\HeaderA{GOMFPARENTS}{Annotation of GO Identifiers to their Molecular Function Parents}{GOMFPARENTS}
\keyword{datasets}{GOMFPARENTS}
\begin{Description}\relax
This data set describes associations between GO molecular function (MF)
terms and their direct parent MF terms, based on the directed acyclic
graph (DAG) defined by the Gene Ontology Consortium. The format is an R
environment mapping the GO MF 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 MF term is mapped to a named vector of GO MF 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.

Molecular function is defined as the tasks performed by individual
gene products; examples are transcription factor and DNA helicase as
defined by the Gene Ontology Consortium.

Mappings were based on data provided by:

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(GOMFPARENTS)
    # Remove GO identifiers that do not have any parent
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # Get the parent GO identifiers for the first elents of xx
        goids <- xx[[1]]
        # Find out the GO terms for the first parent goid
        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}