Anatomical Information Science

The Foundational Model of Anatomy (FMA) is a map of the human body. Like maps of other sorts – including the map-like representations we find in familiar anatomical atlases – it is a representation of a certain portion of spatial reality as it exists at a certain (idealized) instant of time. But unlike other maps, the FMA comes in the form of a sophisticated ontology of its objectdomain, comprising some 1.5 million statements of anatomical relations among some 70,000 anatomical kinds. It is further distinguished from other maps in that it represents not some specific portion of spatial reality (say: Leeds in 1996), but rather the generalized or idealized spatial reality associated with a generalized or idealized human being at some generalized or idealized instant of time. It will be our concern in what follows to outline the approach to ontology that is represented by the FMA and to argue that it can serve as the basis for a new type of anatomical information science. We also draw some implications for our understanding of spatial reasoning and spatial ontologies in general. 1 The Foundational Model of Anatomy The Foundational Model of Anatomy (FMA) is a computer-based representation of the entities and relations which together form the phenotypic structure of the human organism [1,2]. It provides a qualitative spatial reference system for the human body that is designed to be understandable to human beings and also to be navigable by computers. It is intended as a general-purpose resource, which can be used by any biomedical application that requires anatomical information, from radiology (in supporting automatic image analysis) to pharmacokinetics (in representing the pathways of drugs as they are absorbed by, distributed through, metabolized in and excreted from the body). The FMA began its life as a classification of anatomical entities called the University of Washington Digital Anatomist Vocabulary. In recent years it has grown from a list of terms linked by is_a and part_of relations to a sophisticated spatialstructural ontology of the human organism at all biologically salient levels of granularity, comprehending some 1.5 million statements of ontological relations among some 70,000 anatomical universals. The acronym ‘FMA’ is currently used in the biomedical informatics community both for this ontology and also for its representation in computerized form within the Protégé 2000 frame-based ontology editing environment [2,3]. We shall argue in what follows that the FMA provides a starting-point for a new type of anatomical information science, representing a new application domain with potentially valuable implications also for other branches of Spatial Information Theory. 2 Types of Relations The FMA relates exclusively to continuant entities (i.e. to entities, such as molecules, cells, lungs, which endure through time while undergoing changes of various sorts) [4]. The Structural Informatics Group at the University of Washington, which developed and maintains the FMA, has itself initiated work on two complementary ventures, called PRO and PathRO – for ‘Physiology’ and ‘Pathology Reference Ontology’, respectively [5] – which deal with those occurrent processes in which the anatomical entities at different levels of granularity participate. Here, however, we shall concern ourselves exclusively with continuant entities, which exist at the level of particulars or tokens (having determinate spatial locations at each specific point in time) as instantiations of certain corresponding universals or types (kinds, classes). We can distinguish a number of distinct types of relations between continuant universals which are employed in the construction of an ontology like the FMA [3,6]: 1) is_a relations, linking one universal to another (more general) universal in a subsumption hierarchy; examples: liver is_a organ, lacrimal lake is_a anatomical cavity 2) static physical relations between continuant universals; examples: lobe of liver part_of liver, nuclear membrane adjacent_to cytoplasm 3) relations between universals instantiated at different stages in the development of an organism; examples: zygote derives_ from ovum, adult transformation_of child. Cross-cutting all of these are distinctions between: a) instance-level relations (such as the parthood relation between your left thumb and your left hand), which obtain between instances of anatomical universals within the canonical organization of the human body; b) relations involving also non-canonical anatomical instances including instances of pathological anatomical universals such as wounded knee or amputation stump; c) relations involving entities (implants, food, etc.) imported into the human body; d) relations involving entities (biopsied samples, excreta, etc.) exported from the human body. The FMA itself focuses on relations of types 1) and 2) under heading a). In what follows we expand our scope to include also relations of other types, drawing on recent work, summarized in [7, 8], involving not only the FMA’s developers but also representatives of other influential research groups in biomedical ontology.