© 2008

Anatomy Ontologies for Bioinformatics

Principles and Practice

  • Editors
  • Albert Burger
  • Duncan Davidson
  • Richard Baldock

Part of the Computational Biology book series (COBO, volume 6)

Table of contents

  1. Front Matter
    Pages I-XVI
  2. Existing Anatomy Ontologies for Human, Model Organisms and Plants

    1. Front Matter
      Pages 1-1
    2. Katica Ilic, Seung Y. Rhee, Elizabeth A. Kellogg, Peter F. Stevens
      Pages 27-42
    3. Alan L Rector
      Pages 43-57
    4. Cornelius Rosse, José L. V. Mejino Jr
      Pages 59-117
    5. Paul N. Schofield, Björn Rozell, Georgios V. Gkoutos
      Pages 119-130
  3. Engineering and Linking of Anatomy Ontologies

    1. Front Matter
      Pages 131-131
    2. Patrick Lambrix, He Tan
      Pages 133-149
    3. Stuart Aitken, Yin Chen
      Pages 151-162
    4. Albert Burger, Jonathan Bard
      Pages 163-175
    5. Thomas Wächter, Dimitra Alexopoulou, Heiko Dietze, Jörg Hakenberg, Michael Schroeder
      Pages 177-194
  4. Anatomy Ontologies and Spatio-Temporal Atlases

    1. Front Matter
      Pages 195-195
    2. Richard A. Baldock, Albert Burger
      Pages 197-211
    3. Duncan Davidson
      Pages 213-247
    4. Richard Baldock, Duncan Davidson
      Pages 249-265
    5. Maryann E. Martone, Ilya Zaslavsky, Amarnath Gupta, Asif Memon, Joshua Tran, Willy Wong et al.
      Pages 267-286
  5. Anatomy Ontologies – Modelling Principles

    1. Front Matter
      Pages 287-287
    2. Thomas Bittner, Maureen Donnelly, Louis J. Goldberg, Fabian Neuhaus
      Pages 307-326

About this book


Bioinformatics as a discipline has come of age, and there are now numerous databases and tools that are widely used by researchers in the biomedical field. However, successful development of future bioinformatics applications will depend on an appropriately formalised representation of domain knowledge.

This book provides a timely and first-of-its-kind collection of contributed chapters on anatomy ontologies. It is interdisciplinary in its approach, bringing together relevant expertise from computing and biomedical studies, and covering both theoretical and applied aspects, with an emphasis on newer work relevant to the emerging Semantic Web.

Topics and Features:

• Provides a comprehensive discussion of the foundations of anatomical ontologies and the state of the art in existing computational tools and applications

• Considers a number of fundamental modelling principles

• Includes chapters about research on algorithms to systematically align anatomy ontologies and to mine data in the literature, using anatomy terms

• Explains recent efforts to develop a common anatomy reference ontology

• Discusses anatomy in the context of spatio-temporal biomedical atlases

• Describes systems and tools for linking anatomy ontologies with each other and with other on-line resources, such as the biomedical literature

• Highlights the challenges of dealing with anatomy-based information on the Semantic Web

Although primarily written for readers who will be involved in developing the next generation of IT applications in the areas of life sciences, biomedical sciences and health care, this unique volume will be of interest to anyone who will further develop anatomy ontologies, who will use them, and who will be involved in the actual development of relevant (semantic) web applications.


Alignment Biomedical Atlases Biomedical Databases DOM Semantic Web Software Tools and Applications Systems Biology Temporal and Spatial Data Translational Science algorithm algorithms anatomy bioinformatics databases modeling

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