GOTERM {GO} | R Documentation

## Annotation of GO identifiers by terms defined by Gene Ontology Consortium

### Description

This is an R environment (hash table) mapping GO ids to the specific terms in defined by Gene Ontology Consortium

### Details

GO ids are keys and the corresponding GO terms are values. Each value is a GOTerms object with 6 slots (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, Category - the GO ontology category. Can be MF - molecular function, CC - cellular component, or BP - biological process).

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 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/2004-09-01/go_200409-termdb.xml.gz. Built: 2004-09-01

Package built: Mon Jan 10 19:19:56 2005

### 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]])
        }

[Package GO version 1.7.0 Index]