Motivation and organizational principles for anatomical knowledge representation: the digital anatomist symbolic knowledge base

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.

Figure 1

The classification of physical anatomical entities based on the -is a- relationship. The first-generation offspring of Anatomical structure and Organ part are also shown.

Figure 2

The subclasses of Organ and its subclasses, displayed in a screen capture from the hierarchy editor of Knowledge Base Manager, the authoring program for the symbolic knowledge base. The symbol >> indicates that the node in the hierarchy (formed in this instance by the -is a- relationship) has at least one generation of children that is not shown. Double clicking on a term displays its immediate offspring by one tab indentation. Some of the terms denoting organ subclasses are extended by the qualifier “(organ)” because these terms are also used to designate members of other subclasses of Anatomical structure, such as Bone (tissue), Muscle (tissue). The tree is opened up for Viscus, the first Organ subclass, in which examples of canonical instances are displayed to illustrate the classification.

Figure 3

Semantic network constructed with -is a- (solid lines) and -part of- (interrupted lines) relationships to model aspects of knowledge pertaining to the right atrium. Terms denoting parts of the heart are shown in the plane of the shaded quadrangle; the subclasses to which these entities are assigned are displayed above this plane.

Figure 5

Screen capture from the authoring program KB Manager, showing a segment of the -part of- hierarchy for the heart to illustrate concept granularity, term assignments and cross references with other vocabularies. The symbol >> indicates that the node in the hierarchy has at least one generation of children that is not shown. Immediate offspring of a node are shown by one tab indentation. All components of the Conducting system of the heart could, for instance, be displayed by double clicking on the term and the successive generations of its children. Note that those components of the conducting system that are associated with the right atrium are displayed as parts of the Myocardium of right atrium, providing a symbolic representation of useful spatial information. The preferred name of a concept is highlighted in the Hierarchy Editor panel and also appears in the top bar of the Concept Inspector panel. Of the five synonyms associated with the concept, one is highlighted and appears in the Term Inspector panel, which provides information about the term: its role (synonym), concept identifier (UWDA ID) and its SNOMED identifier. Selecting Nodus sinuatrialis among the synonyms would identify the authority for the terms as Nomina Anatomica.

Figure 4

Members of the class Anatomical spatial entity, displayed by KB Manager. The first generation subclasses of Anatomical spatial entity are comprehensive; trees are partially opened up for Body space and Anatomical junction to show their subclasses and some canonical instances of Body space.

Figure 6

Screen capture from the web atlas of Thoracic Viscera, illustrating the association of a term (retrieved from the Symbolic Knowledge Base by the Symbolic Knowledge Server), on the fly, with a structure present in a 3-D reconstruction (retrieved from the Spatial Database by the Web Server and CGI Programs9,43). The term posterior left ventricular branch of left coronary artery was selected in the -branch of- hierarchy of the Symbolic Knowledge Base, accessed by the Web client; clicking on the term provides a list of images in which the concept is present. A lateral view of the heart, reconstructed by Skandha program from 1-mm cryosections of a cadaver,, was chosen; a leader associates the selected term (shown above the image) with the corresponding anatomical structure in the 3-D reconstruction.