\HeaderA{GOALLENTREZID}{Annotation of GO identifiers by all the corresponding Entrez Gene
identifiers}{GOALLENTREZID}
\aliasA{GOALLLOCUSID}{GOALLENTREZID}{GOALLLOCUSID}
\keyword{datasets}{GOALLENTREZID}
\begin{Description}\relax
This is an R environment (hash table) mapping GO identifiers to all the Entrez Gene
identifiers corresponding to the GO identifiers and its direct or indirect
offspring. The direct or indirect offspring of a given GO identifier are the
nodes that are directly linked to the node for the GO identifier or indirectly
linked to the GO identifier through nodes that are linked to the GO identifier based on
the directed acyclic graph defined by Gene Ontology Consortium
\end{Description}
\begin{Details}\relax
GO identifiers are Keys and the corresponding Entrez Gene identifiers are Values. Values
are named vectors of length 1 or greater depending on whether a given
GO identifier can be mapped to one or more Entrez Gene identifiers. Names for
values are the evidence codes for the GO identifier (if an evidence code was
provided by source data). The evidence codes that are 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

NA is assigned to GO identifiers that can not be mapped to any Entrez Gene identifier at
this time.  

Mappings were based on data provided by:

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

Entrez Gene:\url{http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/}. Built: Source data downloaded from Entrez Gene on Tue Sep  5 18:42:30 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") || stop("GO unavailable")
        # Convert the environment object to a list
        xx <- as.list(GOALLENTREZID)
        # Remove GO identifiers that are not mapped to any Entrez Gene identifier
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
                # Get the Entrez Gene identifiers for the first two elents of xx
                llids  <- xx[1:2]
                # Get the evidence code llids
                evds <- sapply(llids, names)
        }

\end{ExampleCode}
\end{Examples}