| Foreword | 6 |
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| Preface | 9 |
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| Contents | 11 |
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| List of Contributors | 13 |
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| Part I Existing Anatomy Ontologies for Human, Model Organisms and Plants | 17 |
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| 1 Anatomical Ontologies for Model Organisms: The Fungi and Animals | 18 |
| 2 Plant Structure Ontology (PSO) A Morphological and Anatomical Ontology of Flowering Plants | 41 |
| 3 Anatomy for Clinical Terminology | 57 |
| 4 The Foundational Model of Anatomy Ontology | 72 |
| 5 Towards a Disease Ontology | 131 |
| Part II Engineering and Linking of Anatomy Ontologies | 143 |
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| 6 Ontology Alignment and Merging | 144 |
| 7 COBrA and COBrA-CT: Ontology Engineering Tools | 161 |
| 8 XSPAN A Cross-Species Anatomy Network | 173 |
| 9 Searching Biomedical Literature with Anatomy Ontologies | 186 |
| Part III Anatomy Ontologies and Spatio-Temporal Atlases | 204 |
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| 10 Anatomical Ontologies: Linking Names to Places in Biology | 205 |
| 11 Time in Anatomy | 220 |
| 12 The Edinburgh Mouse Atlas | 255 |
| 13 The Smart Atlas: Spatial and Semantic Strategies for Multiscale Integration of Brain Data | 272 |
| Part IV Anatomy Ontologies Modelling Principles | 292 |
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| 14 Modelling Principles and Methodologies Relations in Anatomical Ontologies | 293 |
| 15 Modeling Principles and Methodologies - Spatial Representation and Reasoning | 310 |
| 16 CARO The Common Anatomy Reference Ontology | 330 |
| Index | 353 |