\HeaderA{YEASTGO2PROBE}{Mappings between GO identifiers and probe identifiers
representing genes that are directly associated with the GO ids}{YEASTGO2PROBE}
\keyword{datasets}{YEASTGO2PROBE}
\begin{Description}\relax
The Gene Ontology (GO) Consortium maintains a controlled vocabulary of
defined terms to describe gene products. Each of the terms is assigned
a GO id that can be associated with a group of
genes. YEASTGO2PROBE maps each GO id to the probe identifiers
representing genes that are associated with the GO ids
\end{Description}
\begin{Details}\relax
GO terminologies are presented as a directed acyclic graph with root
nodes having more general terms than their children
nodes. YEASTGO2PROBE only maps GO ids to probe ids associated with
nodes specified by the GO ids but not their children nodes. The mapped
probe ids are named vectors. Names of the vectors are the evidence
codes indicating what kind of evidence is found to support the
association between GO ids and genes.

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

A GO id may be mapped to the same probe id more than once but
the evidence code can be different. Mappings between Gene Ontology ids
an Gene Ontology terms and other information are available in a
separate data package named GO. 

Mappings were based on data provided by:

LocusLink Yeast Genome:\url{http://www.yeastgenome.org/DownloadContents.shtml}. Built: Yeast Genome data are built at various time  intervals. Sources used were downloaded  Fri Jan  7 14:56:40 2005 
.

Package built Fri Jan  7 16:12:38 2005
\end{Details}
\begin{References}\relax
\url{ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz}
\end{References}
\begin{Examples}
\begin{ExampleCode}
    # Convert to a list
    xx <- as.list(YEASTGO2PROBE)
    if(length(xx) > 0){
        # Gets the probe ids for the top 2nd and 3nd GO ids
        goids <- xx[2:3]
        # Gets the probe ids for the first element of goids
        goids[[1]]
        # Evidence code for the mappings
        names(goids[[1]])
    }
\end{ExampleCode}
\end{Examples}

