Features chapters on the fundamentals of Gene Ontology, its use in gene annotation, and its application in bioinformatic analyses

Emphasizes providing practical guidance and troubleshooting advice

Assumes no prior knowledge yet serves as an informative and useful text for experts as well

Includes supplementary material: [...]

Part I: Fundamentals

1. Primer on Ontologies

Janna Hastings

2. The Gene Ontology and the Meaning of Biological Function

Paul D. Thomas

3. Primer on the Gene Ontology

Pascale Gaudet, Nives Škunca, James C. Hu, and Christophe Dessimoz

Part II: Making Gene Ontology 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 T. Jones

6. Text Mining to Support Gene Ontology Curation and Vice Versa

Patrick Ruch

7. How Does the Scientific Community Contribute to Gene Ontology?

Ruth C. Lovering

Part III: Evaluating Gene Ontology Annotations

8. Evaluating Computational Gene Ontology Annotations

Nives Škunca, Richard J. Roberts, and Martin Steffen

9. Evaluating Functional Annotations of Enzymes Using the Gene Ontology

Gemma L. Holliday, Rebecca Davidson, Eyal Akiva, and Patricia C. Babbitt10. Community-Based Evaluation of Computational Function Prediction

Iddo Friedberg and Predrag Radivojac

Part IV: Using the Gene Ontology

11. Get GO!: Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools

Monica 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, and Remedies

Pascale Gaudet and Christophe Dessimoz

15. Visualizing GO Annotations

Fran Supek and Nives Škunca

16. A Gene Ontology Tutorial in Python

Alex Warwick Vesztrocy and Christophe Dessimoz

Part V: Advanced Gene Ontology Topics