parsePsimi25Interaction: Parsing PSI-MI 2.5 XML documents into interactions
In alyst/RpsiXML: R interface to PSI-MI 2.5 files

Description Usage Arguments Value Author(s) References See Also Examples

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.

1 2	parsePsimi25Interaction(psimi25file, psimi25source, verbose=TRUE) parsePsimi25Complex(psimi25file, psimi25source, verbose=FALSE)

`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.

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.

Jitao David Zhang <jitao_david.zhang@roche.com>, Tony Chiang <tchiang@ebi.ac.uk>

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/

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

# 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)