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/hsa04330.
> xml<ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa04330.%0Axml>
> "
> > parseKGML(url)
> failed to load external entity
> "
> ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa04330.
> xml<ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa04330.%0Axml>
> "
> Error: 1: failed to load external entity
> "
> ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa04330.
> xml<ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/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
> >
>
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>



-- 
Jitao David Zhang
Biological Statistics and Computational Biology Ph.D.
Division of Molecular Genome Analysis
DKFZ, Heidelberg D-69120, Germany

http://www.NextBioMotif.com/

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