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

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

Get KGML file (url) with KEGG PATHWAY ID and (optional) organism

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="auto", ...)
kgmlNonmetabolicName2MetabolicName(destfile)
getCategoryIndepKGMLurl(pathwayid, organism="hsa", method="auto", ...)

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", "auto" 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 REST API remotely.

Before July 2017, KEGG FTP server was used to download the KGML files. Since then the REST API service of KEGG is used instead.

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.

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) https://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"))

hasConnection <- RCurl::url.exists(getKGMLurl("cel00010"))
if(hasConnection) {
  tmp <- tempfile()
  retrieveKGML(pathwayid='00010', organism='cel', destfile=tmp, method="auto")
} else {
  warnings("No connection to KEGG webservice")
}

Accio/KEGGgraph documentation built on Jan. 13, 2023, 1:03 p.m.