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table_of_contents [2016/07/26 14:01] – Christophe Dessimoztable_of_contents [2016/11/04 13:10] (current) – Christophe Dessimoz
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 ====== Table of Contents ====== ====== Table of Contents ======
  
 +The chapters are all available for individual download from the official [[http://link.springer.com/book/10.1007/978-1-4939-3743-1|Springerlink page]]:
  
 ^  PART I: Fundamentals  ^^^ ^  PART I: Fundamentals  ^^^
 |1|Primer on Ontologies|Janna Hastings| |1|Primer on Ontologies|Janna Hastings|
 |2|The Gene Ontology and the meaning of biological function|Paul Thomas| |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|+|3|Primer on the Gene Ontology ([[http://arxiv.org/abs/1602.01876|preprint]])|Pascale Gaudet, Nives Skunca, James C Hu and Christophe Dessimoz|
 ^  **PART II: Making GO annotations**  ^^^ ^  **PART II: Making GO annotations**  ^^^
 |4|Best practices in manual annotation with the Gene Ontology|Sylvain Poux and Pascale Gaudet| |4|Best practices in manual annotation with the Gene Ontology|Sylvain Poux and Pascale Gaudet|
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 |8|Evaluating computational Gene Ontology annotations|Nives Skunca, Richard J. Roberts and Martin Steffen| |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| |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|+|10|Community-Based Evaluation of Computational Function Prediction ([[http://arxiv.org/abs/1601.01048|preprint]])|Predrag Radivojac and Iddo Friedberg|
 ^  **PART IV: Using the GO**  ^^^ ^  **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| |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| |12|Semantic Similarity in the Gene Ontology|Catia Pesquita|
 |13|Gene-Category Analysis|Sebastian Bauer| |13|Gene-Category Analysis|Sebastian Bauer|
-|14|Gene Ontology: Pitfalls, Biases, Remedies|Pascale Gaudet and Christophe Dessimoz| +|14|Gene Ontology: Pitfalls, Biases, Remedies ([[https://arxiv.org/abs/1602.01875|preprint]])|Pascale Gaudet and Christophe Dessimoz| 
-|15|Visualising GO annotations|Fran Supek and Nives Skunca| +|15|Visualising GO annotations ([[http://arxiv.org/abs/1602.07103|preprint]])|Fran Supek and Nives Skunca| 
-|16|A Gene Ontology Tutorial in Python|Alex Warwick Vesztrocy and Christophe Dessimoz|+|16|A Gene Ontology Tutorial in Python ([[http://nbviewer.jupyter.org/urls/dessimozlab.github.io/go-handbook/GO%20Tutorial%20in%20Python%20-%20Exercises.ipynb|exercises]] and [[http://nbviewer.jupyter.org/urls/dessimozlab.github.io/go-handbook/GO%20Tutorial%20in%20Python%20-%20Solutions.ipynb|solutions]]) |Alex Warwick Vesztrocy and Christophe Dessimoz|
 ^  **PART V: Advanced GO topics**  ^^^ ^  **PART V: Advanced GO topics**  ^^^
 |17|Annotation Extensions|Rachael Huntley and Ruth Lovering| |17|Annotation Extensions|Rachael Huntley and Ruth Lovering|
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 ^  **PART VII: Conclusion**  ^^^ ^  **PART VII: Conclusion**  ^^^
 |21|The vision and challenges of the Gene Ontology|Suzanna E. Lewis| |21|The vision and challenges of the Gene Ontology|Suzanna E. Lewis|
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