\HeaderA{parsePsimi25Interaction}{Parsing PSI-MI 2.5 XML documents into interactions}{parsePsimi25Interaction}
\aliasA{parsePsimi25Complex}{parsePsimi25Interaction}{parsePsimi25Complex}
\keyword{models}{parsePsimi25Interaction}
\begin{Description}\relax
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.

\code{parsePsimi25Interaction} is the parser for interaction data and
\code{parsePsimi25Complex} is the parser for complex data.
\end{Description}
\begin{Usage}
\begin{verbatim}
parsePsimi25Interaction(psimi25file, psimi25source, verbose=TRUE)
parsePsimi25Complex(psimi25file, psimi25source, verbose=FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{psimi25file}] character, file name or URL of the XML document 
\item[\code{psimi25source}] A supported data repository source, see also
\code{\LinkA{psimi25Source-class}{psimi25Source.Rdash.class}} 
\item[\code{verbose}] logical, whether the parsing state should be displayed verbosely.
\end{ldescription}
\end{Arguments}
\begin{Value}
\code{psimi25Interaction} returns a list of \code{psimi25InteractionEntry}
objects, each represents one \code{entry} in the XML document
\code{psimi25Complex} returns a \code{psimi25ComplexEntry} objects,
representing the complex data from one XML document.
\end{Value}
\begin{Author}\relax
Jitao David Zhang <j.zhang@dkfz-heidelberg.de>, Tony Chiang
<tchiang@ebi.ac.uk>
\end{Author}
\begin{References}\relax
\item[PSI-MI XML v2.5 data exchange
format] \url{http://www.psidev.info/index.php?q=node/60}
\item[BioGRID] \url{http://www.thebiogrid.com}
\item[DIP] \url{http://dip.doe-mbi.ucla.edu/}
\item[HPRD] \url{http://www.hprd.org/}
\item[IntAct] \url{http://www.ebi.ac.uk/intact}
\item[MINT] \url{http://mint.bio.uniroma2.it/mint}
\item[MIPS/CORUM] \url{http://mips.gsf.de/}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{psimi25Interaction-class}{psimi25Interaction.Rdash.class}},
\code{\LinkA{psimi25InteractionEntry-class}{psimi25InteractionEntry.Rdash.class}},
\code{\LinkA{psimi25Complex-class}{psimi25Complex.Rdash.class}}
\code{\LinkA{psimi25ComplexEntry-class}{psimi25ComplexEntry.Rdash.class}},
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# 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)

\end{ExampleCode}
\end{Examples}

