GOTERM {GO}R Documentation

Annotation of GO identifiers by terms defined by Gene Ontology Consortium

Description

A GO identifier is associated with several terms defined by the Gene Ontology Consortium. GOTERM contains of GO ids to the terms.

Details

GO ids are keys and the corresponding GO terms are values. Each value is a list of GOTerms objects with 6 slots each (GOID - GO identifier, Term - the specific GO ontology term for the GO id, Synonym - other synonymous terms, Secondary - secondary GO ids that were merged to the primary GO id, Definition - further definition of the GO ontology term, Ontology - the GO ontology category. Can be MF - molecular function, CC - cellular component, or BP - biological process).

Go terms "obsolete molecular function" (GO:0008369), "obsolete cellular component" (GO id GO:0008370), and "obsolete biological process" (GO:0008371) are terms that have been removed from the active process ontology. Each of these GO ids has a group of GO ids as their direct children (nodes directly linked to but below the GO ids along the directed acyclic graph defined by GO) 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:http://www.godatabase.org/dev/database/archive/2004-07-01/go_200407-termdb.xml.gz. Built: 2004-07-01

Package built: Tue Sep 28 11:27:36 2004

References

http://www.ncbi.nlm.nih.gov/LocusLink

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 1.6.5 Index]