GOLOCUSID2GO {GO} | R Documentation

## Entrez Gene to Gene Ontology (GO) mapping

### Description

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

### Details

Each Entrez Gene id is mapped to a list of lists. The names on the outer list are GO ids. Each inner list consists of three named elements: GOID, Ontology, and Evidence.

The GOID element matches the GO id named in the outer list and is included for convenience when processing the data using `lapply`.

The Ontology element indicates which of the three Gene Ontology categories this identifier belongs to. The categories are biological process (BP), cellular component (CC), and molecular function (MF).

The Evidence element contains a code indicating what kind of evidence supports the association of the GO id to the Entrez Gene 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

Entrez Gene ids for which no GO associations exist are left out of the environment.

Mappings were based on data provided by:

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.ncbi.nih.gov/entrez/query.fcgi?db=gene

### Examples

    library("GO")
    ## Select an Entrez Gene id
    egId <- "10043"
    egIdGoData <- GOLOCUSID2GO[[egId]]

    ## Display GO ids associated with the Entrez Gene id
    sapply(egIdGoData, function(x) x$GOID)

    ## The ontology categories of the GO ids
    sapply(egIdGoData, function(x) x$Ontology)

    ## The evidence codes for the GO ids
    sapply(egIdGoData, function(x) x$Evidence)

[Package GO version 1.10.0 Index]