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table_of_contents [2016/07/26 16:00] Christophe Dessimoz created |
table_of_contents [2016/11/04 14:10] (current) Christophe Dessimoz |
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| - | Table of Contents | + | ====== Table of Contents ====== |
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| + | 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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