\HeaderA{org.Sc.sgdENZYME}{Map between ORF IDs and Enzyme Commission (EC) Numbers}{org.Sc.sgdENZYME}
\aliasA{org.Sc.sgdENZYME2ORF}{org.Sc.sgdENZYME}{org.Sc.sgdENZYME2ORF}
\keyword{datasets}{org.Sc.sgdENZYME}
\begin{Description}\relax
org.Sc.sgdENZYME is an R object that provides mappings between
ORF identifiers and EC numbers.
\end{Description}
\begin{Details}\relax
Each ORF identifier maps to a named vector containing the EC number that
corresponds to the enzyme produced by that gene. The name corresponds
to the ORF identifier. If this information is unknown, the vector
will contain an \code{NA}.

Enzyme Commission numbers are assigned by the Nomenclature Committee
of the International Union of Biochemistry and Molecular Biology
\url{http://www.chem.qmw.ac.uk/iubmb/enzyme/} to allow enzymes to be
identified. 

An Enzyme Commission number is of the format EC x.y.z.w, where x, y, z,
and w are numeric numbers. In org.Sc.sgdENZYME2ORF, EC is dropped from the
Enzyme Commission numbers.

Enzyme Commission numbers have corresponding names that describe the
functions of enzymes in such a way that EC x is a more general
description than EC x.y that in turn is a more general description than
EC x.y.z. The top level EC numbers and names are listed below:

EC 1 oxidoreductases

EC 2 transferases

EC 3 hydrolases

EC 4 lyases

EC 5 isomerases

EC 6 ligases

The EC name for a given EC number can be viewed at
\url{http://www.chem.qmul.ac.uk/iupac/jcbn/index.html#6} 

Mappings between ORF identifiers and enzyme identifiers were obtained using files
provided by: KEGG GENOME ( ftp://ftp.genome.jp/pub/kegg/genomes ) on 2008-Apr1


For the reverse map, each EC number maps to a named vector containing
the ORF identifier that corresponds to the gene that produces
that enzyme. The name of the vector corresponds to the EC number.
\end{Details}
\begin{References}\relax
\url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}
\end{References}
\begin{Examples}
\begin{ExampleCode}
    x <- org.Sc.sgdENZYME
    # Get the ORF identifiers that are mapped to an EC number 
    mapped_genes <- mappedkeys(x)
    # Convert to a list
    xx <- as.list(x[mapped_genes])
    if(length(xx) > 0) {
      # Get the ENZYME id for the first five genes
      xx[1:5]
      # Get the first one
      xx[[1]]
    }
    # For the reverse map:
    # Convert to a list
    xx <- as.list(org.Sc.sgdENZYME2ORF)
    if(length(xx) > 0){
       # Gets the ORF identifiers for the first five enzyme
       #commission numbers
       xx[1:5]
       # Get the first one
       xx[[1]]
    }

\end{ExampleCode}
\end{Examples}

