Anatomy Ontologies for Bioinformatics (eBook)

Principles and Practice

Albert Burger, Duncan Davidson, Richard Baldock (Herausgeber)

eBook Download: PDF

2007 | 2008
XVI, 354 Seiten
Springer London (Verlag)
978-1-84628-885-2 (ISBN)

Infos

This book provides a timely and first-of-its-kind collection of papers on anatomy ontologies. It is interdisciplinary in its approach, bringing together the relevant expertise from computing and biomedical studies. The book aims to provide readers with a comprehensive understanding of the foundations of anatomical ontologies and the-state-of-the-art in terms of existing tools and applications. It also highlights challenges that remain today.

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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.

Inhalt

Foreword 6
Preface 9
Contents 11
List of Contributors 13
Part I Existing Anatomy Ontologies for Human, Model Organisms and Plants 17
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
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
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
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

Produkt-Details

• Erscheint lt. Verlag: 20.12.2007
• Reihe/Serie: Computational Biology
• Reihe/Serie: Computational Biology
• Zusatzinfo: XVI, 354 p.
• Verlagsort: London
• Sprache: englisch
• Themenwelt: Mathematik / Informatik ► Informatik ► Datenbanken
• Themenwelt: Mathematik / Informatik ► Informatik ► Theorie / Studium
• Themenwelt: Mathematik / Informatik ► Informatik ► Web / Internet
• Themenwelt: Informatik ► Weitere Themen ► Bioinformatik
• Themenwelt: Medizin / Pharmazie ► Physiotherapie / Ergotherapie ► Orthopädie
• Themenwelt: Studium ► 1. Studienabschnitt (Vorklinik) ► Anatomie / Neuroanatomie
• Themenwelt: Naturwissenschaften ► Biologie
• Themenwelt: Technik ► Medizintechnik
• Schlagworte: algorithm • algorithms • Alignment • anatomy • Bioinformatics • Biomedical Atlases • Biomedical Databases • Databases • Dom • Knowledge Representation • Modeling • Ontologies • semantic web • Software Tools and Applications • systems biology • Temporal and Spatial Data • Translational Science
• ISBN-10: 1-84628-885-1 / 1846288851
• ISBN-13: 978-1-84628-885-2 / 9781846288852