ECO R European Centre for Ontological Research Realist

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ECO R European Centre for Ontological Research Realist Ontology for Electronic Health Records Dr.

ECO R European Centre for Ontological Research 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

ECO R European Centre for Ontological Research Interoperability of electronic health records • By

ECO R 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 e-Healthhealth - makinginformation healthcare bettersystems. for European citizens: An action plan for a European e-Health Area

ECO R European Centre for Ontological Research The O-word in science N. Guarino, P.

ECO R European Centre for Ontological 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.

ECO R The O-word in buzz-speak European Centre for Ontological Research • “An ontology

ECO R The O-word in buzz-speak European Centre for Ontological Research • “An ontology is a classification methodology formalizing a subject's knowledge or belief system in a structured way. Dictionaries and encyclopedias are examples of ontologies. ” (X 1) • “A terminology (or classification) is a kind of ontology by definition and it should preserve (and "understand") the relationships between the 1, 000 s of terms in it or else it would become a mere dictionary (or at best a thesaurus). ” (X 2) • “Ontologies are Web pages that contain a mystical unifying force that gives differing labels common meaning. ” (X 3)

ECO R European Centre for Ontological Research “Ontology” An ontology defines the terms used

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, p 17 OWL Web Ontology Language; and Requirements W 3 C Recommendation 10 February 2004 http: //www. w 3. org/TR/webont-req/

ECO R European Centre for Ontological Research “Ontology” • Ontologies need to specify descriptions

ECO R European Centre for Ontological Research “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 W 3 C Recommendation 10 February 2004 http: //www. w 3. org/TR/webont-req/

ECO R European Centre for Ontological Research "Where there is the sound of a

ECO R European Centre for Ontological Research "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. )

ECO R Concepts come from terminology European Centre for Ontological Research • In Information

ECO R Concepts come from terminology European Centre for Ontological Research • 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 R European Centre for Ontological Research Realist ontology • describes what is fundamental

ECO R European Centre for Ontological Research 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.

ECO R Understanding content (1) European Centre for Ontological Research We see: “John Doe

ECO R 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

ECO R Understanding content (2) European Centre for Ontological Research We see: The XML

ECO R Understanding content (2) European Centre for 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 CEN’s view on EHCR and reality R EHCR-architecture Terminology European Centre for Ontological

ECO CEN’s view on EHCR and reality R 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>

ECO R European Centre for Ontological Research Patient sex • male • female •

ECO R European Centre for Ontological Research Patient sex • male • female • Unknown ? ? ?

ECO R European Centre for Ontological Research Amen !!! • “Give folks a loose

ECO R European Centre for Ontological 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)

ECO R European Centre for Ontological Research XML OWL • XML – Pure syntax

ECO R European Centre for Ontological Research 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 ?

ECO R NCIT’s “Lung” in OWL European Centre for Ontological Research <owl: Class rdf:

ECO R NCIT’s “Lung” in OWL European Centre for Ontological Research <owl: Class rdf: ID="Lung"> <rdfs: label>Lung</rdfs: label> “All instances of lung must be located in at least one instance <code>C 12468</code> of thoracic cavity” <has. Type>primitive</has. Type> Hence: total lung excision is <rdfs: sub. Class. Of rdf: resource="#Organ"/> impossible. <rdfs: sub. Class. Of> <owl: Restriction> <owl: on. Property rdf: resource="#r. Anatomic_Structure_Has_Location"/> <owl: some. Values. From rdf: resource="#Thoracic_Cavity"/> </owl: Restriction> </rdfs: sub. Class. Of>. . . </owl>

ECO R NCIT’s “Lung” in OWL European Centre for Ontological Research <owl: Class rdf:

ECO R NCIT’s “Lung” in OWL European Centre for Ontological Research <owl: Class rdf: ID="Lung"> “every assigned location of <rdfs: label>Lung</rdfs: label> pleura must be an instance of <code>C 12468</code> the class Thoracic Cavity” <has. Type>primitive</has. Type> Allows lungs not to be located <rdfs: sub. Class. Of rdf: resource="#Organ"/> at all. <rdfs: sub. Class. Of> <owl: Restriction> <owl: on. Property rdf: resource="#r. Anatomic_Structure_Has_Location"/> <owl: all. Values. From rdf: resource="#Thoracic_Cavity"/> </owl: Restriction> </rdfs: sub. Class. Of>. . . </owl>

ECO R European Centre for Ontological Research What is our message ? • From

ECO R European Centre for Ontological Research 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