parsePsimi25Interaction {RpsiXML}R Documentation

Parsing PSI-MI 2.5 XML documents into interactions

Description

The PSI-MI 2.5 XML format is used widely by many repositories to record protein-protein interaction data as well as protein complex data. This functions parse such files into interactions or complexes.

parsePsimi25Interaction is the parser for interaction data and parsePsimi25Complex is the parser for complex data.

Usage

parsePsimi25Interaction(psimi25file, psimi25source, verbose=TRUE)
parsePsimi25Complex(psimi25file, psimi25source, verbose=FALSE)

Arguments

psimi25file character, file name or URL of the XML document
psimi25source A supported data repository source, see also psimi25Source-class
verbose logical, whether the parsing state should be displayed verbosely.

Value

psimi25Interaction returns a list of psimi25InteractionEntry objects, each represents one entry in the XML document psimi25Complex returns a psimi25ComplexEntry objects, representing the complex data from one XML document.

Author(s)

Jitao David Zhang <j.zhang@dkfz-heidelberg.de>, Tony Chiang <tchiang@ebi.ac.uk>

References

PSI-MI XML v2.5 data exchange format
http://www.psidev.info/index.php?q=node/60
BioGRID
http://www.thebiogrid.com
DIP
http://dip.doe-mbi.ucla.edu/
HPRD
http://www.hprd.org/
IntAct
http://www.ebi.ac.uk/intact
MINT
http://mint.bio.uniroma2.it/mint
MIPS/CORUM
http://mips.gsf.de/

See Also

psimi25Interaction-class, psimi25InteractionEntry-class, psimi25Complex-class psimi25ComplexEntry-class,

Examples

# parse interaction data
xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")

gridxml <- file.path(xmlDir, "biogrid_200804_test.xml")
gridSet <- parsePsimi25Interaction(gridxml, BIOGRID.PSIMI25)

intactxml <- file.path(xmlDir, "intact_2008_test.xml")
intactSet <- parsePsimi25Interaction(intactxml, INTACT.PSIMI25, verbose=TRUE)

# parse complex data
intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
intactComplexSet <- parsePsimi25Complex(intactComplexxml, INTACT.PSIMI25)


[Package RpsiXML version 1.0.0 Index]