Transcript BS2_From_BFO_to_MedO.. - Buffalo Ontology Site

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
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)
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
How eliminate this nonsense?
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 toplevel look like?