Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences

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Christopher J. O. Baker, Kei-Hoi Cheung
Springer Science & Business Media, Apr 14, 2007 - Science - 446 pages
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The rapid growth of the Web has led to the proliferation of information sources and content accessible via the Internet. While improvements in hardware capabilities continue to help the speed and the flow of information across networked computers, there remains a major problem for the human user to keep up with the rapid expansion of the Web information space. Although there is plenty of room for computers to help humans to discover, navigate, and integrate information in this vast information space, the way the information is currently represented and structured through the Web is not easily readable to computers. To address this issue, the Semantic Web has emerged. It envisions a new information infrastructure that enables computers to better address the information needs of human users. To realize the Semantic Web vision, a number of standard technologies have been developed. These include the Uniform Resource Identifiers (URI) for identifying objects in the Web space as well as Resource Description Framework (RDF) and Web Ontology Language (OWL) for encoding knowledge in the form of standard machine-readable ontologies. The goal is to migrate from the syntactic Web of documents to the semantic Web of ontologies. The leading organization for facilitating, developing, and promoting these Web-based standards is the World Wide Web Consortium (W3C) (http://www. w3. org).
 

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Contents

Dedication
vii
Contributing Authors
xi
Preface
xviii
Acknowledgments
xx
Introduction
1
DATABASE AND LITERATURE INTEGRATION
9
SEMANTIC WEB APPROACH TO DATABASE INTEGRATION IN THE LIFE SCIENCES
10
QUERYING SEMANTIC WEB CONTENTS A CASE STUDY
31
TECHNIQUES FOR ONTOLOGY VISUALIZATION
184
ON VISUALIZATION OF OWL ONTOLOGIES
205
ONTOLOGIES IN ACTION
222
APPLYING OWL REASONING TO GENOMIC DATA
225
CAN SEMANTIC WEB TECHNOLOGIES ENABLE TRANSLATIONAL MEDICINE ?
249
ONTOLOGY DESIGN FOR BIOMEDICAL TEXT MINING
280
USING DISTRIBUTED KNOWLEDGE
314
SEMBOWSER SEMANTIC BIOLOGICAL WEB SERVICES REGISTRY
315

KNOWLEDGE ACQUISITION FROM THE BIOMEDICAL LITERATURE
53
ONTOLOGIES IN THE LIFE SCIENCES
82
BIOLOGICAL ONTOLOGIES
83
CLINICAL ONTOLOGIES FOR DISCOVERY APPLICATIONS
101
ONTOLOGY ENGINEERING FOR BIOLOGICAL APPLICATIONS
120
THE EVALUATION OF ONTOLOGIES
139
OWL FOR THE NOVICE A LOGICAL PERSPECTIVE
159
ONTOLOGY VISUALIZATION
183
AGENT TECHNOLOGIES IN THE LIFE SCIENCES
341
KNOWLEDGE DISCOVERY FOR BIOLOGY WITH TAVERNA
355
ON THE SUCCESS OF THE SEMANTIC WEB IN THE LIFE SCIENCES
396
FACTORS INFLUENCING THE ADOPTION OF THE SEMANTIC WEB IN THE LIFE SCIENCES
397
SEMANTIC WEB STANDARDS LEGAL AND SOCIAL ISSUES AND IMPLICATIONS
413
Index
435
Notes
446
Copyright

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About the author (2007)

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 DecipherITTM 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.

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