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R ealist O ntology for Electronic Health Records

R ealist O ntology for Electronic Health Records. Dr. Werner Ceusters ECOR: European Centre for Ontological Research, Saarbrücken University RAMIT: Research in Advanced Medical Informatics and Telematics. Interoperability of electronic health records.

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R ealist O ntology for Electronic Health Records

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  1. Realist Ontology for Electronic Health Records Dr. Werner Ceusters ECOR: European Centre for Ontological Research, Saarbrücken University RAMIT: Research in Advanced Medical Informatics and Telematics

  2. Interoperability of electronic health records • By end 2006, Member States, in collaboration with the European Commission, shouldidentify and outline interoperability standards for health data messages and electronichealth records, taking into account best practices and relevant standardisation efforts. • Achieving a seamless exchange of health information across Europe requires commonstructures and ontologies of the information transferred between health information systems. e-Health - making healthcare better for European citizens: An action plan for aEuropean e-Health Area COM (2004) 356 final, 30.4.2004, p17

  3. 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.

  4. 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)

  5. “Ontology” An ontology defines the terms used to describe and represent an area of knowledge, and are used bypeople, databases, and applications that need to share domain information (a domain is a specificsubject area, such as health or medicine). e-Health - making healthcare better for European citizens: An action plan for aEuropean e-Health Area COM (2004) 356 final, 30.4.2004, p17 OWL Web Ontology Language; Use Cases and Requirements W3C Recommendation 10 February 2004 http://www.w3.org/TR/webont-req/

  6. “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/

  7. "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.)

  8. concept term referent 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.”

  9. 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.

  10. The machine sees: John Doe has a pyogenic granuloma of the left thumb Understanding content (1) We see: “John Doe has a pyogenic granuloma of the left thumb”

  11. The machine sees: • <record> • <subject>John Doe </subject> • <diagnosis>pyogenic granuloma of the left thumb </diagnosis> • </record> Understanding content (2) The XML misunderstanding We see: • <record> • <patient>John Doe</patient> • <diagnosis>pyogenic granuloma of the left thumb</diagnosis> • </record>

  12. EHCR-architecture Terminology • <129465004><116154003> John Doe </116154003> • < 8319008 > 17372009 <findingsite> 76505004 • <laterality>7771000</laterality> </findingsite> • </ 8319008 > • </129465004> Statements Reality CEN’s view on EHCR and reality

  13. Patient sex • male • female • Unknown ???

  14. 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)

  15. 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 ?

  16. NCIT’s “Lung” in OWL “All instances of lung must be located in at least one instance of thoracic cavity” Hence: total lung excision is impossible. <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>

  17. NCIT’s “Lung” in OWL “every assigned location of pleura must be an instance of the class Thoracic Cavity” Allows lungs not to be located at all. <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>

  18. 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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