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ECO
R
European Centre for
Ontological Research
Using realist
ontology to link
patient records with
terminologies
Dr. W. Ceusters
European Centre for Ontological Research
University of Saarbrücken
ECO
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Affiliations and Partners
European Centre for
Ontological Research
ECO
R
European Centre for
Ontological Research
Management
Strategic Management Board
Directors
Representatives of affiliates
Advisory
Board
ECO
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European Centre for
Ontological Research
Interoperability of
electronic health records
• By end 2006, Member States, in collaboration
with the European Commission, should identify
and outline interoperability standards for health
data messages and electronic health records,
taking into account best practices and relevant
standardisation efforts.
• Achieving a seamless exchange of health
information across Europe requires common
structures and ontologies of the information
transferred between
systems.
e-Healthhealth
- makinginformation
healthcare better
for European
citizens: An action plan for a European e-Health
Area
ECO
R
European Centre for
Ontological Research
“Ontology”
An ontology defines the terms used to
describe and represent an area of
knowledge, and are used by people,
databases, and applications that need to
share domain information (a domain is a
specific subject area, such as health or
medicine). e-Health - making healthcare better for European
citizens: An action plan for a European e-Health
Area
COM
(2004) Use
356 Cases
final, 30.4.2004,
p17
OWL Web Ontology
Language;
and Requirements
W3C Recommendation 10 February 2004
http://www.w3.org/TR/webont-req/
ECO
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European Centre for
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“Ontology”
• Ontologies need to specify descriptions for
the following kinds of concepts:
– Classes (general things) in the many domains
of interest
– The relationships that can exist among things
– The properties (or attributes) those things may
have
OWL Web Ontology Language; Use Cases and Requirements
W3C Recommendation 10 February 2004
http://www.w3.org/TR/webont-req/
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Focus of this presentation
European Centre for
Ontological Research
• Ontology DOES HAVE a role in maximizing
the potential uses of the EHCR
– by making the contents understandable both for
humans and machines in the same way
• Allows us to identify mistakes in current systems
• gives us a methodology to do better
• But only on the condition that the
RIGHT SORT of ontology is used
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Understanding content (1)
European Centre for
Ontological Research
We see:
“John Doe has a pyogenic
granuloma of the left thumb”
The machine sees:
John Doe has a
pyogenic
granuloma of
the left thumb
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Understanding content (2)
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Ontological Research
We see:
The XML misunderstanding
<record>
<patient>John Doe</patient>
<diagnosis>pyogenic granuloma of the left thumb</diagnosis>
</record>
The machine sees:
<record>
<subject> John Doe </subject>
<diagnosis> pyogenic granuloma
of the left thumb </diagnosis>
</record>
ECO
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Understanding content (3)
European Centre for
Ontological Research
<129465004>
<116154003> John Doe </116154003>
< 8319008 > 17372009
<finding site> 76505004
<laterality>7771000</laterality>
</finding site>
</ 8319008 >
</129465004>
XML-tags
give
humans
Codes tell
humans
and
some
context,where
but tell
machines
thethe
machine
nothing
than
“meaning”
canmore
be found
where to store the data
ECO
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European Centre for
Ontological Research
The view of terminology
• In Information Science:
– “An ontology is a
description (like a formal
specification of a program)
of the concepts and
relationships that can exist
for an agent or a community
of agents.”
• In Philosophy:
– “Ontology is the science of
what is, of the kinds and
structures of objects,
properties, events,
processes and relations in
every area of reality.”
concept
term
referent
ECO
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European Centre for
Ontological Research
Summary of current deficiencies in
traditional and formal terminologies
based on the concept paradigm
• Terms often require “reading in context”:
– ICD: stomach for tumor in stomach
• Agrammatical constructions :
– Several systems: Hepatitis, acute
• Semantic drift as one moves between hierarchies:
– UMLS: fever ISA clinical exam ISA measurement ISA data
collection ISA information science
• labels for terms do not correspond with intended
meaning:
– SNOMED-CT: leg for lower limb or lower leg
• underspecification (leading to erroneous classification
in DL-based systems)
• overspecification (leading to wrong assumptions with
respect to instances)
ECO
An underspecification example
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Ontological Research
ECO
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European Centre for
Ontological Research
Current EHCR architectures
and message standards
are not any better !
1. They refer to such terminologies for
most of the content
2. Their structures are built using the
same error-prone approach
CEN ENV 13606
ECO
R CEN’s starting position for ENV
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13606 is ok
“The real world of health and health care is
made up of individual clinical situations
(of which the participants are called
“associate topics”), that are described by an
EHCR author as clinical statements.
Within an EHCR system each clinical
statement will be expressed as an
elementary healthcare record entry.”
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CEN’s view on EHCR and reality
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EHCR-architecture
Terminology
European Centre for
Ontological Research
Statements
Reality
<129465004><116154003> John Doe </116154003>
< 8319008 > 17372009 <finding site> 76505004
<laterality>7771000</laterality>
</finding site>
</ 8319008 >
</129465004>
CEN ENV 13606
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Architectural Component Attributes
European Centre for
Ontological Research
Refer to situations and statements and rely on terminology
Language
Component
unique identifier
0..1
1
Related
date and time
0..n
Component
Status information
1
1
Component
name structure
Architectural
Component
0..n
Related
healthcare
agent
1
Originating
Healthcare
agent
1
1
Originating
date and time
0..n
Distribution
Rule Reference
Subject of care
identifier
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Ontological Research
KMEHR-message
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Ontological Research
KMEHR: element dayperiod/cd
afterbreakfast
afterdinner
evening
afterlunch
afterlunch
morning
afternoon
beforebreakfast night
beforedinner
beforelunch
betweenbreakfastandlunch
betweendinnerandsleep
betweenlunchanddinner
betweenmeals
thehourofsleep
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KMEHR: element duration
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Ontological Research
unit enumeration:
%vv
%wv
mg/dl
amp
bot
box
cap
cc
cnt
ctr
dis
drm
...
