\name{@ANNOBJPREFIX@ENSEMBL}
\alias{@ANNOBJPREFIX@ENSEMBL}
\alias{@ANNOBJPREFIX@ENSEMBL2EG}
\title{Map Ensembl gene accession numbers with Entrez Gene identifiers}  
\description{ 
  @ANNOBJPREFIX@ENSEMBL is an R object that contains mappings between 
  Entrez Gene identifiers and Ensembl gene accession numbers.    
}
\details{
  This object is a simple mapping of Entrez Gene identifiers
  \url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene} to Ensembl
  gene Accession Numbers.
  
  Mappings were based on data provided by BOTH of these sources:
  \url{http://www.ensembl.org/biomart/martview/}
  \url{ftp://ftp.ncbi.nlm.nih.gov/gene/DATA}

  For most species, this mapping is a combination of NCBI to ensembl IDs
  from BOTH NCBI and ensembl.  Users who wish to only use mappings from
  NCBI are encouraged to see the ncbi2ensembl table in the appropriate
  organism package.  Users who wish to only use mappings from ensembl
  are encouraged to see the ensembl2ncbi table which is also found in
  the appropriate organism packages.  These mappings are based upon the
  ensembl table which is contains data from BOTH of these sources in an
  effort to maximize the chances that you will find a match.

  For worms and flies however, this mapping is based only on sources
  from ensembl, as these organisms do not have ensembl to entrez gene
  mapping data at NCBI.
}

\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@ENSEMBL
# Get the entrez gene IDs that are mapped to an Ensembl ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
  # Get the Ensembl gene IDs for the first five genes
  xx[1:5]
  # Get the first one
  xx[[1]]
}
#For the reverse map ENSEMBL2EG:
# Convert to a list
xx <- as.list(@ANNOBJPREFIX@ENSEMBL2EG)
if(length(xx) > 0){
   # Gets the entrez gene IDs for the first five Ensembl IDs
   xx[1:5]
   # Get the first one
   xx[[1]]
}
}
\keyword{datasets}



