GOTERM {GO}R Documentation

Annotation of GO Identifiers to GO Terms

Description

This data set gives mappings between GO identifiers and their respective terms.

Details

Each GO identifier is mapped to a GOTerms object that has 6 slots:

GOID
GO Identifier
Term
The term for that GO id
Synonym
Synonymous terms
Secondary
Secondary terms that have been merged into this term
Definition
Further definition of the GO term
Ontology
One of MF - molecular function, BP - biological process, or CC - cellular component

All the obsolete GO terms are under the nodes "obsolete molecular function" (GO:0008369), "obsolete cellular component" (GO id GO:0008370), and "obsolete biological process" (GO:0008371). Each of these GO identifiers has a group of GO identifiers as their direct children with GO terms that were defined by GO but are deprecated in the current build. These deprecated GO terms were appended by "(obsolete)" when the data package was built.

Mappings were based on data provided by:

Gene Ontology:ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest. Built: Build Information not available

Package built: Mon Apr 7 09:09:39 2008

References

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

Examples

    require("GO") || stop("GO unavailable")
    require("annotate") || stop("annotate unavailable")
    # Convert the environment object to a list
    xx <- as.list(GOTERM)
    if(length(xx) > 0){
        # Get the TERMS for the first elent of xx
        GOID(xx[[1]])
        Term(xx[[1]])
        Synonym(xx[[1]])
        Secondary(xx[[1]])
        Definition(xx[[1]])
        Ontology(xx[[1]])
    }

[Package GO version 2.2.0 Index]