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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]] | ||
| + | * Download [[http://link.springer.com/book/10.1007%2F978-1-4939-3743-1|individual chapters]] | ||
| + | * Electronic version of the GO python tutorial (Chapter 16) | ||
| + | * [[http://nbviewer.jupyter.org/urls/dessimozlab.github.io/go-handbook/GO%20Tutorial%20in%20Python%20-%20Exercises.ipynb| without solutions]] | ||
| + | * [[http://nbviewer.jupyter.org/urls/dessimozlab.github.io/go-handbook/GO%20Tutorial%20in%20Python%20-%20Solutions.ipynb|with solutions]] | ||
| + | * Buy a hardcopy: | ||
| + | * [[http://www.springer.com/us/book/9781493937417|Springer Shop]] (if you have co-authored a chapter in this or any other Springer book, you are entitled to a [[http://www.springer.com/gp/help/discounts-for-authors/510|40% author discount]]) | ||
| + | * 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 ]] | ||
| - | ^ PART I: Fundamentals ^^^ | ||
| - | |1|Primer on Ontologies|Janna Hastings| | ||
| - | |2|The Gene Ontology and the meaning of biological function|Paul Thomas| | ||
| - | |3|Primer on the Gene Ontology|Pascale Gaudet, Nives Skunca, James C Hu and Christophe Dessimoz| | ||
| - | ^ **PART II: Making GO 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 Jones| | ||
| - | |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 III: Evaluating GO 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 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 Ontology: Pitfalls, 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 V: Advanced GO topics** ^^^ | ||
| - | |17|Annotation Extensions|Rachael Huntley and Ruth Lovering| | ||
| - | |18|The Evidence Ontology: Supporting Conclusions & Assertions with Evidence|Marcus Chibucos, Jim Hu, Deborah A. Siegele and Michelle Giglio| | ||
| - | ^ **PART VI: Beyond the GO** ^^^ | ||
| - | |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 Denaxas| | ||
| - | ^ **PART VII: Conclusion** ^^^ | ||
| - | |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. | ||