\HeaderA{psi25interaction}{parser for PSI-MI 2.5 XML documents from EBI intact}{psi25interaction}
\aliasA{psi25complex}{psi25interaction}{psi25complex}
\keyword{models}{psi25interaction}
\begin{Description}\relax
The PSI-MI 2.5 XML format is used by EBI IntAct database to record
protein-protein interaction data and protein complex data. 
\code{psi25interaction} is the parser for interaction data and
\code{psi25complex} is the parser for complex data.
\end{Description}
\begin{Usage}
\begin{verbatim}
psi25interaction(intactFile)
psi25complex(intactFile)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{intactFile}] character, file name or URL of the XML document
\end{ldescription}
\end{Arguments}
\begin{Value}
\code{psi25interaction} returns a list of \code{interactionEntry} 
objects, each represents one \code{entry} in the XML document.
\code{psi25complex} returns an \code{complexEntry} object, which
represents the data from one XML document.
\end{Value}
\begin{Author}\relax
Nianhua Li
\end{Author}
\begin{References}\relax
The IntAct Database \url{http://www.ebi.ac.uk/intact/site/contents/downloads.jsf}.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{interactionEntry-class}{interactionEntry.Rdash.class}}, \code{\LinkA{complexEntry-class}{complexEntry.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# parse complex data
fn <- system.file("PSI25XML/complexSample.xml", package="Rintact")
complexData <- psi25complex(fn)
complexData

# parse interaction data
fn <- system.file("PSI25XML/interactionSample.xml", package="Rintact")
interactionData <- psi25interaction(fn)
interactionData
\end{ExampleCode}
\end{Examples}

