Anatomical Ontologies: Linking Names to Places in Biology

Abstract

An ontology captures knowledge of a domain in a structured and well-defined way. Anatomy provides a conceptual framework for the parts and tissues of an organism including structural (parts and sub-parts), functional (system elements), developmental (change of structure during embryogenesis) and derivation. Anatomy is also used to define place or spatial location. This can be in the form of topological relationships, e.g. adjacency or connectedness, or geometric, e.g. distance and direction. Atlases provide a direct or iconic framework to describe the spatial organisation of an organism with no reference to the conceptual anatomical framework. In this chapter we discuss how anatomical and atlas frameworks can be used to provide a rich ontology encompassing both conceptual, topological and geometric spaces. We also introduce the notion of a natural coordinate system both as a robust tool for navigation within an organism (e.g. the mouse embryo) and as a mechanism for cross-atlas interoperability.