\HeaderA{hgu2beta7GO}{Mappings between probe identifiers and Gene Ontology information}{hgu2beta7GO}
\keyword{datasets}{hgu2beta7GO}
\begin{Description}\relax
The Gene Ontology Consortium maintains a controlled vocabulary of
defined terms to describe gene products. hgu2beta7GO maps probe
identifiers to Gene Ontology information including the ids, evidence
codes, and ontology categories of the terms for the genes represented by
the probe ids.
\end{Description}
\begin{Details}\relax
Each probe id is mapped to a list containing one (mapped to none or
one set of GO information) or more (mapped to more than one sets of GO
information) elements. When a probe id is mapped to at lest one set of
GO information, each element of the list contains a sub list of three
elements named "GOID", "Ontology", and "Evidence". The value for element
"GOID" gives the Gene Ontology identifier the key probe 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 ontology category the GO id belongs to. The
value for element "Evidence" contains an evidence code indicating what
kind of evidence is found to support the association of the GO id to
the gene represented by the key probe 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

Mappings between probe ids and GO information were obtained through
their mappings to LocusLink ids. NAs are assigned to probe identifiers
that can not be mapped to any Gene Ontology information. 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:\url{ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz}. Built: February 16, 2005

Gene Ontology:\url{http://www.godatabase.org/dev/database/archive/daily/go_daily-termdb.rdf-xml.gz}. Built: http://www.godatabase.org/dev/database/archive/daily/go_daily-termdb.rdf-xml.gz

Package built Wed Feb 16 23:32:20 2005
\end{Details}
\begin{Examples}
\begin{ExampleCode}
    # Convert to a list
    xx <- as.list(hgu2beta7GO)
    # Remove all the NAs
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
            # Try the firest one
            got <- xx[[1]]           
            got[[1]][["GOID"]]
            got[[1]][["Ontology"]]
            got[[1]][["Evidence"]]

    }
\end{ExampleCode}
\end{Examples}

