Anatomy Ontologies for Bioinformatics

1. Front Matter

   Pages I-XVI

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2. Existing Anatomy Ontologies for Human, Model Organisms and Plants

   1. Front Matter

      Pages 1-1

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   2. Anatomical Ontologies for Model Organisms: The Fungi and Animals

      • Jonathan Bard

      Pages 3-25

   3. Plant Structure Ontology (PSO)— A Morphological and Anatomical Ontology of Flowering Plants

      • Katica Ilic, Seung Y. Rhee, Elizabeth A. Kellogg, Peter F. Stevens

      Pages 27-42

   4. Anatomy for Clinical Terminology

      • Alan L Rector

      Pages 43-57

   5. The Foundational Model of Anatomy Ontology

      • Cornelius Rosse, José L. V. Mejino Jr

      Pages 59-117

   6. Towards a Disease Ontology

      • Paul N. Schofield, Björn Rozell, Georgios V. Gkoutos

      Pages 119-130

3. Engineering and Linking of Anatomy Ontologies

   1. Front Matter

      Pages 131-131

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   2. Ontology Alignment and Merging

      • Patrick Lambrix, He Tan

      Pages 133-149

   3. COBrA and COBrA-CT: Ontology Engineering Tools

      • Stuart Aitken, Yin Chen

      Pages 151-162

   4. XSPAN — A Cross-Species Anatomy Network

      • Albert Burger, Jonathan Bard

      Pages 163-175

   5. Searching Biomedical Literature with Anatomy Ontologies

      • 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

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   2. Anatomical Ontologies: Linking Names to Places in Biology

      • Richard A. Baldock, Albert Burger

      Pages 197-211

   3. Time in Anatomy

      • Duncan Davidson

      Pages 213-247

   4. The Edinburgh Mouse Atlas

      • Richard Baldock, Duncan Davidson

      Pages 249-265

   5. The Smart Atlas: Spatial and Semantic Strategies for Multiscale Integration of Brain Data

      • 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

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   2. Modelling Principles and Methodologies – Relations in Anatomical Ontologies

      • Fabian Neuhaus, Barry Smith

      Pages 289-306

   3. Modeling Principles and Methodologies - Spatial Representation and Reasoning

      • Thomas Bittner, Maureen Donnelly, Louis J. Goldberg, Fabian Neuhaus

      Pages 307-326

This book is about the ontology of anatomy. With respect to the individual ?elds of ontology and anatomy, the ontology of anatomy has aspects of both an old and a new topic area. A new aspect for anatomy is that the ontology of anatomy brings medicine together with molecular biology and its related subjects. Similarly, for the ?eld of ontology, biomedical informatics has seen an explosion in the use of onto- gies and ontology-like resources. There has been a particular interest in ontologies for human anatomy and also the anatomy of other types of organism. This explosion has pushed the ?eld of ontology into the limelight, with new practical applications of ontology being developed and new formalisms to accommodate the things that biologists need to say. The ontology of anatomy covers a broad spectrum of life sciences, but why should medics and geneticists, molecular biologists, etc. really be so interested in anatomy? For medics, the reason for this interest is seemingly self evident—medical things happen to bodies and bits of the body. Surgical procedures are carried out on body parts; illnesses and injuries happen to the body and parts of the body. So, if we are to describe medicine, we need to start with anatomy. For molecular biologists, it is often not immediately obvious that biology and medicine join at the level of anatomy, especially in the study of disease processes and the treatment of disease, particularly through drug action.

• 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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