GOTERM {GO}R Documentation

Annotation of GO identifiers by the textural description of genes represented by the GO identifiers

Description

This is an R environment (hash table) mapping GO ids to the specific textural description of the biological process, cellular component, or molecular function the genes represented by the GO ids are involved

Details

GO ids are keys and the corresponding GO textural descriptions are values. Values are name vectors of length 1. Names of the vectors indicating the GO category a term belongs to (MF = mocular function, BP = biological process, and CC = cellular component).

All the obsolete GO textural descriptions 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 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:

LocusLink built: March 3, 2004. ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.ga

Package built: Wed Mar 3 16:27:29 2004

References

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

Examples

        require("GO") || stop("GO unavailable")
        # Convert the environment object to a list
        xx <- as.list(GOTERM)
        if(length(xx) > 0){
                # Get the TERMS for the first two elents of xx
                terms <- xx[1:2]
                # Get the GO category the terms belong to 
                sapply(terms, names)
        }

[Package GO version 1.5.1 Index]