hgu2beta7GO {hgu2beta7} | R Documentation |
The Gene Ontology Consortium maintains a controlled vocabulary of defined terms to describe gene products. hgu2beta7GO maps probe identifiers to Gene Ontology information including the ids, evidence codes, and ontology categories of the terms for the genes represented by the probe ids.
Each probe id is mapped to a list containing one (mapped to none or one set of GO information) or more (mapped to more than one sets of GO information) elements. When a probe id is mapped to at lest one set of GO information, each element of the list contains a sub list of three elements named "GOID", "Ontology", and "Evidence". The value for element "GOID" gives the Gene Ontology identifier the key probe 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 ontology category the GO id belongs to. The value for element "Evidence" contains an evidence code indicating what kind of evidence is found to support the association of the GO id to the gene represented by the key probe 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
Mappings between probe ids and GO information were obtained through their mappings to LocusLink ids. NAs are assigned to probe identifiers that can not be mapped to any Gene Ontology information. Mappings between Gene Ontology ids an Gene Ontology terms and other information are available in a separate data package named GO.
Mappings were based on data provided by:
LocusLink:ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz. Built: February 16, 2005
Gene Ontology:http://www.godatabase.org/dev/database/archive/daily/go_daily-termdb.rdf-xml.gz. Built: http://www.godatabase.org/dev/database/archive/daily/go_daily-termdb.rdf-xml.gz
Package built Wed Feb 16 23:32:20 2005
# Convert to a list xx <- as.list(hgu2beta7GO) # Remove all the NAs xx <- xx[!is.na(xx)] if(length(xx) > 0){ # Try the firest one got <- xx[[1]] got[[1]][["GOID"]] got[[1]][["Ontology"]] got[[1]][["Evidence"]] }