eco r european centre for ontological research using realist ontology to link patient records with...

ECOREuropean Centre forOntological Research

Using realist ontology to link

patient records with terminologies

Dr. W. CeustersEuropean Centre for Ontological Research

University of Saarbrücken

ECOREuropean Centre forOntological Research Affiliations and Partners

ECOREuropean Centre forOntological Research Management

Directors Representatives of affiliates

AdvisoryBoard

Strategic Management Board

ECOREuropean Centre forOntological 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 health information systems.

e-Health - making healthcare better for European citizens: An action plan for a European e-Health Area

COM (2004) 356 final, 30.4.2004, p17


“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).

OWL Web Ontology Language; Use Cases and RequirementsW3C Recommendation 10 February 2004

http://www.w3.org/TR/webont-req/

e-Health - making healthcare better for European citizens: An action plan for a European e-Health Area

COM (2004) 356 final, 30.4.2004, p17


“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 RequirementsW3C Recommendation 10 February 2004

http://www.w3.org/TR/webont-req/


Focus of this presentation

• 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


Understanding content (1)

“John Doe has a pyogenic granuloma of the left thumb”

We see:

The machine sees:



<record><patient>John Doe</patient>

<diagnosis>pyogenic granuloma of the left thumb</diagnosis>

</record>

The XML misunderstandingWe see:

< >

< > </ >

< > </ >

</ >

The machine sees:



<129465004><116154003> John Doe </116154003>

< 8319008 > 17372009

<finding site> 76505004

<laterality>7771000</laterality>

</finding site>

</ 8319008 >

</129465004>XML-tags give humans some context, but tell the machine nothing more than where to store the data

Codes tell humans and machines where the “meaning” can be found


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

ECOREuropean Centre forOntological Research Summary of current deficiencies in

traditional and formal terminologiesbased 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)


An underspecification example


Current EHCR architecturesand 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’s starting position for ENV13606 is ok

CEN ENV 13606

“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.”


CEN’s view on EHCR and reality

Reality

EHCR-architecture Terminology

Statements

<129465004><116154003> John Doe </116154003>< 8319008 > 17372009 <finding site> 76505004

<laterality>7771000</laterality> </finding site></ 8319008 >

</129465004>


Architectural Component Attributes

CEN ENV 13606

ArchitecturalComponent

Componentunique identifier

OriginatingHealthcare

agent Originating

date and time

Relatedhealthcare

agent

Relateddate and time

Componentname structure

Subject of careidentifier

ComponentStatus information

DistributionRule Reference

Language

11

10..n

0..n

1

11

0..n

0..1

Refer to situations and statements and rely on terminology

ECOREuropean Centre forOntological Research KMEHR-message


KMEHR: element dayperiod/cd

afterbreakfast afterdinner evening

afterlunch afterlunch morning

afternoon beforebreakfast night

beforedinner beforelunch

betweenbreakfastandlunch

betweendinnerandsleep

betweenlunchanddinner

betweenmeals thehourofsleep


KMEHR: element duration

unit enumeration: %vv %wv %ww 1 000/mm3mg/dl amp bag bol bot box c can cap cc cm cmmcnt ctr daily day dis drm fl fld ...


Patient sex

• male

• female

• Unknown ???


From Speech Acts to Information Model

HL7-RIM

Entity

LanguageCommunication

CommunicationFunction

Role

Participation

Act

ContextStructure

RoleLink ActLink

Living subject person nonPersonLSPlaceOrganisationMaterial ManufacteredM Device Container

EmployeePatient

LicensedEntityAccess

ManagedParticipation

PatientEncounterControlActSupply DietWorkingListProcedureObservation PublicHealthcare DiagnosticImage

DeviceTaskSubstanceAdministrationFinancialContractAccountFinancialTransactionInvoiceElement


Account ActRelationship ControlAct DeviceTask DiagnosticImage FinancialContract FinancialTransaction InvoiceElement ManagedParticipation Observation Participation PatientEncounter Procedure PublicHealthCase SubstanceAdministration Supply WorkingList Diet Act

A collection of classes including the Act class and its specializations. These relate to the actions and events that constitute health care services.

HL7: Acts contains :


HL7: Acts contains :

Account ActRelationship ControlAct DeviceTask DiagnosticImage FinancialContract FinancialTransaction InvoiceElement ManagedParticipation Observation Participation PatientEncounter Procedure PublicHealthCase SubstanceAdministration Supply WorkingList Diet Act

A collection of classes including the Act class and its specializations. These relate to the actions and events that constitute health care services.


Messy hierarchy

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

Acts: A collection of classes including the Act class and its specializations. These relate to the actions and events that constitute health care services.


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.

My use of the word ontology,or: what we really need


A look in the operating theatre

Haydom Lutheran Hospital, Tanzania

This surgeon

This amputation stump

A lot ofobjects present

This mask

This hand

with some relations

Part of


A look in the operating theatre

Haydom Lutheran Hospital, Tanzania

This wound being closed by holding ...

That wound fluid

drained

A lot ofprocesses going on

This kocher being held in that hand of that surgeon

with some relations

Part of

ECOREuropean Centre forOntological Research “Axiom”

• 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 part-relationship between that hand and that surgeon, and the processes going on, were equally real.

epistemology

ontology


The blurr of possible worlds

Reality

EHCR-architecture Terminology

Statements

<129465004><116154003> John Doe </116154003>< 8319008 > 17372009 <finding site> 76505004

<laterality>7771000</laterality> </finding site></ 8319008 >

</129465004>

Observation(interpretation)


“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, ...


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”

• ...


Ontology versusDescription 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


(Simplified) Logic of classes• 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:


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

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