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This book provides a practical and§self-contained overview of the Gene Ontology (GO), the leading project to§organize biological knowledge on genes and their products across genomic§resources. Written for biologists and bioinformaticians, it covers the§state-of-the-art of how GO annotations are made, how they are evaluated, and§what sort of analyses can and cannot be done with the GO. In the spirit of the Methods§in Molecular Biology book series, there is an emphasis throughout the§chapters on providing practical guidance and troubleshooting advice. Authoritative§and accessible, The Gene Ontology§Handbook serves non-experts as well as seasoned GO users as a thorough§guide to this powerful knowledge system.