Albert Burger & Duncan Davidson 
Anatomy Ontologies for Bioinformatics [PDF ebook] 
Principles and Practice

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.

Mục lục

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.- COBr A and COBr A-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.