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[email protected] [email protected] http://www.geneontology.org http://www.ebi.ac.uk The Gene Ontology is a structured controlled vocabulary that can be used to describe gene product attributes in the domains of function, location and process in a species-neutral manner. It is used by an ever-increasing number of biological databases and has become the de facto standard for the annotation of genes and gene products. By providing a standardized biological language, the GO facilitates the capture and dissemination of information across species and database boundaries. The aims of the Gene Ontology project are threefold: - to compile vocabularies to describe components, functions and processes - to produce tools to query and annotate using GO - to associate gene products with GO terms (annotation) SERVING SUGGESTIONS The following tools can be used to enjoy the Gene Ontology at its best: DAG-Edit (top right) - standalone tool for creating, editing, browsing and searching ontologies. INGREDIENTS - includes dictionary, CVS, spellchecker GO employs three ontologies to describe gene product attributes: Cellular component: the location of a gene product within or outside a cell and GO database access plugins - as used in the EBI GO editorial office eg. extracellular, mitochondrion, ribosome, enzyme complex Molecular function: elemental activities described at a molecular level eg. glucose binding, carotenoid isomerase activity, transporter activity Biological process: the ‘bigger picture’; the broader goal or purpose which groups a set of functions eg. signal transduction, behavior, glycolysis, regulation of cell size GO terms are made up of a term name, a unique ID, and (for 90% of terms) a definition. GO terms may also have synonyms, which can be either identical or related concepts; the relationship between the term and synonym is stored in the ontology flat file. Additionally, there may be cross-references to terms in other databases (eg. MetaCyc metabolic pathways, EC enzymes) if the GO term has an exact equivalent in another classification system. GO terms are linked together by two relationships, is-a and part-of. The ontologies are in the form of a directed acyclic graph, where any term may have one or more parents and zero, one, or more children. GO is hierarchical, meaning that child terms are more specific than parent terms. QuickGO (not pictured) - fast web-based GO browser at the EBI AmiGO (right and below) - web based or downloadable versions - accesses the GO database to provide ontology and annotation information - search/browse terms or gene products - pie chart view of annotation distribution - GOst blast server for querying GO DB See the Tools section of the GO website for more on these tools and many others. The term information and position in the process ontology of the GO term GO:0042746. DIET GO GO slims are low calorie versions of GO which contain a set of high level GO terms. You can build your own GO slim for your organism or area of interest or use existing generic or organism-specific GO slims. The map2slim.pl script can be used to map an annotation data set to GO slim terms to see an overview of the distribution of annotations. GO slims also serve as a good introduction to GO by showing the high level concepts without all the detail underneath. NUTRITIONAL COMPOSITION The GO Consortium is the databases that contribute to the development of the Gene Ontology. The current members are as follows: FlyBase Berkeley Drosophila Genome Project Saccharomyces Genome Database Mouse Genome Informatics The Arabidopsis Information Resource WormBase EBI GOA project (UniProt Knowledgebase, InterPro) Rat Genome Database DictyBase GeneDB S. pombe GeneDB for protozoa Genome Knowledgebase TIGR Gramene Compugen The Zebrafish Information Network COMMENTS, QUESTIONS OR SUGGESTIONS? The GO Consortium welcomes feedback from all users on the resources it provides and to this end, there are several channels in place for providing input. SourceForge (http://geneontology.sf.net/) for GO content items, such as new term requests or ontology edits. There are also trackers for annotation questions, and DAG-Edit and AmiGO bug reports and feature requests. GO mailing list (details on the website) for discussions of ontology content or annotation issues. The GO Friends list for is used for general GO announcements. GO meetings (restricted to lucky consortium members) for in depth discussion of sticky points that are not resolved on the mailing list. This does not affect your statutory rights. RELATED PRODUCTS The Gene Ontology is one of a growing set of controlled vocabularies held in Open Biological Ontologies, an umbrella organization for freely available bio-ontologies. For an ontology to be included in OBO, it must adhere to the following criteria: - it must be universally and freely available - must be represented in one or more commonly accepted ontology syntaxes - not overlap conceptually with any existing OBO ontologies - must have unique, stable identifiers for all concepts - concepts must be rigorously defined Visit http://obo.sf.net/ for more on OBO. Comprehensive details on the Gene Ontology can be found on the GO website at http://www.geneontology.org or from [email protected]. - It’s the real thing.