Annotating with GO: an overview http://www.geneontology.org/ 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: http://www.geneontology.org/#annotations 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: http://www.geneontology.org/doc/GO.xrf_abbs 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).