The Gene Ontology Handbook by Christophe Dessimoz
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The Gene Ontology Handbook

The Gene Ontology Handbook


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About the Book

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 Skunca, 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 Skunca, 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. Babbitt

10. 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 Skunca

16. A Gene Ontology Tutorial in Python

Alex Warwick Vesztrocy and Christophe Dessimoz

Part V: Advanced Gene Ontology Topics 17. Annotation Extensions

Rachael P. Huntley and Ruth C. Lovering

18. The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations

Marcus C. Chibucos, Deborah A. Siegele, James C. Hu, and Michelle Giglio

Part VI: Beyond the Gene Ontology

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 C. Denaxas

Part VII: Conclusion

21. The Vision and Challenges of the Gene Ontology

Suzanna E. Lewis

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Product Details
  • ISBN-13: 9781493981267
  • Publisher: Humana Press
  • Publisher Imprint: Humana Press
  • Height: 254 mm
  • No of Pages: 305
  • Series Title: Methods in Molecular Biology
  • Weight: 607 gr
  • ISBN-10: 1493981269
  • Publisher Date: 23 Jun 2018
  • Binding: Paperback
  • Language: English
  • Returnable: N
  • Spine Width: 17 mm
  • Width: 178 mm

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