%ww 1
bag
c
cm
daily
fl
000/mm3
bol
can
cmm
day
fld
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Ontological Research
Patient sex
• male
• female
• Unknown ???
HL7-RIM
ECO
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Living subject
person
nonPersonLS
Place
Organisation
Material
ManufacteredM
Device
Container
Managed PatientEncounter
Employee
Participation ControlAct
Patient
LicensedEntity
Supply
Access
Diet
WorkingList
Procedure
Observation
Entity
PublicHealthcare
DiagnosticImage
DeviceTask
SubstanceAdministration
FinancialContract
Account
FinancialTransaction
InvoiceElement
Role
Role
Link
Language
Communication
Participation
ActLink
Communication
Function
Act
Context
Structure
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HL7: Acts contains :
A collection of classes including the Act class
and its specializations. These relate to the
actions and events that constitute health care
services.
Account
ControlAct
DiagnosticImage
FinancialTransaction
ManagedParticipation
Participation
Procedure
SubstanceAdministration
WorkingList
Act
ActRelationship
DeviceTask
FinancialContract
InvoiceElement
Observation
PatientEncounter
PublicHealthCase
Supply
Diet
ECO
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European Centre for
Ontological Research
HL7: Acts contains :
A collection of classes including the Act class
and its specializations. These relate to the
actions and events that constitute health care
services.
Account
ControlAct
DiagnosticImage
FinancialTransaction
ManagedParticipation
Participation
Procedure
SubstanceAdministration
WorkingList
Act
ActRelationship
DeviceTask
FinancialContract
InvoiceElement
Observation
PatientEncounter
PublicHealthCase
Supply
Diet
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European Centre for
Ontological Research
Messy hierarchy
Acts: A collection of classes including the Act
class and its specializations. These relate to the
actions and events that constitute health care
services.
Act: A record of something that is being done,
has been done, can be done, or is intended or
requested to be done
Financial contract: A contract whose value is
measured in monetary terms.
Examples: Insurance; Purchase agreement
ECO
My use of the word ontology,
R
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Ontological Research
or: what we really need
a representation of REALITY that is
understandable for a computer and
reflects the properties of the objects
within its domain in such a way that
there obtain substantial and systematic
correlations between reality and the
ontology itself.
ECO
R A look in the operating theatre
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Ontological Research
A lot of
objects present
This
surgeon
with some relations
Part of
This mask
This
amputatio
n stump
This hand
Haydom Lutheran Hospital, Tanzania
ECO
R A look in the operating theatre
European Centre for
Ontological Research
A lot of
processes going on
This wound
being closed
by holding ...
with some relations
Part of
That wound
fluid
drained
This kocher
being held in
that hand of
that surgeon
Haydom Lutheran Hospital, Tanzania
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European Centre for
Ontological Research
“Axiom”
epistemology
• If the picture is not a fake, we (i.e., me and
this audience) KNOW that that hand, that
surgeon, ... EXISTED, i.e. WERE REAL.
• But importantly: that hand, surgeon, kocher,
mask, ... EXISTED independently of our
knowledge about them and also the partrelationship between that hand and that
surgeon, and the processes going on, were
equally real.
ontology
ECOThe blurr of possible worlds
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EHCR-architecture
Terminology
European Centre for
Ontological Research
Statements
Observation
(interpretation)
Reality
<129465004><116154003> John Doe </116154003>
< 8319008 > 17372009 <finding site> 76505004
<laterality>7771000</laterality>
</finding site>
</ 8319008 >
</129465004>
ECO
R
European Centre for
Ontological Research
“Axiom”
• Concept-based terminology (and standardisation
thereof) is there as a mechanism to improve
understanding of messages by humans.
• It is NOT the right device
– to explain why reality is what it is, how it is organised,
etc., (although it is needed to allow communication),
– to reason about reality,
– to make machines understand what is real,
– to integrate across different views, languages,
conceptualisations, ...
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Why not ?
• Does not take care of universals and particulars
appropriately
• Concepts not necessarily correspond to
something that (will) exist(ed)
– Sorcerer, unicorn, leprechaun, ...
• Definitions set the conditions under which terms
may be used, and may not be abused as
conditions an entity must satisfy to be what it is
• Language can make strings of words look as if it
were terms
– “Middle lobe of left lung”
• ...
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Ontology versus
Description Logics
• In the Description Logic world
– terms and definitions come first,
– the job is to validate them and reason with them by
means of a model
– but whether the model correspond to reality is not its
problem (Workshop on DL, Saarbrücken, 22-23/11/2004)
• In the realist ontology world
– robust ontology (with all its reasoning power) comes
first
– terms, term-hierarchies and record architectures must
be subjected to the constraints of ontological
coherence
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(Simplified) Logic of classes
European Centre for
Ontological Research
• primitive:
– entities: particulars versus universals
– relation inst such that:
• all classes are universals; all instances are
particulars
• some particulars are not instances; e.g.
some mereological sums
• subsumption defined resorting to instances:
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What is our message ?
• From “Good Characteristics of a EHCR” (Eurorec 1997,
Paris) to “Good characteristics of an Ontology”
– Crucial: how does an “ontology” relate to reality
• Pragmatism is no excuse for sloppiness
• Philosophical is no synonym for useless
• Subject EHCR standards that deal with semantics
to a sound ontological analysis
• EHCR is an ideal domain, because it deals with
real patients in real situations.
• When building “models”, they should be related to
reality in the right way