Table of Contents

The chapters are all available for individual download from the official Springerlink page:

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