The Gene Ontology Handbook

Primer on Ontologies.- The Gene Ontology and the Meaning of Biological Function.- Primer on the Gene Ontology.- Best Practices in Manual Annotation with the Gene Ontology.- Computational Methods for Annotation Transfers from Sequence.- Text Mining to Support Gene Ontology Curation and Vice Versa.- How Does the Scientific Community Contribute to Gene Ontology?.- Evaluating Computational Gene Ontology Annotations.- Evaluating Functional Annotations of Enzymes Using the Gene Ontology.- Community-Based Evaluation of Computational Function Prediction.- Get GO!: Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools.- Semantic Similarity in the Gene Ontology.- Gene-Category Analysis.- Gene Ontology: Pitfalls, Biases, and Remedies.- Visualizing GO Annotations.- A Gene Ontology Tutorial in Python.- Annotation Extensions.- The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.- Complementary Sources of Protein Functional Information: The Far Side of GO.- Integrating Bio-Ontologies and Controlled Clinical Terminologies: From Base Pairs to Bedside Phenotypes.- The Vision and Challenges of the Gene Ontology.