GOLOCUSID2ALLGO {GO}R Documentation

Annotation of LocusLink identifiers by specific and derived gene ontology information regarding the genes corresponding to the LocusLink identifiers

Description

This is an R environment (hash table) mapping LocusLink ids to gene ontology information regarding the genes represented by the LocusLink identifiers. Gene ontology information includes those stated directly by NCBI and those derived based on the directed acyclic GO graph defined by Gene Ontology Consortium

Details

LocusLink ids are keys and the corresponding GO information are values. Association of LocusLink ids to GO information were obtained by including those reported by NCBI (specific) and those that were derived through the parent-child relations among GO nodes on the directed acyclic GO graph. If a given GO node had been reported to be associated with a LocusLink id, all the offspring of that GO node were considered to be associated with the LocusLink id as well.

Each locusLink id is mapped to a list with one (mapped to none or one GO id) or more (mapped to more than one GO ids) sub lits. Each sub list contains three elements named "GOID", "Ontology", and "Evidence". The value for element "GOID" gives the Gene Ontology identifier the key LocusLink id corresponds to. The value for element "Ontology" can be an abbreviation of MF (mocular function), BP (biological process),or CC (cellular component) for the GO category the GO id belongs to. The values for element "Evidence" contains an evidence code indicating what kind of evidence is found to support the association of the GO id to the LocusLink id. The evidence codes 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 LocusLink id that can not be mapped to any GO id at this time.

Mappings were based on data provided by:

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.ncbi.nlm.nih.gov/LocusLink

Examples

        require("GO") || stop("GO unavailable")
        # Convert the environment object to a list
        xx <- as.list(GOLOCUSID2ALLGO)
        # Remove LocusLink ids that are not mapped to any GO id
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
                # Get the GO ids for the first two elents of xx
                goids  <- xx[1:2]
                # Get the evidence code goids
                evds <- sapply(goids, names)
        }

[Package GO version 1.6.5 Index]