Get KGML file (url) with KEGG PATHWAY ID and (optional) organism
The function simply returns the KGML file url given KEGG PATHWAY ID. If the KEGG PATHWAY ID contains no organism prefix, user can specify the 'organism' parameter. Otherwise the 'organism' option is ignored.
retrieveKGML is a simple wrapper to getKGMLurl, which downloads the
KGML file with
download.file in utils package.
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KEGG PATHWAY ID, e.g. 'hsa00020'
three-alphabet organism code, if pathwayid contains the ocde this option is ignored
Destination file, to which the remote KGML file should be saved
Method to be used for downloading files, passed to
Parameters passed to download.file
getKGMLurl takes the pathway identifier (can be in the form of
'hsa00020' or with 'pathway' prefix, for example 'path:hsa00020'), and
returns the url to download KGML file.
The mapping between pathway identifier and pathway name can be found by KEGGPATHNAME2ID (or reversed mappings) in KEGG.db package. See vignette for example.
download.file to download the KGML
file from KEGG FTP remotely.
Since July 2011 the KGML is downloaded directly from the HTTP main page of each pathway, instead of from the FTP server. The FTP server is only open to subscribers. Commercial and other users should consider support the KEGG database by subscribing to the FTP service. See the references section below.
KGML File URL of the given pathway.
So far the function does not check the correctness of the 'organism' prefix, it is the responsibility of the user to garantee the right spelling.
For Windows users, it is necessary to download and install
(http://gnuwin32.sourceforge.net/packages/wget.htm) to use the
wget method to download files. Sometimes it may be necessary to
modify searching path to add GnuWin32 folder (where
execution file is located) and re-install R to make
Some user may experience difficulty of retrieving KGML files when the download method is set to ‘auto’. In this case setting the method to ‘wget’ may solve the problem (thanks to the report by Gilbert Feng).
There were a period when the metabolic and non-metabolic pathways were
saved separately in different directories, and
able to handle them.
kgmlNonmetabolicName2MetabolicName is used to translate
non-metabolic pathway KGML URL to that of metabolic
getCategoryIndepKGMLurl determines the correct URL to
download by attempting both possibilities. They were mainly called
internally. Now since the KGML file is to be downloaded in each
pathway's main page instead from the FTp server, these functions are
no more needed and will be removed in the next release.
Jitao David Zhang mailto:firstname.lastname@example.org
Plea from KEGG (available as of Aug 2011) http://www.genome.jp/kegg/docs/plea.html
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