zebrafishGO {zebrafish}R Documentation

Mappings between probe identifiers and Gene Ontology information


The Gene Ontology Consortium maintains a controlled vocabulary of defined terms to describe gene products. zebrafishGO 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: September 16, 2004

Gene Ontology:http://www.godatabase.org/dev/database/archive/2004-07-01/go_200407-termdb.xml.gz. Built: 2004-07-01

Package built Fri Sep 17 09:37:03 2004


    # Convert to a list
    xx <- as.list(zebrafishGO)
    # Remove all the NAs
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
            # Try the firest one
            got <- xx[[1]]           


[Package zebrafish version 1.6.5 Index]