Table of Contents
The chapters are all available for individual download from the official Springerlink page:
| PART I: Fundamentals | ||
|---|---|---|
| 1 | Primer on Ontologies | Janna Hastings |
| 2 | The Gene Ontology and the meaning of biological function | Paul Thomas |
| 3 | Primer on the Gene Ontology (preprint) | Pascale Gaudet, Nives Skunca, James C Hu and Christophe Dessimoz |
| PART II: Making GO annotations | ||
| 4 | Best practices in manual annotation with the Gene Ontology | Sylvain Poux and Pascale Gaudet |
| 5 | Computational methods for annotation transfers from sequence | Domenico Cozzetto and David Jones |
| 6 | Text Mining to Support Gene Ontology Curation and Back | Patrick Ruch |
| 7 | How does the scientific community contribute to Gene Ontology? | Ruth Lovering |
| PART III: Evaluating GO annotations | ||
| 8 | Evaluating computational Gene Ontology annotations | Nives Skunca, Richard J. Roberts and Martin Steffen |
| 9 | Evaluating functional annotations of enzymes using the Gene Ontology | Gemma Holliday, Rebecca Davidson, Eyal Akiva and Patricia Babbitt |
| 10 | Community-Based Evaluation of Computational Function Prediction (preprint) | Predrag Radivojac and Iddo Friedberg |
| PART IV: Using the GO | ||
| 11 | Get GO! Retrieving GO data using AmiGO, QuickGO, API, Files, and Tools. | Monica C Munoz-Torres and Seth Carbon |
| 12 | Semantic Similarity in the Gene Ontology | Catia Pesquita |
| 13 | Gene-Category Analysis | Sebastian Bauer |
| 14 | Gene Ontology: Pitfalls, Biases, Remedies (preprint) | Pascale Gaudet and Christophe Dessimoz |
| 15 | Visualising GO annotations (preprint) | Fran Supek and Nives Skunca |
| 16 | A Gene Ontology Tutorial in Python (exercises and solutions) | Alex Warwick Vesztrocy and Christophe Dessimoz |
| PART V: Advanced GO topics | ||
| 17 | Annotation Extensions | Rachael Huntley and Ruth Lovering |
| 18 | The Evidence Ontology: Supporting Conclusions & Assertions with Evidence | Marcus Chibucos, Jim Hu, Deborah A. Siegele and Michelle Giglio |
| PART VI: Beyond the GO | ||
| 19 | Complementary Sources Of Protein Functional Information: The Far Side Of GO | Nicholas Furnham |
| 20 | Integrating bio-ontologies and controlled clinical terminologies: from base pairs to bedside phenotypes | Spiros Denaxas |
| PART VII: Conclusion | ||
| 21 | The vision and challenges of the Gene Ontology | Suzanna E. Lewis |