GOGO2LL {GO} | R Documentation |
This is an R environment (hash table) mapping GO ids to the LocusLink ids corresponding to the GO id.
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 Consortium built: 2004-02-01.http://www.godatabase.org/dev/database/archive/2004-02-01/go_200402-termdb.xml.gz
LocusLink built: March 3, 2004. ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.ga
Package built: Wed Mar 3 16:27:29 2004
http://www.geneontology.org/ and http://www.ncbi.nlm.nih.gov/LocusLink
require("GO") || stop("GO unavailable") # Convert the environment object to a list xx <- as.list(GOGO2LL) # 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) }