1. Annotating with GO: an overview
What is a Gene Ontology (GO) annotation?
Databases external to GO make cross-links between GO terms and objects in their databases (typically, gene products, or their surrogates, genes), and then provide tables of these links to GO. The GO itself contains no information about genes or gene products. The GO annotation (‘gene association’) files are all publicly available:
A gene product is annotated to one or
more terms in each of the three
ontologies; biological process, cellular
component and molecular function.
Database name abbreviation
Gene products are annotated to the most specific GO term possible for the information available.
Abbreviations used by GO are described here:
Example annotation:
A gene product is annotated
with terms reflecting only its normal
activities, locations and processes.
Database Object identifier. A Database Object is usually a gene product, but can also be a gene or a transcript.
When there is no information regarding one or more aspects of a gene product, the gene product is annotated to the GO term ‘unknown’.
Fields highlighted in grey are mandatory
Used when it is specified in the source that that a gene product is NOT associated with a particular gene product e.g. “we have found that protein Z is not involved in the X cascade”.
Annotation of a gene product to one ontology is independent of its annotation to the other two ontologies.
Gene Ontology term identifier
Object type: gene, transcript or protein
The
annotation of
gene products to GO
terms is performed according to
two main principles: the recording of the
source of the annotation and the type
of evidence on which
the annotation was
based.
P = biological process, F = molecular function and C = cellular component.
Taxonomic identifier for gene product
The evidence describes how the annotation was created, and provides a way of measuring its strength or reliability. GO has developed a set of standard evidence codes which form a loose hierarchy, with ‘inferred by electronic annotation’ (IEA) being the least reliable type of evidence, followed by ‘inferred by sequence similarity’ (ISS).
The source of an annotation may be a literature reference, a database record or the type of computational anaylsis. Literature references are entered as an accession number, either from the database in question and/or from PubMed. Annotations based on computational analysis include a reference to the method of analysis.
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
Evidence codes
IC inferred by curator
IMP inferred from mutant phenotype
IGI inferred from genetic interaction
IPI inferred from physical interaction
ISS inferred from sequence similarity
Collaborating databases
Many important databases produce GO annotations and contribute to the development of the GO. These include:
FlyBase (database for the fruitfly Drosophila melanogaster), Berkeley Drosophila Genome Project (Drosophila informatics; GO database & software), Saccharomyces Genome Database (SGD) (database for the budding yeast Saccharomyces cerevisiae), Mouse Genome Database (MGD) & Gene Expression Database (GXD) (databases for the mouse Mus musculus), The Arabidopsis Information Resource (TAIR) (database for the brassica family plant Arabidopsis thaliana), WormBase (database for the nematode Caenorhabditis elegans), PomBase (database for the fission yeast Schizosaccharomyces pombe), Rat Genome Database (RGD) (database for the rat Rattus norvegicus), DictyBase (informatics resource for the slime mold Dictyostelium discoideum), The Pathogen Sequencing Unit (The Wellcome Trust Sanger Institute), Genome Knowledge Base (GKB) (Cold Spring Harbor Laboratory), EBI : InterPro - SWISS-PROT - TrEMBL groups, The Institute for Genomic Research (TIGR), Gramene (A Comparative Mapping Resource for Monocots), Compugen (with its Internet Research Engine).