\HeaderA{agGO2ALLPROBES}{Map Between Gene Ontology (GO) Identifiers and all Manufacturer
Identifiers in the subtree}{agGO2ALLPROBES}
\keyword{datasets}{agGO2ALLPROBES}
\begin{Description}\relax
agGO2ALLPROBES is an R environment that provides mappings
between a given GO identifier and all manufactuerer identifiers annotated at that
GO term or one of its children in the GO ontology.
\end{Description}
\begin{Details}\relax
GO consists of three ontologies---molecular function (MF),
biological process (BP), and cellular component (CC).  All ontologies
are structured as directed acyclic graphs (DAGs).  Each node in
each DAG (tree) is a GO term (id) associated with a named vector of
manufacturer identifiers.  The name associated with each manufacturer id
corresponds to the evidence code for that GO identifier.  This environment
agGO2ALLPROBES maps between a given GO identifier and all manufactuerer
identifiers annotated at that GO term or one of its children in the GO ontology.  

The evidence code indicates what kind of evidence supports the
association between the GO and Entrez Gene identifiers. Evidence codes
currently 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 identifier may be mapped to the same manufacturer identifier more than once but the
evidence code can be different. Mappings between Gene Ontology identifiers and
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

Package built Fri Aug 24 17:42:16 2007
\end{Details}
\begin{References}\relax
\url{ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/}
\end{References}
\begin{Examples}
\begin{ExampleCode}
    # Convert to a list
    xx <- as.list(agGO2ALLPROBES)
    if(length(xx) > 0){
        # Gets the probe identifiers for the top 2nd and 3nd GO identifiers
        goids <- xx[2:3]
        # Gets all the probe identifiers for the first element of goids
        goids[[1]]
        # Evidence code for the mappings
        names(goids[[1]])
    }
\end{ExampleCode}
\end{Examples}

