\HeaderA{GOBPPARENTS}{Annotation of GO identifiers by the GO identifiers of their
direct parents}{GOBPPARENTS}
\keyword{datasets}{GOBPPARENTS}
\begin{Description}\relax
This is an R environment (hash table) mapping GO ids to the GO
ids of their direct parents under biological process (BP). Direct
parents of a given GO id are those GO ids correponding to all the parents
nodes that have direct link to the node for the GO id of
concern based on the directed acyclic graph defined by Gene Ontology
Consortium. GO terms for parent nodes are more general than that of the
child nods
\end{Description}
\begin{Details}\relax
GO ids are keys and the corresponding parent GO ids are values. Values are
named vectors of length 1 or greater depending on whether the GO id of
concern has only one or more parents. The name(s) of value(s) is(are)
the association code (isa or partof) between the GO id and its direct
parents.GO ids that do not have any parent node are assigned NA as the
values.

Biological process is defined as the broad biological goals, such as
mitosis or purine metabolism, that are accomplished by ordered
assemblies of molecular functions as defined by Gene Ontology
Consortium.

Mappings were based on data provided:

Gene Ontology:\url{http://www.godatabase.org/dev/database/archive/2004-09-01/go_200409-termdb.xml.gz}. Built: 2004-09-01

Package built: Mon Jan 10 19:19:56 2005
\end{Details}
\begin{References}\relax
\url{http://www.geneontology.org/} and
\url{http://www.ncbi.nlm.nih.gov/LocusLink}
\end{References}
\begin{Examples}
\begin{ExampleCode}
  require("GO", character.only = TRUE) || stop("GO unavailable")
  require("annotate", character.only = TRUE) || stop("annoate unavailable")
  # Convert the environment object to a list
  xx <- as.list(GOBPPARENTS)
  # Remove GO ids that do not have any parent
  xx <- xx[!is.na(xx)]
  if(length(xx) > 0){
     # Get the children GO ids 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]]])
  }
\end{ExampleCode}
\end{Examples}

