GOALLLOCUSID {GO}R Documentation

Annotation of GO identifiers by all the corresponding LocusLink identifiers

Description

This is an R environment (hash table) mapping GO ids to all the LocusLink ids corresponding to the GO id and its direct or indirect offspring. The direct or indirect offspring of a given GO id are the nodes that are directly linked to the node for the GO id or indirectly linked to the GO id through nodes that are linked to the GO id based on the directed acyclic graph defined by Gene Ontology Consortium

Details

GO ids are Keys and the corresponding LocusLink ids are values. Values are named vectors of length 1 or greater depending on whether a given GO id can be mapped to only one or more LocusLink ids. Names for values are the evidence codes for the GO id (if evidence code was provided by source data). The evidence codes that are 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

NA is assigned to GO ids that can not be mapped to any LocusLink id at this time.

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

LocusLink:/scratch/homes/jzhang/R/library/AnnBuilder/temp/file643c9869LL_tmpl. Built: Built: September 15, 2005

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

References

http://www.geneontology.org/ and http://www.ncbi.nlm.nih.gov/LocusLink

Examples

        require("GO") || stop("GO unavailable")
        # Convert the environment object to a list
        xx <- as.list(GOALLLOCUSID)
        # Remove GO ids that are not mapped to any LocusLink id
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
                # Get the LocusLink ids for the first two elents of xx
                llids  <- xx[1:2]
                # Get the evidence code llids
                evds <- sapply(llids, names)
        }


[Package GO version 1.6.5 Index]