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Cover image for Semantic web : revolutionizing knowledge discovery in the life sciences
Title:
Semantic web : revolutionizing knowledge discovery in the life sciences
Publication Information:
New York, NY : Springer, 2007
Physical Description:
xx, 445 p. : ill., digital ; 25 cm.
ISBN:
9780387484365

9780387484389
General Note:
Also available online version
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30000010139650 TK5105.88815 S45 2007 Open Access Book Book
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Summary

Summary

This book introduces advanced semantic web technologies, illustrating their utility and highlighting their implementation in biological, medical, and clinical scenarios. It covers topics ranging from database, ontology, and visualization to semantic web services and workflows. The volume also details the factors impacting on the establishment of the semantic web in life science and the legal challenges that will impact on its proliferation.


Author Notes

Christopher Baker is a Principle Investigator at the Knowledge Discovery Department of the Institute for Infocomm Research (I2R), a member of the Agency for Science, Technology and Research (A*STAR) in Singapore. Dr Baker was formerly Bioinformatics Project Manager of the Génome Québec funded project, 'Ontologies, the semantic web and intelligent systems for genomics' where he coordinated the application of knowledge management technologies to fungal genomic data sets. Prior to this he was Group Leader In-silico Discovery at Ecopia BioSciences Inc. where he masterminded key portions of the DecipherIT(tm) bioinformatics software suite and managed the genomic annotation team. Dr Baker received post doctoral training at Iogen Corporation and the University of Toronto after completing his Ph. D. studies in Environmental Microbiology and Enzymology at the University of Wales, Cardiff, UK.

Dr. Cheung is currently an Associate Professor at the Center for Medical Informatics, Yale University School of Medicine. Dr. Cheung is a bioinformatician with a Ph.D. in Computer Science. He has established a broad base of collaboration with life scientists, computational biologists, and computer scientists. Dr. Cheung has published extensively in the field of bioinformatics. He is one of the core faculty members in the Yale Ph.D. Program in Computational Biology and Bioinformatics. In addition, he is a Principal Investigator of two research grants (one was awarded by the National Institutes of Health and the other was awarded by the National Science Foundation). Dr. Cheung's research interests include biological database and tool integration. Recently, Dr. Cheung has embarked on the research and development of Semantic Web in the bioscience domain.


Table of Contents

Kei-Hoi Cheung and Andrew K. Smith and Kevin Y. L. Yip and Christopher J. O. Baker and Mark B. GersteinLoic Royer and Benedikt Linse and Thomas Wachter and Tim Furch and Francois Bry and Michael SchroederLynette Hirschman and William Hayes and Alfonso ValenciaPatrick Lambrix and He Tan and Vaida Jakoniene and Lena StrombackYves Lussier and Olivier BodenreiderLarisa N. Soldatova and Ross D. KingLeo Obrst and Werner Ceusters and Inderjeet Mani and Steve Ray and Barry SmithJeff PanXiaoshu Wang and Jonas AlmeidaSerguei Krivov and Ferdinando Villa and Richard Williams and Xindong WuKaty Wolstencroft and Robert Stevens and Volker HaarslevVipul Kashyap and Tonya HongsermeierRene Witte and Thomas Kappler and Christopher J. O. BakerSatya S. Sahoo and Amit P. Sheth and Blake Hunter and William S. YorkAlbert BurgerCarole Goble and Katy Wolstencroft and Antoon Goderis and Duncan Hull and Jun Zhao and Pinar Alper and Phillip Lord and Chris Wroe and Khalid Belhajjame and Daniele Turi and Robert Stevens and Tom Oinn and David De RoureToni KazicDov Greenbaum and Mark B Gerstein
Dedicationp. v
Contributing Authorsp. xi
Prefacep. xix
Acknowledgmentsp. xxi
Introductionp. 1
Part I Database and Literature Integrationp. 9
Chapter 1 Semantic Web Approach to Database Integration in the Life Sciencesp. 11
Chapter 2 Querying Semantic Web Contents: A Case Studyp. 31
Chapter 3 Knowledge Acquisition from the Biomedical Literaturep. 53
Part II Ontologies in the Life Sciencesp. 83
Chapter 4 Biological Ontologiesp. 85
Chapter 5 Clinical Ontologies for Discovery Applicationsp. 101
Chapter 6 Ontology Engineering for Biological Applicationsp. 121
Chapter 7 The Evaluation of Ontologies: Toward Improved Semantic Interoperabilityp. 139
Chapter 8 OWL for the Novice: A Logical Perspectivep. 159
Part III Ontology Visualizationp. 183
Chapter 9 Techniques for Ontology Visualizationp. 185
Chapter 10 On Visualization of OWL Ontologiesp. 205
Part IV Ontologies in Actionp. 223
Chapter 11 Applying OWL Reasoning to Genomic Datap. 225
Chapter 12 Can Semantic Web Technologies Enable Translational Medicine?p. 249
Chapter 13 Ontology Design for Biomedical Text Miningp. 281
Part V Using Distributed Knowledgep. 315
Chapter 14 SemBOWSER - Semantic Biological Web Services Registryp. 317
Chapter 15 Agent Technologies in the Life Sciencesp. 341
Chapter 16 Knowledge Discovery for Biology with Taverna: Producing and Consuming Semantics in the Web of Sciencep. 355
Part VI On the Success of Semantic Web in the Life Sciencesp. 397
Chapter 17 Factors Influencing the Adoption of the Semantic Webin theLife Sciencesp. 399
Chapter 18 Semantic Web Standards: Legal and Social Issues and Implicationsp. 413
Indexp. 435
Notesp. 446
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