\HeaderA{GOCCPARENTS}{Annotation of GO Identifiers to their Cellular Component Parents}{GOCCPARENTS}
\keyword{datasets}{GOCCPARENTS}
\begin{Description}\relax
This data set describes associations between GO molecular function (CC)
terms and their direct parent CC terms, based on the directed acyclic
graph (DAG) defined by the Gene Ontology Consortium. The format is an R
environment mapping the GO CC terms to all direct parent terms, where a
direct parent term is a more general GO term that immediately precedes
the given GO term in the DAG.
\end{Description}
\begin{Details}\relax
Each GO CC term is mapped to a named vector of GO CC terms. The name
associated with the parent term will be either \emph{isa}, \emph{hasa} or \emph{partof},
where \emph{isa} indicates that the child term is a more specific version
of the parent, and \emph{hasa} and \emph{partof} indicate that the
child term is a part of the parent. For example, a telomere is part of
a chromosome.

Cellular component is defined as the subcellular structures,
locations, and macromolecular complexes; examples include nucleus,
telomere, and origin recognition complex as defined b y Gene Ontology
Consortium.

Mappings were based on data provided:

Gene Ontology:\url{http://gopher5/compbio/annotationSourceData/archive.godatabase.org/latest/}. Built: 08-Aug-2006

Package built: Tue Sep  5 18:42:30 2006
\end{Details}
\begin{References}\relax
\url{http://www.geneontology.org/} and
\url{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene}
\end{References}
\begin{Examples}
\begin{ExampleCode}
  require("GO", character.only = TRUE) || stop("GO unavailable")
  require("annotate", character.only = TRUE) || stop("annotate unavailable")
  # Convert the environment object to a list
  xx <- as.list(GOCCPARENTS)
  # Remove GO IDs that do not have any parent
  xx <- xx[!is.na(xx)]
  if(length(xx) > 0){
     goids <- xx[[1]]
     # Find out the GO terms for the first parent go ID
     GOID(GOTERM[[goids[1]]])
     Term(GOTERM[[goids[1]]])
     Synonym(GOTERM[[goids[1]]])
     Secondary(GOTERM[[goids[1]]])
     Definition(GOTERM[[goids[1]]])
     Ontology(GOTERM[[goids[1]]])
  }
\end{ExampleCode}
\end{Examples}