GOENTREZID {GO} | R Documentation |
This data set gives mappings between GO identifiers and Entrez Gene identifiers as reported by NCBI. The format is an R environment mapping GO identifiers to a vector of Entrez Gene identifiers that are associated with it. In addition to the Entrez Gene identifier. the evidence code (the reason for the association) is also given.
Each GO identifier is mapped to a named vector of Entrez Gene identifiers. The name associated with each Entrez Gene identifier corresponds to the evidence code for that GO identifier. The evidence code indicates what kind of evidence supports the association between the GO and Entrez Gene identifiers. 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 identifiers that can not be mapped to any Entrez Gene identifier at this time.
Mappings were based on data provided by:
Gene Ontology:http://gopher5/compbio/annotationSourceData/archive.godatabase.org/latest/. Built: 08-Aug-2006
Entrez Gene:http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Tue Sep 5 18:42:30 2006
Package built: Tue Sep 5 18:42:30 2006
http://www.geneontology.org/ and http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
require("GO") || stop("GO unavailable") # Convert the environment object to a list xx <- as.list(GOENTREZID) # Remove GO identifiers that are not mapped to any Entrez Gene id xx <- xx[!is.na(xx)] if(length(xx) > 0){ # Get the Entrez Gene identifiers for the first two elents of xx llids <- xx[1:2] # Get the evidence code llids evds <- sapply(llids, names) }