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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: Database name abbreviation A gene product is annotated to one or more terms in each of the three ontologies; biological process, cellular component and molecular function. http://www.geneontology.org/#annotations Abbreviations used by GO are described here: http://www.geneontology.org/doc/GO.xrf_abbs Gene products are annotated to the most specific GO term possible for the information available. Example annotation: A gene product is annotated Database Object identifier. A Database Object is usually a gene product, but can also be a gene or a transcript. 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”. DB DB_Object_ID DB_Object_ Symbol SGD S0000296 PHO3 SGD S0000296 PHO3 [NOT] GO:0015888 Κ Κ Κ Κ DB:Reference (|DB:Reference) go_id GO:0003993 SGD:8789|PMID:267 6709 SGD:8789|PMID:267 6709 Evidence With IMP IMP Aspect DB_Object_Name (|Name) P ΚΚ Κ Κ F Κ Κ Κ Κ DB_Object_Synonym (|Synonym) DB_Object_ Type Taxo n (|taxon) Date YBR092C gene taxon:4932 20001122 YBR092C gene taxon:4932 20001122 Fields highlighted in grey are mandatory Gene Ontology term identifier with terms reflecting only its normal activities, locations and processes. When there is no information regarding one or more aspects of a gene product, the gene product is annotated to the GO term ‘unknown’. Object type: gene, transcript or protein Annotation of a gene product to one ontology is independent of its annotation to the other two ontologies. The annotation of P = biological process, F = Taxonomic identifier for gene molecular function and C = cellular gene products to GO product component. 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. The source of an annotation may be a literature reference, a The evidence describes how the annotation was created, and database record or the type of computational anaylsis. Literature provides a way of measuring its strength or reliability. GO has references are entered as an accession number, either from the developed a set of standard evidence codes which form a loose database in question and/or from PubMed. Annotations based on hierarchy, with ‘inferred by electronic annotation’ (IEA) being the computational analysis include a reference to the method of least reliable type of evidence, followed by ‘inferred by sequence analysis. similarity’ (ISS). Evidence codes IDA inferred from direct assay IC IEP inferred from expression pattern IMP inferred from mutant phenotype IEA inferred from electronic annotation IGI inferred from genetic interaction TAS traceable author statement IPI inferred from physical interaction NAS non-traceable author statement ISS inferred from sequence similarity ND inferred by curator no biological data available 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).