\HeaderA{GOLOCUSID2ALLGO}{Annotation of LocusLink identifiers by specific and derived gene
ontology information regarding the genes corresponding to the
LocusLink identifiers}{GOLOCUSID2ALLGO}
\keyword{datasets}{GOLOCUSID2ALLGO}
\begin{Description}\relax
This is an R environment (hash table) mapping LocusLink ids to gene
ontology information regarding the genes represented by the LocusLink
identifiers. Gene ontology information includes those stated directly
by NCBI and those derived based on the directed acyclic GO graph defined by
Gene Ontology Consortium
\end{Description}
\begin{Details}\relax
LocusLink ids are keys and the corresponding GO information are
values. Association of LocusLink ids to GO information were obtained
by including those reported by NCBI (specific) and those that were
derived through the parent-child relations among GO nodes on the
directed acyclic GO graph. If a given GO node had been reported to be
associated with a LocusLink id, all the offspring of that GO node were
considered to be associated with the LocusLink id as well. 

Each locusLink id is mapped to a list with one (mapped to none or one GO id)
or more (mapped to more than one GO ids) sub lits. Each sub list contains
three elements named "GOID", "Ontology", and "Evidence". The value for
element "GOID" gives the Gene Ontology identifier the key LocusLink id 
corresponds to. The value for element "Ontology" can be an
abbreviation of MF (mocular function), BP (biological process),or CC
(cellular component) for the GO category the GO id belongs to. The
values for element "Evidence" contains an evidence code indicating
what kind of evidence is found to support the association of the GO id
to the LocusLink id. The evidence codes 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 LocusLink id that can not be mapped to any GO id at
this time.

Mappings were based on data provided by:

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.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(GOLOCUSID2ALLGO)
        # Remove LocusLink ids that are not mapped to any GO id
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
                # Get the GO ids for the first two elents of xx
                goids  <- xx[1:2]
                # Get the evidence code goids
                evds <- sapply(goids, names)
        }
\end{ExampleCode}
\end{Examples}

