Book Volume 1446 2017
Open Access This content is freely available online to anyone, anywhere at any time.

The Gene Ontology Handbook

Editors:

ISBN: 978-1-4939-3741-7 (Print) 978-1-4939-3743-1 (Online)

Table of contents (21 protocols)

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  1. Front Matter

    Pages i-xii

  2. Fundamentals

    1. Front Matter

      Pages 1-1

    2. Protocol

      Pages 3-13

      Primer on Ontologies

    3. Protocol

      Pages 15-24

      The Gene Ontology and the Meaning of Biological Function

    4. Protocol

      Pages 25-37

      Primer on the Gene Ontology

  3. Making Gene Ontology Annotations

    1. Front Matter

      Pages 39-39

    2. Protocol

      Pages 41-54

      Best Practices in Manual Annotation with the Gene Ontology

    3. Protocol

      Pages 55-67

      Computational Methods for Annotation Transfers from Sequence

    4. Protocol

      Pages 69-84

      Text Mining to Support Gene Ontology Curation and Vice Versa

    5. Protocol

      Pages 85-93

      How Does the Scientific Community Contribute to Gene Ontology?

  4. Evaluating Gene Ontology Annotations

    1. Front Matter

      Pages 95-95

    2. Protocol

      Pages 97-109

      Evaluating Computational Gene Ontology Annotations

    3. Protocol

      Pages 111-132

      Evaluating Functional Annotations of Enzymes Using the Gene Ontology

    4. Protocol

      Pages 133-146

      Community-Wide Evaluation of Computational Function Prediction

  5. Using the Gene Ontology

    1. Front Matter

      Pages 147-147

    2. Protocol

      Pages 149-160

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

    3. Protocol

      Pages 161-173

      Semantic Similarity in the Gene Ontology

    4. Protocol

      Pages 175-188

      Gene-Category Analysis

    5. Protocol

      Pages 189-205

      Gene Ontology: Pitfalls, Biases, and Remedies

    6. Protocol

      Pages 207-220

      Visualizing GO Annotations

    7. Protocol

      Pages 221-229

      A Gene Ontology Tutorial in Python

  6. Advanced Gene Ontology Topics

    1. Front Matter

      Pages 231-231

    2. Protocol

      Pages 233-243

      Annotation Extensions

    3. Protocol

      Pages 245-259

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

  7. Beyond the Gene Ontology

    1. Front Matter

      Pages 261-261

    2. Protocol

      Pages 263-274

      Complementary Sources of Protein Functional Information: The Far Side of GO

    3. Protocol

      Pages 275-287

      Integrating Bio-ontologies and Controlled Clinical Terminologies: From Base Pairs to Bedside Phenotypes

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