\name{@ANNOBJPREFIX@GO2ALLORFS}
\alias{@ANNOBJPREFIX@GO2ALLORFS}
\title{Map Between Gene Ontology (GO) Identifiers and all ORF
  Identifiers in the subtree}
\description{
  @ANNOBJPREFIX@GO2ALLORFS is an R object that provides mappings
  between a given GO identifier and all ORF identifiers annotated at that
  GO term or one of its children in the GO ontology.
}
\details{
  GO consists of three ontologies---molecular function (MF),
  biological process (BP), and cellular component (CC).  All ontologies
  are structured as directed acyclic graphs (DAGs).  Each node in
  each DAG (tree) is a GO term (id) associated with a named vector of
  manufacturer identifiers.  The name associated with each ORF id
  corresponds to the evidence code for that GO identifier.  This object
  @ANNOBJPREFIX@GO2ALLORFS maps between a given GO identifier and all ORF
  identifiers annotated at that GO term or one of its children in the GO ontology.  

  The evidence code indicates what kind of evidence supports the
  association between the GO and ORF identifiers. Evidence codes
  currently in use include:

  IMP - inferred from mutant phenotype  

  IGI - inferred from genetic interaction

  IPI - inferred from physical interaction  

  ISS - inferred from sequence similarity  

  IDA - inferred from direct assay  

  IEP - inferred from expression pattern  

  IEA - inferred from electronic annotation  

  TAS - traceable author statement  

  NAS - non-traceable author statement  

  ND - no biological data available  

  IC - inferred by curator

  A GO identifier may be mapped to the same ORF identifier more than once but the
  evidence code can be different. Mappings between Gene Ontology identifiers and
  Gene Ontology terms and other information are available in a separate
  data package named GO.  
  
  Mappings were based on data provided by: @GO2ALLORFSSOURCE@
  For GO2ALL style mappings, the intention is to return all the genes
  that are the same kind of term as the parent term (based on the idea
  that they are more specific descriptions of the general term).
  However because of this intent, not all relationship types will be
  counted as offspring for this mapping.  Only "is a" and "has a" style
  relationships indicate that the genes from the child terms would be
  the same kind of thing.
}

\references{
\url{ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/}
}

\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:
# Convert to a list
xx <- as.list(@ANNOBJPREFIX@GO2ALLORFS)
if(length(xx) > 0){
    # Gets the ORF identifiers for the top 2nd and 3nd GO identifiers
    goids <- xx[2:3]
    # Gets all the ORF identifiers for the first element of goids
    goids[[1]]
    # Evidence code for the mappings
    names(goids[[1]])
}
}

\keyword{datasets}

