getKGMLurl: Get KGML file (url) with KEGG PATHWAY ID and (optional)...

In KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

Description

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.

Usage

getKGMLurl(pathwayid, organism = "hsa")
retrieveKGML(pathwayid, organism, destfile,method="wget", ...)
kgmlNonmetabolicName2MetabolicName(destfile)
getCategoryIndepKGMLurl(pathwayid, organism="hsa", method="wget", ...)

Arguments

pathwayid	KEGG PATHWAY ID, e.g. 'hsa00020'
organism	three-alphabet organism code, if pathwayid contains the ocde this option is ignored
destfile	Destination file, to which the remote KGML file should be saved
method	Method to be used for downloading files, passed to download.file function. Currently supports "internal", "wget" and "lynx"
...	Parameters passed to download.file

Details

The function 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.

retrieveKGML calls 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.

Since July 2017, the function uses the REST API service of KEGG.

Value

KGML File URL of the given pathway.

Note

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 wget program (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 wget execution file is located) and re-install R to make wget work.

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 KEGGgraph was able to handle them. kgmlNonmetabolicName2MetabolicName is used to translate non-metabolic pathway KGML URL to that of metabolic pathway. 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.

Author(s)

Jitao David Zhang mailto:[e-mail]

References

Plea from KEGG (available as of Aug 2011) http://www.genome.jp/kegg/docs/plea.html

Examples

getKGMLurl("hsa00020")
getKGMLurl("path:hsa00020")
getKGMLurl("00020",organism="hsa")
getKGMLurl(c("00460", "hsa:00461", "path:hsa00453", "path:00453"))

## NOT RUN
## Not run: 
  tmp <- tempfile()
  retrieveKGML(pathwayid='00010', organism='cel', destfile=tmp, method="wget")

## End(Not run)
## END

Example output

Attaching package: ‘KEGGgraph’

The following object is masked from ‘package:graphics’:

    plot

The following object is masked from ‘package:base’:

    plot

[1] "http://rest.kegg.jp/get/hsa00020/kgml"
[1] "http://rest.kegg.jp/get/hsa00020/kgml"
[1] "http://rest.kegg.jp/get/hsa00020/kgml"
[1] "http://rest.kegg.jp/get/hsa00460/kgml"
[2] "http://rest.kegg.jp/get/hsa00461/kgml"
[3] "http://rest.kegg.jp/get/hsa00453/kgml"
[4] "http://rest.kegg.jp/get/hsa00453/kgml"
KGML cannot be retrieved, cannot open URL 'http://rest.kegg.jp/get/cel00010/kgml'.

KEGGgraph documentation built on Nov. 8, 2020, 5:42 p.m.