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

The GOID element matches the GO identifier named in the outer list and is
included for convenience when processing the data using 'lapply'.

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 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

Mappings between probe identifiers and GO information were obtained through
their mappings to Entrez Gene identifiers. NAs are assigned to probe identifiers
that can not be mapped to any Gene Ontology information. Mappings
between Gene Ontology identifiers an Gene Ontology terms and other information
are available in a separate data package named GO.

Mappings were based on data provided by:

Tair: \url{ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_AG_array_elements-2006-07-14.txt}
Tair: \url{ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes}
Tair: \url{ftp://ftp.arabidopsis.org/home/tair/User_Requests/LocusPublished.02022007}
Built: N/A

Tair: \url{ftp://ftp.arabidopsis.org/home/tair/Ontologies/Gene_Ontology/ATH_GO_GOSLIM.20070224.txt}
Built: N/A

Package built Fri Aug 24 17:42:16 2007
\end{Details}
\begin{Examples}
\begin{ExampleCode}
    # Convert to a list
    xx <- as.list(agGO)
    # 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}

