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.
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
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.
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 Representation and Reasoning.- CARO – The Common Anatomy Reference Ontology.