\name{@ANNOBJPREFIX@PATH}
\alias{@ANNOBJPREFIX@PATH}
\alias{@ANNOBJPREFIX@PATH2ORF}
\title{Mappings between ORF identifiers and KEGG pathway identifiers}
\description{
  KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data
  for various organisms. @ANNOBJPREFIX@PATH maps ORF identifiers to the
  identifiers used by KEGG for pathways.  The reverse map
  @ANNOBJPREFIX@PATH2ORF maps back from KEGG pathway IDs to the ORF
  identifiers.
}
\details{
  Each KEGG pathway has a name and identifier. Pathway name for a given pathway
  identifier 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 identifiers as
  keys.   

  Mappings were based on data provided by: @PATHSOURCE@

}

\references{
  \url{http://www.genome.ad.jp/kegg/}
}

\seealso{
  \itemize{
    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
          the \code{select()} interface.
  }
}

\examples{
## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
x <- @ANNOBJPREFIX@PATH
# Get the ORF identifiers that are mapped to a KEGG pathway ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
  # Get the PATH for the first five genes
  xx[1:5]
  # Get the first one
  xx[[1]]
}
# Convert the object to a list
xx <- as.list(@ANNOBJPREFIX@PATH2ORF)
# Remove pathway identifiers that do not map to any ORF id
xx <- xx[!is.na(xx)]
if(length(xx) > 0){
    # The ORF identifiers for the first two elements of XX
    xx[1:2]
    # Get the first one
    xx[[1]]
}
}

\keyword{datasets}


