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  • Book
  • Open Access
  • © 2017

The Gene Ontology Handbook

  • 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 of the book series: Methods in Molecular Biology (MIMB, volume 1446)

Buying options

Softcover Book USD 59.99
Price excludes VAT (USA)
Hardcover Book USD 59.99
Price excludes VAT (USA)

Table of contents (21 protocols)

  1. Front Matter

    Pages i-xii
  2. Fundamentals

    1. Front Matter

      Pages 1-1
    2. Primer on Ontologies

      • Janna Hastings
      Pages 3-13Open Access
    3. The Gene Ontology and the Meaning of Biological Function

      • Paul D. Thomas
      Pages 15-24Open Access
    4. Primer on the Gene Ontology

      • Pascale Gaudet, Nives Škunca, James C. Hu, Christophe Dessimoz
      Pages 25-37Open Access
  3. Making Gene Ontology Annotations

    1. Front Matter

      Pages 39-39
    2. Best Practices in Manual Annotation with the Gene Ontology

      • Sylvain Poux, Pascale Gaudet
      Pages 41-54Open Access
    3. Computational Methods for Annotation Transfers from Sequence

      • Domenico Cozzetto, David T. Jones
      Pages 55-67Open Access
    4. How Does the Scientific Community Contribute to Gene Ontology?

      • Ruth C. Lovering
      Pages 85-93Open Access
  4. Evaluating Gene Ontology Annotations

    1. Front Matter

      Pages 95-95
    2. Evaluating Computational Gene Ontology Annotations

      • Nives Škunca, Richard J. Roberts, Martin Steffen
      Pages 97-109Open Access
    3. Evaluating Functional Annotations of Enzymes Using the Gene Ontology

      • Gemma L. Holliday, Rebecca Davidson, Eyal Akiva, Patricia C. Babbitt
      Pages 111-132Open Access
    4. Community-Wide Evaluation of Computational Function Prediction

      • Iddo Friedberg, Predrag Radivojac
      Pages 133-146Open Access
  5. Using the Gene Ontology

    1. Front Matter

      Pages 147-147
    2. Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools

      • Monica Munoz-Torres, Seth Carbon
      Pages 149-160Open Access
    3. Semantic Similarity in the Gene Ontology

      • Catia Pesquita
      Pages 161-173Open Access
    4. Gene-Category Analysis

      • Sebastian Bauer
      Pages 175-188Open Access
    5. Gene Ontology: Pitfalls, Biases, and Remedies

      • Pascale Gaudet, Christophe Dessimoz
      Pages 189-205Open Access
    6. Visualizing GO Annotations

      • Fran Supek, Nives Škunca
      Pages 207-220Open Access

About this book

This book is open access under a CC BY 4.0 license.

This book provides a practical and self-contained overview of the Gene Ontology (GO), the leading project to organize biological knowledge on genes and their products across genomic resources. Written for biologists and bioinformaticians, it covers the state-of-the-art of how GO annotations are made, how they are evaluated, and what sort of analyses can and cannot be done with the GO. In the spirit of the Methods in Molecular Biology book series, there is an emphasis throughout the chapters on providing practical guidance and troubleshooting advice. 
Authoritative and accessible, The Gene Ontology Handbook serves non-experts as well as seasoned GO users as a thorough guide to this powerful knowledge system.


  • Bioinformatics
  • GO annotations
  • Enrichment analysis
  • Computational predictions
  • Gene function

Editors and Affiliations

  • Department of Genetics Evolution and Environment, University College of London, London, United Kingdom

    Christophe Dessimoz

  • Department of Computer Science, ETH Zurich, Zurich, Switzerland

    Nives Škunca

Bibliographic Information

  • Book Title: The Gene Ontology Handbook

  • Editors: Christophe Dessimoz, Nives Škunca

  • Series Title: Methods in Molecular Biology

  • DOI:

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s) 2017

  • License: CC BY

  • Hardcover ISBN: 978-1-4939-3741-7Published: 22 November 2016

  • Softcover ISBN: 978-1-4939-8126-7Published: 23 June 2018

  • eBook ISBN: 978-1-4939-3743-1Published: 01 November 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 305

  • Number of Illustrations: 6 b/w illustrations, 50 illustrations in colour

  • Topics: Bioinformatics

Buying options

Softcover Book USD 59.99
Price excludes VAT (USA)
Hardcover Book USD 59.99
Price excludes VAT (USA)