\HeaderA{gahgu95cGO}{Map between custom probeset IDs and Gene Ontology (GO)}{gahgu95cGO}
\keyword{datasets}{gahgu95cGO}
\begin{Description}\relax
gahgu95cGO is an R environment that provides mappings between
custom probeset identifiers and the GO identifiers that they are
directly associated with.
\end{Description}
\begin{Details}\relax
Each custom probeset identifier is mapped to a list of lists.  The names on
the outer list are GO identifiers.  Each inner list contains of five
named elements: GOID, Ontology, Term, Evidence and PMIDS.

The GOID element matches the GO identifier named in the outer list.

The Ontology element indicates which of the three Gene Ontology
categories this identifier belongs to.  The categories are
biological process (BP), cellular component (CC), and molecular
function (MF).

The Term element indicates the name of GO cathegory correspoding to the
GO identifier named in the outer list.

The Evidence element contains a code indicating what kind of
evidence supports the association of the GO identifier to the Entrez Gene
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

The PMIDS element indicates the Pubmed IDs of references in the literature, if relevant,
obtained from EntrezGene.

NAs are assigned to probe identifiers that can not be mapped to any Gene Ontology
information. Other information concerning Gene Ontology classification are available
in a separate data package named GO.


Mappings were based on data provided by:

GeneCards database - www.genecards.org

Package built Mon Aug 25 17:09:56 2008
\end{Details}
\begin{References}\relax
\url{www.genecards.org}
\end{References}
\begin{Examples}
\begin{ExampleCode}
    # Convert to a list
    xx <- as.list(gahgu95cGO)
    # Remove all the NAs
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
            # Try the first one
            got <- xx[[1]]           
            got[[1]][["GOID"]]
            got[[1]][["Ontology"]]
            got[[1]][["Evidence"]]

    }
\end{ExampleCode}
\end{Examples}

