Motivation and Organizational Principles for Anatomical Knowledge Representation: The Digital Anatomist Symbolic Knowledge Base

TLDR

The study aims to create a machine‑parseable ontology that represents the macroscopic physical objects and spaces of the human body in a form understandable to both experts and novices. The ontology was built by extending the UMLS Semantic Network, defining classes and subclasses with partitive and spatial attributes, and validated through a thorax instantiation that employed transitive relationships to model its physical organization. The ontology classifies all anatomical entities into three top‑level categories—Anatomical structure, Anatomical spatial entity, and Body substance—while supporting systemic, regional, and diverse naming conventions, and it is extensible to microscopic levels and other body parts, thereby establishing a foundational standard for anatomical concept representation.

Abstract

Objective: Conceptualization of the physical objects and spaces that constitute the human body at the macroscopic level of organization, specified as a machine-parseable ontology that, in its human-readable form, is comprehensible to both expert and novice users of anatomical information. Design: Conceived as an anatomical enhancement of the UMLS Semantic Network and Metathesaurus, the anatomical ontology was formulated by specifying defining attributes and differentia for classes and subclasses of physical anatomical entities based on their partitive and spatial relationships. The validity of the classification was assessed by instantiating the ontology for the thorax. Several transitive relationships were used for symbolically modeling aspects of the physical organization of the thorax. Results: By declaring Organ as the macroscopic organizational unit of the body, and defining the entities that constitute organs and higher level entities constituted by organs, all anatomical entities could be assigned to one of three top level classes (Anatomical structure, Anatomical spatial entity and Body substance). The ontology accommodates both the systemic and regional (topographical) views of anatomy, as well as diverse clinical naming conventions of anatomical entities. Conclusions: The ontology formulated for the thorax is extendible to microscopic and cellular levels, as well as to other body parts, in that its classes subsume essentially all anatomical entities that constitute the body. Explicit definitions of these entities and their relationships provide the first requirement for standards in anatomical concept representation. Conceived from an anatomical viewpoint, the ontology can be generalized and mapped to other biomedical domains and problem solving tasks that require anatomical knowledge.