Anatomy Ontologies for Bioinformatics

Bioinformatics as a discipline has come of age. There are now numerous databases and tools that are widely used by researchers in biomedicine. However, successful development of future bioinformatics applications depends on a formalized 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 expertise from computing and biomedical studies. The book covers both theoretical and applied aspects, with an emphasis on newer work relevant to the emerging semantic web. Although written for readers involved in developing the next generation of IT applications in life sciences, biomedicine and health care, this unique book is of interest to anyone who develops and uses anatomy ontologies or is involved in the actual development of relevant semantic web applications.

A timely and first-of-its-kind tightly-edited collection of papers on anatomy ontologies Highlights the challenges that remain today and which will have to be considered when dealing with anatomy-based information on the Semantic Web 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 Includes supplementary material: sn.pub/extras

Klappentext

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.

Inhalt
Existing Anatomy Ontologies for Human, Model Organisms and Plants.- Anatomical Ontologies for Model Organisms: The Fungi and Animals.- Plant Structure Ontology (PSO) A Morphological and Anatomical Ontology of Flowering Plants.- Anatomy for Clinical Terminology.- The Foundational Model of Anatomy Ontology.- Towards a Disease Ontology.- Engineering and Linking of Anatomy Ontologies.- Ontology Alignment and Merging.- COBrA and COBrA-CT: Ontology Engineering Tools.- XSPAN A Cross-Species Anatomy Network.- Searching Biomedical Literature with Anatomy Ontologies.- Anatomy Ontologies and Spatio-Temporal Atlases.- Anatomical Ontologies: Linking Names to Places in Biology.- Time in Anatomy.- The Edinburgh Mouse Atlas.- The Smart Atlas: Spatial and Semantic Strategies for Multiscale Integration of Brain Data.- Anatomy Ontologies Modelling Principles.- Modelling Principles and Methodologies Relations in Anatomical Ontologies.- Modeling Principles and Methodologies - Spatial Representationand Reasoning.- CARO The Common Anatomy Reference Ontology.