Your browser version is outdated. We recommend that you update your browser to the latest version.


The first aspect of ontology that I like to get straight is the difference between realist and other ontologies. Realist ontologies data from Aristotle. The guiding principle is that entities in the ontology must accurately reflect real world entities. Each entity is from one of three possible types. L1 entities are first order (real) entities. L2 entities are representations (imaginary) entities. L3 entities are written representations of L2 entities. In your hierarchy of entities you must maintain these distinctions. An L2 entity, for example a physicians diagnosis for a given patient, cannot be the parent of an L1 entity, for example a patient's symptom.

I think this distinction between entity types is fundamental to any possible knowledge representation. It is so fundamental that we do not notice we are doing it. When we name an object we do not think of that name as an abstract entity. We in some way re-experience the object itself. Making this connection underlies our ability to communicate.

Photo credit: credit:

In this way, we do not get confused about whether the diagnosis creates the symptoms. Studies find that 3 year old children know that physical objects can be seen and touched, but mental objects cannot (Carrick & Quas, 2006). The higher a child's verbal intelligence the better they make the fantasy-reality distinction.

Unfortunately, maintaining level of reality is not the only requirement. Each hierarchical relationship must be rigorously investigated based on the definitions of the entities involved. If disease is defined as resulting from a pathophysiologic process then a disorder with unknown pathophysiology should not be a disease. Similarly, a diagnosis of exclusion, in which the main point is that the patient's symptomology does not conform to known pathophysiology, cannot itself be a diagnosis.

Carrick, N., & Quas, J. A. (2006). Effects of discrete emotions on young children's ability to discern fantasy and reality. Developmental Psychology, 42(6), 1278–1288.

MUS Ontology

This was work done with Dr. Werner Ceusters, with assistance from Dr. Matt Samore, and Dr. Stéphane Meystre.


The past decade has witnessed an increased interest in what are called “medically unexplained syndromes” (MUS). We address the question of whether structuring the domain knowledge for MUS can be achieved by applying the principles of Ontological Realism in light of criticisms about their useful- ness in areas where science has not yet led to insights univocally endorsed by the relevant communities. We analyzed whether the different perspectives held by MUS researchers can be represented without taking any particular stance and whether existing ontologies based on Ontological Realism can be further built upon. We did not find refutation of the applicability of the principles. We found the Ontology of General Med- ical Science and Information Artifact Ontology to provide useful frameworks for analyzing certain MUS controversies, although leaving other questions open. 

Table 4 - Foundational units for an MUS ontology

CLINICAL REPRESENTATION =def. – A (IAO) REPRESENTATIONAL ARTIFACT of a PHENOTYPE that is inferred from the combination of laboratory, image, and clinical findings about a given patient.

UNEXPLAINED CLINICAL REPRESENTATION =def. – A CLINICAL REPRESENTATION that when used as input for an interpretive process does not lead to a DIAGNOSIS.

DIAGNOSIS OF MUS =def. – A (IAO) REPRESENTATION of the conclusion of an interpretive process that has as input an UNEXPLAINED CLINICAL REPRESENTATION of a given patient and as output an assertion to the effect that no DIAGNOSIS has been established.