\HeaderA{agPATH}{Mappings between probe identifiers and KEGG pathway identifiers}{agPATH}
\keyword{datasets}{agPATH}
\begin{Description}\relax
KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data
for various organisms. agPATH maps probe identifiers to the
identifiers used by KEGG for pathways in which the genes represented
by the probe identifiers are involved
\end{Description}
\begin{Details}\relax
Each KEGG pathway has a name and id. Pathway name for a given pathway
id can be obtained using the KEGG data package that can either be
built using AnnBuilder or downloaded from Bioconductor
\url{http://www.bioconductor.org}.

Graphic presentations of pathways are searchable at
url{http://www.genome.ad.jp/kegg/pathway.html} by using pathway ids as
keys.   

Mappings were based on data provided by:

KEGG:\url{http://gopher5/compbio/annotationSourceData/kegg/pathways}. Built: Release 34.0 (April 2005)

Entrez Gene:\url{http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/}. Built: Source data downloaded from Entrez Gene on Tue May 17 18:26:20 2005

Package built Tue May 17 18:29:49 2005
\end{Details}
\begin{References}\relax
\url{http://www.genome.ad.jp/kegg/}
\end{References}
\begin{Examples}
\begin{ExampleCode}
    # Convert the environment to a list
    xx <- as.list(agPATH)
    # Remove probe ids that do not map to any pathway id
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The pathway ids for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    } 
\end{ExampleCode}
\end{Examples}

