Keywords:
Bioinformatics.
;
Ontologies (Information retrieval).
;
Electronic books.
Description / Table of Contents:
Introduction to Bio-Ontologies explores the computational background of ontologies. Emphasizing computational and algorithmic issues surrounding bio-ontologies, this self-contained text helps readers understand ontological algorithms and their applications. The first part of the book defines ontology and bio-ontologies. It also explains the importance of mathematical logic for understanding concepts of inference in bio-ontologies, discusses the probability and statistics topics necessary for understanding ontology algorithms, and describes ontology languages, including OBO (the preeminent language for bio-ontologies), RDF, RDFS, and OWL. The second part covers significant bio-ontologies and their applications. The book presents the Gene Ontology; upper-level ontologies, such as the Basic Formal Ontology and the Relation Ontology; and current bio-ontologies, including several anatomy ontologies, Chemical Entities of Biological Interest, Sequence Ontology, Mammalian Phenotype Ontology, and Human Phenotype Ontology. The third part of the text introduces the major graph-based algorithms for bio-ontologies. The authors discuss how these algorithms are used in overrepresentation analysis, model-based procedures, semantic similarity analysis, and Bayesian networks for molecular biology and biomedical applications. With a focus on computational reasoning topics, the final part describes the ontology languages of the Semantic Web and their applications for inference. It covers the formal semantics of RDF and RDFS, OWL inference rules, a key inference algorithm, the SPARQL query language, and the state of the art for querying OWL ontologies. Web Resource Software and data designed to complement material in the text are available on the book's website: http://bio-ontologies-book.org The site provides the R Robo package developed for the book, along with a
Type of Medium:
Online Resource
Pages:
1 online resource (514 pages)
Edition:
1st ed.
ISBN:
9781439836668
Series Statement:
Chapman and Hall/CRC Mathematical and Computational Biology Series
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=1633237
DDC:
610.285
Language:
English
Note:
Front Cover -- Dedication -- Preface -- Contents -- List of Figures -- List of Tables -- Symbol Description -- I. Basic Concepts -- 1. Ontologies and Applications of Ontologies in Biomedicine -- 2. Mathematical Logic and Inference -- 3. Probability Theory and Statistics for Bio-Ontologies -- 4. Ontology Languages -- II. Bio-Ontologies -- 5. The Gene Ontology -- 6. Upper-Level Ontologies -- 7. A Selective Survey of Bio-Ontologies -- III. Graph Algorithms for Bio-Ontologies -- 8. Overrepresentation Analysis -- 9. Model-Based Approaches to GO Analysis -- 10. Semantic Similarity -- 11. Frequency-Aware Bayesian Network Searches in Attribute Ontologies -- IV. Inference in Ontologies -- 12. Inference in the Gene Ontology -- 13. RDFS Semantics and Inference -- 14. Inference in OWL Ontologies -- 15. Algorithmic Foundations of Computational Inference -- 16. SPARQL -- Appendices -- A. An Overview of R -- B. Information Content and Entropy -- C. W3C Standards: XML, URIs, and RDF -- D. W3C Standards: OWL -- Glossary -- C -- D -- F -- H -- J -- M -- N -- O -- P -- Q -- R -- T -- W -- Bibliography.
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