML(gsub("_","-",url)) KEGG Pathway [ Title ]: Notch signaling pathway [ Name ]: path:hsa04330 [ Organism ]: hsa [ Number ] :04330 [ Image ] :http://www.genome.jp/kegg/pathway/hsa/hsa04330.png [ Link ] :http://www.genome.jp/kegg-bin/show_pathway?hsa04330 ------------------------------------------------------------ Statistics: 30 node(s) 16 edge(s) 0 reaction(s) ------------------------------------------------------------ > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices datasets utils methods base other attached packages: [1] KEGGgraph_1.2.0 Rgraphviz_1.24.0 graph_1.24.0 XML_2.6-0 rcom_2.2-1 rscproxy_1.3-1 loaded via a namespace (and not attached): [1] tools_2.10.0 >

Hi Fraser, Thanks for the reporting. The reason for this is that since April 2009 the KEGG server saves the non-metabolic and metabolic pathways in two different sub-directory separatedly, and so far as I know there is no way to tell whether the pathway is metabolic alone from the pathway id. Therefore 'getKGMLurl' can NOT garantee to return the correct address. However, 'retrieveKGML' tries both metabolic and non-metabolic pathway directories, therefore it is able to download the file remotely. To retrieve the URL for a pathway, use 'getCategoryIndepKGMLurl' function, which tries both non-metabolic and metabolic directories. 'getKGMLurl' will be hidden from the next release. I hope my answer solves your question. Best wishes, David 2009/11/20 Fraser Sim <fjsim@buffalo.edu> > I have found a problem with how 'getKGMLurl' constructs the URL for > retrieving the KGML files. It looks like the '_' should be '-' in > non_metabolic portion of the generated url. I am using the current release > versions, R2.10.0 and KEGGgraph 1.2.0. > > Thanks, > Fraser > > > library(KEGGgraph) > Loading required package: XML > Loading required package: graph > > Attaching package: 'graph' > > > The following object(s) are masked from package:XML : > > addNode > > Loading required package: Rgraphviz > Loading required package: grid > > url <- getKGMLurl('04330', organism = "hsa") > > url > [1] > " > ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hs a04330. > xml<ftp: ftp.genome.jp="" pub="" kegg="" xml="" kgml="" non_metabolic="" organisms="" hs="" a="" hsa04330.%0axml=""> > " > > parseKGML(url) > failed to load external entity > " > ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hs a04330. > xml<ftp: ftp.genome.jp="" pub="" kegg="" xml="" kgml="" non_metabolic="" organisms="" hs="" a="" hsa04330.%0axml=""> > " > Error: 1: failed to load external entity > " > ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hs a04330. > xml<ftp: ftp.genome.jp="" pub="" kegg="" xml="" kgml="" non_metabolic="" organisms="" hs="" a="" hsa04330.%0axml=""> > " > > parseKGML(gsub("_","-",url)) > KEGG Pathway > [ Title ]: Notch signaling pathway > [ Name ]: path:hsa04330 > [ Organism ]: hsa > [ Number ] :04330 > [ Image ] :http://www.genome.jp/kegg/pathway/hsa/hsa04330.png > [ Link ] :http://www.genome.jp/kegg-bin/show_pathway?hsa04330 > ------------------------------------------------------------ > Statistics: > 30 node(s) > 16 edge(s) > 0 reaction(s) > ------------------------------------------------------------ > > sessionInfo() > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] grid stats graphics grDevices datasets utils methods > base > > other attached packages: > [1] KEGGgraph_1.2.0 Rgraphviz_1.24.0 graph_1.24.0 XML_2.6-0 > rcom_2.2-1 rscproxy_1.3-1 > > loaded via a namespace (and not attached): > [1] tools_2.10.0 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jitao David Zhang Biological Statistics and Computational Biology Ph.D. Division of Molecular Genome Analysis DKFZ, Heidelberg D-69120, Germany http://www.NextBioMotif.com/ [[alternative HTML version deleted]]