parsePsimi25Interaction: 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.

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/

Examples

Run this code

# 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)

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