\HeaderA{YEASTGO2ALLPROBES}{Mappings between GO identifiers and all the probe idifiers
representing genes associated with the GO ids}{YEASTGO2ALLPROBES}
\keyword{datasets}{YEASTGO2ALLPROBES}
\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 directly or indirectly
through the children GO ids of the GO id. YEASTGO2ALLPROBES maps
GO ids to genes (represented by probe identifiers) that are directly
or indirectly mapped to the GO ids by traversing the GO tree.
\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. Therefore, a
GO id can be mapped to genes corresponding to the term of that
particular GO id as well as genes corresponding to the terms of all the
children GO ids.

YEASTGO2ALLPROBES maps a GO id to all the probe ids representing
genes mapped by traversing the GO tree. 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 and
Gene Ontology terms and other information are available in a separate
data package named GO.  

Mappings were based on data provided:

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(YEASTGO2ALLPROBES)
    if(length(xx) > 0){
        # Gets the probe ids for the top 2nd and 3nd GO ids
        goids <- xx[2:3]
        # Gets all the probe ids for the first element of goids
        goids[[1]]
        # Evidence code for the mappings
        names(goids[[1]])
    }
\end{ExampleCode}
\end{Examples}

