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Welcome to the website of the “Gene Ontology Handbook”, a handbook on the fundamentals of Gene Ontology, its use in gene annotation, and its application in bioinformatic analyses.

PART I: Fundamentals
Primer on OntologiesJanna Hastings
The Gene Ontology and the meaning of biological functionPaul Thomas
Primer on the Gene OntologyPascale Gaudet, Nives Skunca, James C Hu and Christophe Dessimoz
PART II: Making GO annotations
Best practices in manual annotation with the Gene OntologySylvain Poux and Pascale Gaudet
Computational methods for annotation transfers from sequenceDomenico Cozzetto and David Jones
Text Mining to Support Gene Ontology Curation and BackPatrick Ruch
How does the scientific community contribute to Gene Ontology?Ruth Lovering
PART III: Evaluating GO annotations
Evaluating computational Gene Ontology annotationsNives Skunca, Richard J. Roberts and Martin Steffen
Evaluating functional annotations of enzymes using the Gene OntologyGemma Holliday, Rebecca Davidson, Eyal Akiva and Patricia Babbitt
Community-Based Evaluation of Computational Function PredictionPredrag Radivojac and Iddo Friedberg
PART IV: Using the GO
Get GO! Retrieving GO data using AmiGO, QuickGO, API, Files, and Tools.Monica C Munoz-Torres and Seth Carbon
Semantic Similarity in the Gene OntologyCatia Pesquita
Gene-Category AnalysisSebastian Bauer
Gene Ontology: Pitfalls, Biases, RemediesPascale Gaudet and Christophe Dessimoz
Visualising GO annotationsFran Supek and Nives Skunca
A Gene Ontology Tutorial in PythonAlex Warwick Vesztrocy and Christophe Dessimoz
PART V: Advanced GO topics
Annotation ExtensionsRachael Huntley and Ruth Lovering
The Evidence Ontology: Supporting Conclusions & Assertions with EvidenceMarcus Chibucos, Jim Hu, Deborah A. Siegele and Michelle Giglio
PART VI: Beyond the GO
Complementary Sources Of Protein Functional Information: The Far Side Of GONicholas Furnham
Integrating bio-ontologies and controlled clinical terminologies: from base pairs to bedside phenotypesSpiros Denaxas
PART VII: Conclusion
The vision and challenges of the Gene OntologySuzanna E. Lewis