Foundational Model of Anatomy (FMA)
RDFBones uses the Foundational Model of Anatomy (FMA) to model skeletal anatomy and to provide options for analysis in wider anatomical contexts. The FMA is a purpose-built ontology for use in other ontologies that require a well-structured model of anatomical concepts. Though vast and in-depth simultaneously, it is also intended to be generalisable and able to be filtered to suit a specific need [Rosse2003].
The FMA only refers to canonical anatomical concepts and does not by itself harbour instantiated anatomy. This means that pathologies and malformations, just as any specific instance of an anatomical part of an actual human individual, are not included in the ontology’s entities. The FMA is in fact only intended to be a foundation (hence the name) for the representation of instantiated anatomy.
The ontogenesis of the human body is a central point of orientation when it comes to organising the FMA: the most basic category, which contains all individual material anatomical structures, ‘Anatomical Structure’, is based on the concept of a physical entity which has an inherent three-dimensional shape, which itself is “generated by a coordinated expression of the organism’s own structural genes”. This ontogenetics-based system is the first principle upon which the representation in the FMA is built upon. The second principle is the organisation into units. “Units” here refers to a structural element of the whole, such as the classes ‘Organ’ or ‘Cell’, with the entity representing the ‘whole’ being the class ‘Body’. This concept expands to aggregates of these units, such as the classes ‘Organ system’ and ‘Anatomical cluster’, or to parts of units, such as the classes ‘Body part’ and ‘Organ part’. The FMA also accommodates descriptors of physical entities, like cavities and surfaces of organs, and more abstract concepts such as terms, coordinates, and relationships between entities. As relationships are a basic and important aspect of anatomical representation, the FMA is intended to be more specific in describing relationships than most structured vocabularies, which it does through a diverse set of logical rules and inheritance patterns.
Generally, the most reasonable way to represent the body, human or otherwise, is in part-whole relationships. These relationships however differ quite often in their organisation between disciplines and applications such that they end up conflicting each other; there are many ways to define e.g. the concept of ‘upper arm’ - is the head of the femur part of the arm, or part of the shoulder joint? Taking every possible definition into consideration may reduce an anatomical ontology to a sort of dictionary void of any relational information. The FMA keeps the logical approach of part-whole relationships while attempting to “accommodate various views and conventions while remaining consistent and logical” [MejinoJr2003].
A set of rules defines how part-whole relationships are applied in the FMA. The rule of ‘Dimensionality Consistency’ calls for distinction between boundary and partonomy relationships. Part-whole axioms can only be applied for entities that share the same dimensionality:
The statement {‘Right ventricle’ -has part- ‘Wall of right ventricle’} is valid, as both subject and object are 3D.
The statement {‘Right ventricle’ -has part- ‘Surface of right ventricle’} is not, as the subject is 3D and the object is 2D. This relationship would instead have to be presented with the axiom:
{‘Right ventricle’ -bounded by- ‘Surface of right ventricle’}. The predicate ‘bounded by’ allows for a difference of one dimension.
The rule of ‘Containment/Part Distinction’ likewise delimits ‘contains’ and ‘contained-in’ relationships. These two rules suffice within classes such as ‘Conceptual anatomical entity’ and ‘Body substance’, but in the class ‘Anatomical structure’ more specifications are needed. These specifications are set by the class itself so that they may be inherited by the according subclasses [MejinoJr2003].
Further important attributes for partonomy are the attributes ‘constitutional part’ and ‘regional part’. ‘Constitutional part’ pertains to what is best described as larger, yet simpler-than-the-whole structural compounds of an organ/anatomical structure. Partitions are based on composition, not spatial factors. ‘Regional part’ pertains to spatial subdivisions. These subdivisions partition constitutional parts which are in shared locations into sets. Subdivision of the body into functional systems is a common method in anatomy and clinical medicine. However, the FMA defines the class ‘Organ system’ in a structural context and constrains the parts of such a system to organs and their primary regional parts. ‘Systemic part’ relations are used as a secondary partition which can be displayed transitively in a partonomy hierarchy, as can constitutional and regional parts.
RDFBones uses classes from the FMA to represent skeletal elements featured in osteological investigations. Studies involving osteological research data can make recourse to the rich semantic information of the FMA in order to analyse skeletal elements within their anatomical context.
Mejino Jr, José LV, Agoncillo, Augusto V, Rickard, Kurt L, and Rosse, Cornelius, “Representing complexity in part-whole relationships within the foundational model of anatomy”, in AMIA Annual Symposium Proceedings vol. 2003, (2003), pp. 450.
Rosse, Cornelius and Mejino, José L.V., “A reference ontology for biomedical informatics: the Foundational Model of Anatomy”, Journal of Biomedical Informatics 36, 6 (2003), pp. 478–500.