\HeaderA{GOALLLOCUSID}{Annotation of GO identifiers by all the corresponding LocusLink
identifiers}{GOALLLOCUSID}
\keyword{datasets}{GOALLLOCUSID}
\begin{Description}\relax
This is an R environment (hash table) mapping GO ids to all the LocusLink
ids corresponding to the GO id and its direct or indirect
offspring. The direct or indirect offspring of a given GO id are the
nodes that are directly linked to the node for the GO id or indirectly
linked to the GO id through nodes that are linked to the GO id based on
the directed acyclic graph defined by Gene Ontology Consortium
\end{Description}
\begin{Details}\relax
GO ids are Keys and the corresponding LocusLink ids are values. Values
are named vectors of length 1 or greater depending on whether a given
GO id can be mapped to only one or more LocusLink ids. Names for
values are the evidence codes for the GO id (if 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 ids that can not be mapped to any LocusLink id at
this time.  

Mappings were based on data provided by:

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

LocusLink:\url{ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz}. Built: January 10, 2005

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") || stop("GO unavailable")
        # Convert the environment object to a list
        xx <- as.list(GOALLLOCUSID)
        # Remove GO ids that are not mapped to any LocusLink id
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
                # Get the LocusLink ids for the first two elents of xx
                llids  <- xx[1:2]
                # Get the evidence code llids
                evds <- sapply(llids, names)
        }

\end{ExampleCode}
\end{Examples}

