[BioC] KEGGgraph bug

Fraser Sim fjsim at buffalo.edu
Mon Dec 7 20:36:07 CET 2009


Hi David,

Thanks. That doesn’t solve the problem though, try to get the KEGG pathway
‘hsa03010’ using 

>getCategoryIndepKGMLurl(‘03010’,organism = ‘hsa’)

It doesn’t produce a valid html link. It should find
‘ftp://ftp.genome.jp/pub/kegg/xml/kgml/non-metabolic/organisms/hsa/hsa03010.
xml’ which is correct but because 'getKGMLurl' returns the invalid
‘ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms/hsa/hsa03010.
xml’, it then returns
‘ftp://ftp.genome.jp/pub/kegg/xml/kgml/metabolic/organisms/hsa/hsa03010.xml’
which does not exist. 

Note the substitution of "_" with "-". I’m pretty sure it’s a bug in
getKGMLurl.

Thanks,
Fraser

From: Jitao David Zhang [mailto:davidvonpku at gmail.com] 
Sent: Monday, November 23, 2009 5:58 AM
To: Fraser Sim
Cc: bioc
Subject: Re: [BioC] KEGGgraph bug

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

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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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