eco r european centre for ontological research realist ontology for electronic health records dr....

ECOREuropean Centre forOntological Research

Realist Ontology for Electronic Health

Records

Dr. Werner CeustersECOR: European Centre for Ontological Research, Saarbrücken University

RAMIT: Research in Advanced Medical Informatics and Telematics

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

ECOREuropean Centre forOntological Research The O-word in science

N. Guarino, P. Giaretta, "Ontologies and Knowledge Bases: Towards a Terminological Clarification". In Towards Very Large Knowledge Bases: Knowledge Building and Knowledge Sharing, N. Mars (ed.), pp 25-32. IOS Press, Amsterdam, 1995.

ECOREuropean Centre forOntological Research The O-word in buzz-speak

• “An ontology is a classification methodology for formalizing a subject's knowledge or belief system in a structured way. Dictionaries and encyclopedias are examples of ontologies.”

(X1)

• “A terminology (or classification) is a kind of ontology by definition and it should preserve (and "understand") the relationships between the 1,000s of terms in it or else it would become a mere dictionary (or at best a thesaurus).”

(X2)

• “Ontologies are Web pages that contain a mystical unifying force that gives differing labels common meaning.”

(X3)


“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/


"Where there is the sound of a blow, there is respect”

(Pashtun proverb)

• “I repeatedly get confused by the (in my opinion structurally confusing) terminology of those people (like Y) who try to do ontology but end up just studying concepts.”

(X, pers. comm.)


Concepts come from 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


Realist ontology

• describes what is fundamental in the totality of what exists,

• defines the most general categories to which we need to refer in constructing a description of reality,

• tells us how these categories are related.

• is able to be used to describe reality at any point in time.


Understanding content (1)

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

We see:

The machine sees:


Understanding content (2)

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

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

</record>

The XML misunderstandingWe see:

< >

< > </ >

< > </ >

</ >

The machine sees:


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>


Patient sex

• male

• female

• Unknown ???

ECOREuropean Centre forOntological Research Amen !!!

• “Give folks a loose standard and the first thing many of them do is exploit its weaknesses for their personal gain.”

NICHOLAS PETRELEY Computerworld

• “Give folks a loose standard and the first thing the clever ones do is exploit the ignorance of the others for their personal gain.”

WERNER CEUSTERS (in a vicious mood)


XML OWL

• XML– Pure syntax– Simulated semantics

• OWL:– Very precise semantics– But is the semantics of the right sort to faithfully

describe simple medical facts ?

ECOREuropean Centre forOntological Research NCIT’s “Lung” in OWL

<owl:Class rdf:ID="Lung"><rdfs:label>Lung</rdfs:label><code>C12468</code><hasType>primitive</hasType><rdfs:subClassOf rdf:resource="#Organ"/><rdfs:subClassOf>

<owl:Restriction><owl:onProperty

rdf:resource="#rAnatomic_Structure_Has_Location"/><owl:someValuesFrom rdf:resource="#Thoracic_Cavity"/>

</owl:Restriction></rdfs:subClassOf>...</owl>

“All instances of lung must be located in at least one

instance of thoracic cavity”Hence: total lung excision is

impossible.

ECOREuropean Centre forOntological Research NCIT’s “Lung” in OWL

<owl:Class rdf:ID="Lung"><rdfs:label>Lung</rdfs:label><code>C12468</code><hasType>primitive</hasType><rdfs:subClassOf rdf:resource="#Organ"/><rdfs:subClassOf>

<owl:Restriction><owl:onProperty

rdf:resource="#rAnatomic_Structure_Has_Location"/><owl:allValuesFrom rdf:resource="#Thoracic_Cavity"/>

</owl:Restriction></rdfs:subClassOf>...</owl>

“every assigned location of pleura must be an instance of

the class Thoracic Cavity”Allows lungs not to be

located at all.


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

eco r european centre for ontological research realist ontology for electronic health records dr....

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