\HeaderA{agENZYME}{Map between Manufacturer IDs and Enzyme Commission (EC) Numbers}{agENZYME}
\keyword{datasets}{agENZYME}
\begin{Description}\relax
agENZYME is an R object that provides mappings between
manufacturer identifiers and EC numbers.
\end{Description}
\begin{Details}\relax
Each manufacturer identifier maps to a named vector containing the EC number that
corresponds to the enzyme produced by that gene. The name corresponds
to the manufacturer 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 agENZYME2PROBE, 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 probe identifiers and enzyme identifiers were obtained using files
provided by: Tair ( ftp://ftp.arabidopsis.org/Pathways/aracyc\_dump\_20070703 ) on 2007-Aug2
\end{Details}
\begin{References}\relax
\url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}
\end{References}
\begin{Examples}
\begin{ExampleCode}
        x <- agENZYME
        # Get the probe identifiers that are mapped to an EC number 
        mapped_probes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_probes])
        if(length(xx) > 0) {
          # Get the ENZYME for the first five probes
          xx[1:5]
          # Get the first one
          xx[[1]]
        }
\end{ExampleCode}
\end{Examples}

