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home [2016/07/26 15:59]
Christophe Dessimoz
home [2016/11/05 22:49]
Christophe Dessimoz
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-====== Welcome ====== +{{ :​go_book_cover.jpeg?​direct&​400|}}
 Welcome to the website of the "Gene Ontology Handbook",​ a handbook on the fundamentals of Gene Ontology, its use in gene annotation, and its application in bioinformatic analyses. Welcome to the website of the "Gene Ontology Handbook",​ a handbook on the fundamentals of Gene Ontology, its use in gene annotation, and its application in bioinformatic analyses.
-{{ :​go_book_cover.jpeg?​direct&​400|}} +   * [[Table ​of Contents]] 
- +   ​Download ​the book for free (open access): [[http://​link.springer.com/​content/​pdf/​10.1007%2F978-1-4939-3743-1.pdf|PDF]] [[http://​link.springer.com/​download/​epub/​10.1007/​978-1-4939-3743-1.epub|EPUB]] 
-^  PART I: Fundamentals ​ ^^^ +   ​Download [[http://​link.springer.com/book/10.1007%2F978-1-4939-3743-1|individual chapters]] 
-|1|Primer on Ontologies|Janna Hastings| +   ​Electronic version of the GO python tutorial (Chapter 16)  
-|2|The Gene Ontology and the meaning ​of biological function|Paul Thomas| +     [[http://​nbviewer.jupyter.org/​urls/​dessimozlab.github.io/​go-handbook/​GO%20Tutorial%20in%20Python%20-%20Exercises.ipynbwithout solutions]] 
-|3|Primer on the Gene Ontology|Pascale Gaudet, Nives Skunca, James C Hu and Christophe Dessimoz| +     * [[http://​nbviewer.jupyter.org/​urls/​dessimozlab.github.io/​go-handbook/​GO%20Tutorial%20in%20Python%20-%20Solutions.ipynb|with solutions]] ​ 
-^  ​**PART II: Making GO annotations** ​ ^^^ +   * Buy a hardcopy: 
-|4|Best practices in manual annotation with the Gene Ontology|Sylvain Poux and Pascale Gaudet| +      Amazon [[https://​www.amazon.com/​Ontology-Handbook-Methods-Molecular-Biology/​dp/​1493937413/ ​.com ]] / [[https://​www.amazon.co.uk/​Ontology-Handbook-Methods-Molecular-Biology/​dp/​1493937413/ ​| .co.uk ]] / [[https://​www.amazon.fr/​Ontology-Handbook-Methods-Molecular-Biology/​dp/​1493937413/ ​.fr ]] / [[https://​www.amazon.de/​Ontology-Handbook-Methods-Molecular-Biology/​dp/​1493937413/ ​.de ]] 
-|5|Computational methods ​for annotation transfers from sequence|Domenico Cozzetto and David Jones| +   ​[[http://​www.springer.com/​us/​book/​9781493937417|Book page at the publisher]]
-|6|Text Mining to Support Gene Ontology Curation and Back|Patrick Ruch+
-|7|How does the scientific community contribute to Gene Ontology?​|Ruth Lovering| +
-^  **PART IIIEvaluating GO annotations** ​ ^^^ +
-|8|Evaluating computational Gene Ontology annotations|Nives Skunca, Richard JRoberts and Martin Steffen| +
-|9|Evaluating functional annotations of enzymes using the Gene Ontology|Gemma Holliday, Rebecca Davidson, Eyal Akiva and Patricia Babbitt| +
-|10|Community-Based Evaluation of Computational Function Prediction|Predrag Radivojac and Iddo Friedberg+
-^  ​**PART IV: Using the GO**  ^^^ +
-|11|Get GO! Retrieving GO data using AmiGO, QuickGO, API, Files, and Tools.|Monica C Munoz-Torres and Seth Carbon| +
-|12|Semantic Similarity in the Gene Ontology|Catia Pesquita| +
-|13|Gene-Category Analysis|Sebastian Bauer+
-|14|Gene OntologyPitfalls, Biases, Remedies|Pascale Gaudet and Christophe Dessimoz| +
-|15|Visualising ​GO annotations|Fran Supek and Nives Skunca+
-|16|A Gene Ontology Tutorial in Python|Alex Warwick Vesztrocy and Christophe Dessimoz| +
-^  ​**PART VAdvanced GO topics** ​ ^^^ +
-|17|Annotation Extensions|Rachael Huntley and Ruth Lovering| +
-|18|The Evidence ​Ontology: Supporting Conclusions & Assertions with Evidence|Marcus Chibucos, Jim Hu, Deborah ASiegele and Michelle Giglio| +
-^  **PART VIBeyond the GO**  ^^^ +
-|19|Complementary Sources Of Protein Functional InformationThe Far Side Of GO|Nicholas Furnham| +
-|20|Integrating bio-ontologies and controlled clinical terminologies:​ from base pairs to bedside phenotypes|Spiros Denaxas+
-^  ​**PART VIIConclusion** ​ ^^^ +
-|21|The vision and challenges of the Gene Ontology|Suzanna E. Lewis|+
 +The 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.