\name{org.Sc.sgdPATH}
\alias{org.Sc.sgdPATH}
\alias{org.Sc.sgdPATH2ORF}
\title{Mappings between ORF identifiers and KEGG pathway identifiers}
\description{
  KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data
  for various organisms. org.Sc.sgdPATH maps ORF identifiers to the
  identifiers used by KEGG for pathways.  The reverse map
  org.Sc.sgdPATH2ORF 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: KEGG GENOME  
  ftp://ftp.genome.jp/pub/kegg/genomes  
  With a date stamp from the source of: 2010-Sep7

}
\references{
  \url{http://www.genome.ad.jp/kegg/}
}
\examples{
    x <- org.Sc.sgdPATH
    # 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(org.Sc.sgdPATH2ORF)
    # 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}