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Welcome
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 Ontologies | Janna Hastings |
| The Gene Ontology and the meaning of biological function | Paul Thomas |
| Primer on the Gene Ontology | Pascale Gaudet, Nives Skunca, James C Hu and Christophe Dessimoz |
| PART II: Making GO annotations | |
| Best practices in manual annotation with the Gene Ontology | Sylvain Poux and Pascale Gaudet |
| Computational methods for annotation transfers from sequence | Domenico Cozzetto and David Jones |
| Text Mining to Support Gene Ontology Curation and Back | Patrick Ruch |
| How does the scientific community contribute to Gene Ontology? | Ruth Lovering |
| PART III: Evaluating GO annotations | |
| Evaluating computational Gene Ontology annotations | Nives Skunca, Richard J. Roberts and Martin Steffen |
| Evaluating functional annotations of enzymes using the Gene Ontology | Gemma Holliday, Rebecca Davidson, Eyal Akiva and Patricia Babbitt |
| Community-Based Evaluation of Computational Function Prediction | Predrag 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 Ontology | Catia Pesquita |
| Gene-Category Analysis | Sebastian Bauer |
| Gene Ontology: Pitfalls, Biases, Remedies | Pascale Gaudet and Christophe Dessimoz |
| Visualising GO annotations | Fran Supek and Nives Skunca |
| A Gene Ontology Tutorial in Python | Alex Warwick Vesztrocy and Christophe Dessimoz |
| PART V: Advanced GO topics | |
| Annotation Extensions | Rachael Huntley and Ruth Lovering |
| The Evidence Ontology: Supporting Conclusions & Assertions with Evidence | Marcus Chibucos, Jim Hu, Deborah A. Siegele and Michelle Giglio |
| PART VI: Beyond the GO | |
| Complementary Sources Of Protein Functional Information: The Far Side Of GO | Nicholas Furnham |
| Integrating bio-ontologies and controlled clinical terminologies: from base pairs to bedside phenotypes | Spiros Denaxas |
| PART VII: Conclusion | |
| The vision and challenges of the Gene Ontology | Suzanna E. Lewis |