Semantic Web Revolutionizing Knowledge Discovery in the Life Sciences

About this book

The Semantic Web provides a common framework that allows data to be shared and reused across application, enterprise, and community boundaries. Advanced Semantic Web technologies are now enabling a wide range of tasks of central importance to the management of life science information. This book introduces these technologies to life science and bioinformatics professionals, illustrating their utility and highlighting their implementation in biological, medical and clinical scenarios. In six parts the book covers the topics of database and literature integration, knowledge representation, knowledge visualization, the utilization of formal knowledge representations, and access to distributed knowledge. The factors impacting on the establishment of the semantic web in life science and the legal challenges that will impact on its proliferation are addressed in the concluding part.

Contents

- Introduction: The Semantic Web concept and its benefits in life sciences
- Identifying the toolkit of the Semantic Web
- Assembling semantic webs
- How and when to use the semantic web
- Applications of the semantic web
- Establishing the semantic web: Knowledge Representation Formalisms
- Knowledge Acquisition
- Database Federation
- Distributed Data Access
- Semantic Querying and Reasoning
- Computational Challenges
- Homo sapiens and Semantics
- Current practice of the semantic web in Life Sciences (Examples): A KnowledgeBase Project for Alzheimer Disease Research
- Semantic Web Technology in Support of Bioinformatics for Glycan Expression
- Semantic Web Technologies for Analysis of Transcriptome
- Ontology-driven similarity approaches to supporting gene functional assessment
- The Ontology of the Gene Ontology
- Integrating Ontologies with Three-Dimensional Models of Anatomy
- YeastHub
- Using Ontologies to provide semantic richness in biological image databases
- BioDash
- BioPAX

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Biography

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 Genome Quebec 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.