GOLOCUSID {GO}R Documentation

Annotation of GO identifiers by the corresponding LocusLink identifiers

Description

This is an R environment (hash table) mapping GO ids to the LocusLink ids corresponding to the GO id.

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.

Only specific mappings (not derived from the directed acyclic graph of Gene Ontology) between GO and LocusLink ids were included. Non-specific mappings (derived from the directed acyclic graph of Gene Ontology. e. g. GO ids are mapped to LocusLink ids that are mapped to their children) are provided by a separate environment named GOALLLL.

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(GOLOCUSID)
    # 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]