\HeaderA{psimi25Source-class}{Class "psimi25Source"}{psimi25Source.Rdash.class}
\aliasA{parseComplex,psimi25Source-method}{psimi25Source-class}{parseComplex,psimi25Source.Rdash.method}
\aliasA{parseExperiment,psimi25Source-method}{psimi25Source-class}{parseExperiment,psimi25Source.Rdash.method}
\aliasA{parseInteractor,psimi25Source-method}{psimi25Source-class}{parseInteractor,psimi25Source.Rdash.method}
\aliasA{uniprot,psimi25Source-method}{psimi25Source-class}{uniprot,psimi25Source.Rdash.method}
\keyword{classes}{psimi25Source-class}
\begin{Description}\relax
A class representing data source compatible with PSI-MI
2.5 XML data exchange format
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("psimi25Source", ...)}
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{label}:] Object of class \code{"character"}, a
meaningful unique label of the database, does not necessarily have to be
the identifier used in the PSI-MI files. The value is advised to
be overwritten by the objects
\item[\code{sourceDb}:] Object of class \code{"character"}, the
character string used in the PSI-MI files to identify the source
database. The value must be overwritten by the object, depending
on the database identifier used in the PSI-MI file.
\item[\code{uniprotSymbol}:] Object of class \code{"character"}, the
identifier of UniProf reference in "primaryRef" or "secondaryRef"
attributes of the interactors, telling the parser where to find
UniProt symbol of the interactors. The value must be overwritten by
the objects.
\item[\code{parseExperiment}:] Object of class \code{"function"},
the function to parse experiment from the PSI-MI 2.5 file. Except
for special need this function should not be overwritten by the
objects, since it parses the experiment node strictly according
the PSI-MI standard 
\item[\code{parseInteractor}:] Object of class \code{"function"},
the function to parse interactor from the PSI-MI 2.5 file. Except
for special need this function should not be overwritten by the
objects, since it parses the interactor node strictly according
the PSI-MI standard  
\item[\code{parseComplex}:] Object of class \code{"function"},
the function to parse complex from the PSI-MI 2.5 file. Except
for special need this function should not be overwritten by the
objects, since it parses the complex node strictly according
the PSI-MI standard 
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[parseComplex] \code{signature(x = "psimi25Source")}: parse
complex node of PSI-MI 2.5 file 
\item[parseExperiment] \code{signature(x = "psimi25Source")}: parse
experiment node of PSI-MI 2.5 file
\item[parseInteractor] \code{signature(x = "psimi25Source")}: parse
interactor node of PSI-MI 2.5 file
\item[sourceDb] \code{signature(x = "psimi25Source")}: returns the
source database
\item[uniprot] \code{signature(x = "psimi25Source")}: returns the
uniprot identifier of the PSI-MI 2.5 XML file 
}
\end{Section}
\begin{Note}\relax
In case of a new data repository, you can first try creating a
new object of the class with \code{label}, \code{sourceDb} and
\code{uniprotSymbol} adjusted as needed. Try parsing a function with
this new psimi25Source object. In case of warnings or errors, it may
mean that the file provided is not strictly compatible with PSI-MI 2.5
data exchange format standard, please then contact the data provider.

By 02.06.08, six sources have been registered in the release version
of \code{RpsiXML}:  BIOGRID.PSIMI25, DIP.PSIMI25, HPRD.PSIMI25, INTACT.PSIMI25,,
MINT.PSIMI25,MIPS.PSIMI25. Along the development we will implement
more data sources under PSI-MI 25 standard.
\end{Note}
\begin{Author}\relax
Jitao David Zhang <j.zhang@dkfz.de>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{parsePsimi25Interaction}{parsePsimi25Interaction}},
\code{\LinkA{parsePsimi25Complex}{parsePsimi25Complex}},
\code{\LinkA{psimi25XML2Graph}{psimi25XML2Graph}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
showClass("psimi25Source")
\end{ExampleCode}
\end{Examples}

