VT

From Basic Formal Ontology to Medicine Barry Smith and Anand Kumar

UMLS Semantic Network a tool to find our way around the UMLS Metathesaurus (January 2003 version consists of 132 Semantic Types + 54 links) can be arranged in the form of a graph whose vertices are the Semantic Types and whose edges are the links.

UMLS Semantic Network arranged in a double tree structure, with two superclasses: Entities and Events. Entity = “A broad type for grouping physical and conceptual entities”. Event = “A broad type for grouping activities, processes and states”.

Basic Formal-Ontological Distinctions 1. Continuant vs. Occurrent (= SNAP vs. SPAN) 2. Dependent vs. Independent 3. Universals vs. Particulars

Basic Formal-Ontological Distinctions 1. Continuant vs. Occurrent (= SNAP vs. SPAN) 2. Dependent vs. Independent 3. Universals vs. Particulars

Continuant vs. Occurrent (= SNAP vs. SPAN) continuants = entities which continue to exist through time, e.g. organisms, cells, chromosomes occurrents = entities which unfold themselves through time in successive temporal phases, e.g. an intravenous drug infusion continuant/occurrent = (roughly) UMLS distinction between Entity and Event

Basic Formal-Ontological Distinctions 1. Continuant vs. Occurrent (= SNAP vs. SPAN) 2. Dependent vs. Independent 3. Universals vs. Particulars

Dependent vs. Independent independent = has an inherent ability to exist without reference to other entities – e.g. molecules, organisms, planets dependent = require a support from other entities in order to exist – e.g. cellular motion (which requires reference to a cell which moves), or viral infection (which requires reference to some carrier)

Need to find ways to deal with time in medical informatics Guidelines Workflow  need to be clear about the distinction between continuants and occurrents

occurrents (in medicine) are always dependent entities. Thus of the four abstractly possible combinations only three are instantiated

Independent and Dependent Continuants Independent Continuants = substances, objects, things Dependent Continuants = qualities (your height, your skin-color) states or conditions (your diabetes) roles (your role as student, as doctor) functions (of a drug, of a machine)

UMLS Semantic Network Conceptual Entity, with subclasses: Organism Attribute Finding Idea or Concept Occupation or Discipline Organization Group Group Attribute Intellectual Product Language

Conceptual Entities are dependent on minds but Organism Attributes can exist without minds and Groups (e.g. a group of macac monkeys) can exist without minds

UMLS Semantic Tree with root Event Event has subclasses: Activity Phenomenon or Process Natural Phenomenon or Process Biologic Function Physiologic Function Pathologic Function runs together functions, which are continuants, with processes, which are occurrents

Functions are continuants Functions exist self-identically through time; they have no temporal phases and exist even when not being exercised The exercise of a function unfolds itself through its temporal phases The compilers of UMLS have confused what exists dispositionally in a thing, and is the product of design or evolution, with what the thing does episodically, and is the product of intentionality or immediate causal influence

UMLS Semantic Type Collections Chen, Perl et al. and Geller, Perl et al. partition the UMLS Semantic Network into more meaningful units called Semantic Type Collections. problems revealed by the BFO analysis especially in: Pathologic Function Physiologic Function Idea or Concept

Subclasses of Pathologic Function Experimental Model of Disease Cell or Molecular Dysfunction Disease or Syndrome Mental or Behavioral Dysfunction

Subclasses of Physiologic Function Organ or Tissue Function Mental Process Molecular Function Mental Process Genetic Function Cell Function

Subclasses of Idea or Concept Functional Concept Body System Temporal Concept Qualitative Concept Quantitative Concept Spatial Concept Geographic Area Body Location or Region Molecular Sequence Carbohydrate Sequence Amino Acid Sequence Body Space or Junction Nucleotide Sequence

CIRCULATORY SYSTEM bodily systems are parts of organisms (like fingers and hands)

Case Study: Regulation of Blood Pressure UMLS: hypertension is a Disease or Syndrome or a Sign or Symptom blood pressure is an Organism Function. Both are dependent SNAP entities: they endure identically for a certain period of time and they depend for their existence on their bearer.

The hydraulic equation: BP = CO*PVR arterial blood pressure is directly proportional to the product of blood flow (cardiac output, CO) and peripheral vascular resistance (PVR). UMLS: blood flow is an Organism Function cardiac output is a Laboratory or Test Result (SNAP) and a Diagnostic Procedure (SPAN)

How eliminate this nonsense? Blood pressure is_proportional_to_a laboratory or test result? Blood pressure is_proportional_to_a diagnostic procedure? An amino acid sequence is_an idea or concept St. Malo is_a spatial concept

Basic Formal-Ontological Distinctions 1. Continuant vs. Occurrent (= SNAP vs. SPAN) 2. Dependent vs. Independent 3. Universals vs. Particulars

Replace concepts in peoples’ heads (e.g. in UMLS) with universals in re teach medical terminology systems the distinction between universals and particulars distinguish clearly between ontology (the study of reality) and epistemology/psychology (the study of peoples’ concepts)

UMLS confuses epistemology with ontology it confuses the results of our attempts to gain knowledge of specific aspects of the organism (functions, qualities, processes) with those aspects themselves.

What would a better UMLS top- level look like?