GOLOCUSID {GO} | R Documentation

## Gene Ontology (GO) to Entrez Gene Mapping

### Description

This data set gives mappings between GO identifiers and Entrez Gene identifiers as reported by NCBI. The format is an R environment mapping GO ids to a vector of Entrez Gene ids that are associated with it. In addition to the Entrez Gene id, the evidence code (the reason for the association) is also given.

### Details

Each GO id is mapped to a named vector of Entrez Gene ids. The name associated with each Entrez Gene id corresponds to the evidence code for that GO id. The evidence code indicates what kind of evidence supports the association between the GO and Entrez Gene ids. Evidence codes currently 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 Entrez Gene id at this time.

Mappings were based on data provided by:

Gene Ontology:http://gopher5/compbio/annotationSourceData/archive.godatabase.org/latest/. Built: 200509

Entrez Gene:http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Fri Sep 30 02:51:32 2005

Package built: Fri Sep 30 02:51:32 2005

### References

http://www.geneontology.org/ and http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

### 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 Entrez Gene id
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
            # Get the Entrez Gene ids for the first two elents of xx
            llids  <- xx[1:2]
            # Get the evidence code llids
            evds <- sapply(llids, names)
        }

[Package GO version 1.10.0 Index]