Semantic Web

Revolutionizing Knowledge Discovery in the Life Sciences

  • Christopher J. O. Baker
  • Kei-Hoi Cheung

Table of contents

  1. Front Matter
    Pages i-xxi
  2. Introduction

    1. Pages 1-8
  3. Database and Literature Integration

    1. Front Matter
      Pages 9-9
    2. Kei-Hoi Cheung, Andrew K. Smith, Kevin Y. L. Yip, Christopher J. O. Baker, Mark B. Gerstein
      Pages 11-30
    3. Loïc Royer, Benedikt Linse, Thomas Wächter, Tim Furch, François Bry, Michael Schroeder
      Pages 31-52
    4. Lynette Hirschman, William S. Hayes, Alfonso Valencia
      Pages 53-81
  4. Ontologies in the Life Sciences

    1. Front Matter
      Pages 83-83
    2. Patrick Lambrix, He Tan, Vaida Jakoniene, Lena Strömbäck
      Pages 85-99
    3. Yves A. Lussier, Olivier Bodenreider
      Pages 101-119
    4. Larisa N. Soldatova, Ross D. King
      Pages 121-137
    5. Leo Obrst, Werner Ceusters, Inderjeet Mani, Steve Ray, Barry Smith
      Pages 139-158
    6. Jeff Z. Pan
      Pages 159-182
  5. Ontology Visualization

    1. Front Matter
      Pages 183-183
    2. Xiaoshu Wang, Jonas S. Almeida
      Pages 185-203
    3. Serguei Krivov, Ferdinando Villa, Richard Williams, Xindong Wu
      Pages 205-221
  6. Ontologies in Action

    1. Front Matter
      Pages 223-223
    2. Katy Wolstencroft, Robert Stevens, Volker Haarslev
      Pages 225-248
    3. Vipul Kashyap, Tonya Hongsermeier
      Pages 249-279
    4. René Witte, Thomas Kappler, Christopher J. O. Baker
      Pages 281-313
  7. Using Distributed Knowledge

    1. Front Matter
      Pages 315-315
    2. Satya S. Sahoo, Amit Sheth, Blake Hunter, William S. York
      Pages 317-340
    3. Albert Burger
      Pages 341-354
    4. Carole Goble, Katy Wolstencroft, Antoon Goderis, Duncan Hull, Jun Zhao, Pinar Alper et al.
      Pages 355-395
  8. On the Success of the Semantic Web in the Life Sciences

    1. Front Matter
      Pages 397-397
    2. Dov Greenbaum, Mark Gerstein
      Pages 413-433
  9. Back Matter
    Pages 435-446

About this book


The Semantic Web is now a research discipline in its own right and commercial interest in applications of Semantic Web technologies is strong. The advantages of the Semantic Web lie in its ability to present and provide access to complex knowledge in a standardized form making interoperability between distributed databases and middleware achievable.

Life Scientists have much to gain from the emergence of the Semantic Web since their work is strongly knowledge-based. Unambiguous, semantically-rich, structured declarations of information have long been a fundamental cornerstone of scientific discourse. To have such information available in machine-readable form makes a whole new generation of scientific software possible. The value that the Semantic Web offers to the Life Sciences is currently under appreciated. A pedagogical oasis is required for interested scientists and bioinformatics professionals, where they can learn about and draw inspiration from the Semantic Web and its component technologies. In this context this book seeks to offer students, researchers, and professionals a glimpse of the technology, its capabilities and the reach of its current implementation in the Life Sciences. This collection of representative topics, written by leading experts, documents important and encouraging first steps showing the utility of the Semantic Web to Life Science research.

Semantic Web: Revolutionizing Knowledge Discovery in Life Sciences is divided into six parts that cover the topics of: knowledge integration, knowledge representation, knowledge visualization, utilization of formal knowledge representations, and access to distributed knowledge. The final part considers the viability of the semantic web in life science and the legal challenges that will impact on its establishment.

This book may be approached from technical, scientific or application specific perspectives. Component technologies of the Semantic Web (including RDF databases, ontologies, ontological languages, agent systems and web services) are described throughout the book. They are the basic building blocks for creating the Semantic Web infrastructure. Other technologies, such as natural language processing and text mining, which are becoming increasingly important to the Semantic Web, are also discussed. Scientists reading the book will see that the complex needs of biology and medicine are being addressed. Moreover, pioneering Life Scientists have joined forces with Semantic Web developers to build valuable semantic resources for the scientific community. Different areas of computer science (e.g., artificial intelligence, database integration, and visualization) are also being recruited to advance this vision. The ongoing synergy between the Life Sciences and Computer Science is poised to deliver revolutionary discovery tools and new capabilities.

As well as providing the background material and critical evaluation criteria for the design and use of meaningful Semantic Web implementations a multitude of examples are provided. These illustrate the diversity of life science tasks that are benefiting from the use of Semantic Web infrastructure and serve to demonstrate the great potential of the Semantic Web in the Life Sciences.


Evolution Radiologieinformationssystem bioinformatics biology computer science genome knowledge knowledge discovery knowledge representation life sciences ontology science semantic web

Editors and affiliations

  • Christopher J. O. Baker
    • 1
  • Kei-Hoi Cheung
    • 2
  1. 1.Knowledge Discovery DepartmentInstitute for Infocomm ResearchSingapore
  2. 2.Center for Medical InformaticsYale University School of MedicineNew HavenUSA

Bibliographic information