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The "Bio-Ontology" The Bio-Ontology § Answer to the problem of inconsistencies in the annotations § Controlled vocabulary § Hierarchical classification between the terms of the controlled vocabulary The Gene Ontology § molecular function ontology § process ontology § cellular component ontology http://www.geneontology.org/ Source: Jacques v an Helden Gene Ontology: processes Gene Ontology: molecular functions Gene Ontology: cellular compartments Current status of Gene Ontology § § Term definitions § Biological process terms ................... § Molecular function terms ................... § Cellular component terms ................ § Obsolete terms ................................ 23928 9467 3050 1692 Comprehensive functional annotation for 12 "key" genomes Excludes annotations from UniProt, which represent 261 annotated proteomes. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across s pecies. PLoS Comput. Biol. 5: e1000431, 2009. § Annotated gene products § Total ................................................... > 20 000 000 (*) § § Automatically Filtered (taxon-specific, non-redundant........... c.a. 600 000 Manually curated ................................................................... c.a. 100 000 (**) Statistics from 19/9/2012 - taken on 10/2/2013 (*) Mostly imported from UniProt (**) To Check Adapted from Jacques v an Helden Gene Ontology: example Example: MSN2 in S. cerevisiae Query Search GO term or gene/protein. Here we search for the transcription factor MSN2 of yeast. http://www.geneontology.org/ Gene Ontology: example Example: MSN2 in S. cerevisiae You obtain general informations (gene name, synonymous, brief description), as well as the nucleic and proteic sequences. By clicking on "term associations", you get the list of GO terms corresponding to your gene (see next page). Gene Ontology: example Example: MSN2 in S. cerevisiae cellular component molecular function biological process Gene Ontology: example Example: "Osmotic stress" Query Search GO term or gene/protein. Here we search for the GO term "osmotic stress" http://www.geneontology.org/ Gene Ontology: example Example: "Osmotic stress" We get the classification of "osmotic stress" in the GO hierarchy. We can also get the list of genes associated to "osmotic stress". NB: the results can be filtered. For example, it is possible to retrieve only genes from S. cerevisiae.