\HeaderA{org.EcK12.egPATH}{Mappings between Entrez Gene identifiers and KEGG pathway identifiers}{org.EcK12.egPATH}
\aliasA{org.EcK12.egPATH2EG}{org.EcK12.egPATH}{org.EcK12.egPATH2EG}
\keyword{datasets}{org.EcK12.egPATH}
\begin{Description}\relax
KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data
for various organisms. org.EcK12.egPATH maps entrez gene identifiers to the
identifiers used by KEGG for pathways
\end{Description}
\begin{Details}\relax
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 ) on 2008-Sep2
\end{Details}
\begin{References}\relax
\url{http://www.genome.ad.jp/kegg/}
\end{References}
\begin{Examples}
\begin{ExampleCode}
    x <- org.EcK12.egPATH
    # Get the entrez gene 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]]
    }

    # For the reverse map:
    # Convert the object to a list
    xx <- as.list(org.EcK12.egPATH2EG)
    # Remove pathway identifiers that do not map to any entrez gene id
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The entrez gene identifiers for the first two elements of XX
        xx[1:2]
        # Get the first one
        xx[[1]]
    }
\end{ExampleCode}
\end{Examples}

