Ebook: Anatomy Ontologies for Bioinformatics: Principles and Practice

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.

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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.

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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.

Content:
Front Matter....Pages I-XVI
Front Matter....Pages 1-1
Anatomical Ontologies for Model Organisms: The Fungi and Animals....Pages 3-25
Plant Structure Ontology (PSO)— A Morphological and Anatomical Ontology of Flowering Plants....Pages 27-42
Anatomy for Clinical Terminology....Pages 43-57
The Foundational Model of Anatomy Ontology....Pages 59-117
Towards a Disease Ontology....Pages 119-130
Front Matter....Pages 131-131
Ontology Alignment and Merging....Pages 133-149
COBrA and COBrA-CT: Ontology Engineering Tools....Pages 151-162
XSPAN — A Cross-Species Anatomy Network....Pages 163-175
Searching Biomedical Literature with Anatomy Ontologies....Pages 177-194
Front Matter....Pages 195-195
Anatomical Ontologies: Linking Names to Places in Biology....Pages 197-211
Time in Anatomy....Pages 213-247
The Edinburgh Mouse Atlas....Pages 249-265
The Smart Atlas: Spatial and Semantic Strategies for Multiscale Integration of Brain Data....Pages 267-286
Front Matter....Pages 287-287
Modelling Principles and Methodologies – Relations in Anatomical Ontologies....Pages 289-306
Modeling Principles and Methodologies - Spatial Representation and Reasoning....Pages 307-326
CARO – The Common Anatomy Reference Ontology....Pages 327-349
Back Matter....Pages 351-354

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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.

Content:
Front Matter....Pages I-XVI
Front Matter....Pages 1-1
Anatomical Ontologies for Model Organisms: The Fungi and Animals....Pages 3-25
Plant Structure Ontology (PSO)— A Morphological and Anatomical Ontology of Flowering Plants....Pages 27-42
Anatomy for Clinical Terminology....Pages 43-57
The Foundational Model of Anatomy Ontology....Pages 59-117
Towards a Disease Ontology....Pages 119-130
Front Matter....Pages 131-131
Ontology Alignment and Merging....Pages 133-149
COBrA and COBrA-CT: Ontology Engineering Tools....Pages 151-162
XSPAN — A Cross-Species Anatomy Network....Pages 163-175
Searching Biomedical Literature with Anatomy Ontologies....Pages 177-194
Front Matter....Pages 195-195
Anatomical Ontologies: Linking Names to Places in Biology....Pages 197-211
Time in Anatomy....Pages 213-247
The Edinburgh Mouse Atlas....Pages 249-265
The Smart Atlas: Spatial and Semantic Strategies for Multiscale Integration of Brain Data....Pages 267-286
Front Matter....Pages 287-287
Modelling Principles and Methodologies – Relations in Anatomical Ontologies....Pages 289-306
Modeling Principles and Methodologies - Spatial Representation and Reasoning....Pages 307-326
CARO – The Common Anatomy Reference Ontology....Pages 327-349
Back Matter....Pages 351-354
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