Ontological Realism for Biomedical Ontologies and Electronic Health - PowerPoint PPT Presentation

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Center of Ce of E of E Exce Exce celle celle llence llence ce i ce i in in Bioi Bi Bi Bioi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces Tutorial-style Workshop Ontological Realism for Biomedical Ontologies and Electronic Health Records August 29, 2011; 11.30 AM – 01.00 PM Radisson Blu Scandinavia Hotel Oslo, Norway W. CEUSTERS 1 , M. BROCHHAUSEN 2 , S. SCHULZ 3 1 Ontology Research Group, and Department of Psychiatry, University at Buffalo, NY 2 University of Arkansas for Medical Sciences, Little Rock, AR 3 Institut für Medizinische Informatik Statistik und Dokumentation, Medical University, Graz, Austria.

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Ce Center of Center of Ce of E of E Exce Exce celle celle llence llence ce i ce i in in Bi Bi Bioi Bioi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces Program • Ontology and ontologies (5 min, WC): the distinction between ‘Ontology’ as scientific discipline and as representational artifacts; • Ontological Realism & ontologies (25 min, MB): – Ontological Realism as basis for upper ontologies, focusing on BFO. – Entities and relations recognized by Ontological Realism (e.g. ACGT), – Quality criteria for OBO Foundry Ontologies; • Ontology authoring and evaluation (30 min, SS): application of ontological realism in detecting and avoiding common mistakes in formal representations; • Ontological Realism and EHRs (20 min, WC): how to improve EHR data by means of ontological realism; • Roundup and future collaborations (10 min) Ceusters W. - MIE 2011 2

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Ce Center of of E of E Exce Exce celle celle llence llence ce i ce i in in Bioi Bi Bi Bioi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces The distinction between ‘ontology’ as scientific discipline and ‘ontologies’ as representational artifacts W. Ceusters 3

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Ce Center of Center of Ce of E of E Exce Exce celle celle llence llence ce i ce i in in Bioi Bioi Bi Bi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces What’s in a name? • In philosophy: – Ontology (no plural) is the study of what entities exist and how they relate to each other; • In computer science and many biomedical informatics applications: – An ontology (plural: ontologies ) is a shared and agreed upon conceptualization of a domain; • The realist view of the presenters combines the two: – We use Ontological Realism , a specific methodology that uses ontology as the basis for building high quality ontologies , using reality as benchmark. Ceusters W. - MIE 2011

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Center of Ce of E of E Exce Exce celle celle llence llence ce i ce i in in Bioi Bi Bi Bioi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces Ontologies and Software Ontology Computer Science create approach to Authoring ‘ontology’ Tools Reasoners Domain Ontologies Semantic ‘Philosophical’ use Applications approach to ontology Ceusters W. - MIE 2011 5

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Center of Ce of E of E Exce Exce celle celle llence llence ce i ce i in in Bioi Bioi Bi Bi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces The basic axioms of Ontological Realism 1. There is an external reality which is ‘objectively’ the way it is; 2. That reality is accessible to us; 3. We build in our brains cognitive representations of reality; 4. We communicate with others about what is there, and what we believe there is there. Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Ceusters W. - MIE 2011 Biomedical Domain. Proceedings of KR-MED 2006, Biomedical Ontology in Action, November 8, 2006, Baltimore MD, USA

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Center of Ce of E of E Exce Exce celle celle llence llence ce i ce i in in Bioi Bi Bioi Bi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces Three levels of reality in Ontological Realism L3: linguistic Representations representations about (1), (2) or (3) L2: clinicians’ beliefs about (1) L1: entities with objective existence First Order Reality Ceusters W. - MIE 2011

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Ce Center of of E of E Exce Exce celle celle llence llence ce i ce i in in Bi Bi Bioi Bioi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces A crucial distinction: data and what they are about data First- organization Order i s a b o u Reality t model development observation & Representation measurement further R&D verify (instrument and use add study optimization) Δ = Generic outcome beliefs application Ceusters W. - MIE 2011 8

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Center of Ce of E of E Exce Exce celle celle llence llence ce i ce i in in Bioi Bi Bi Bioi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces Distinguish what is generic and what is specific. Generic Generic Specific Specific L3. ‘person’ ‘drug’ ‘insulin’ ‘W. Ceusters’ ‘my sugar’ Representation L2. Beliefs DIAGNOSIS my doctor’s my doctor’s (knowledge) work plan INDICATION diagnosis L1. my doctor my doctor’s PATHOLOGICAL PERSON computer STRUCTURE First-order me DISEASE my NIDDM DRUG reality my blood PORTION OF MOLECULE glucose level INSULIN Realism-based Ontology Referent Tracking Ceusters W. - MIE 2011 9

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Ce Center of of E of E Exce Exce celle celle llence llence ce i ce i in in Bioi Bi Bioi Bi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces The distinction between ‘ontology’ as scientific discipline and ‘ontologies’ as representational artifacts W. Ceusters (5 min.) 10

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Ce Center of of E of E Exce Exce celle celle llence llence ce i ce i in in Bi Bioi Bi Bioi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces Ontological Realism & Ontologies Mathias Brochhausen (25 min.) 11

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Ce Center of of E of E Exce Exce celle celle llence llence ce i ce i in in Bi Bioi Bi Bioi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces Ontology authoring and evaluation Stefan Schulz (30 min.) 12

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Ce Center of of E of E Exce Exce celle celle llence llence ce i ce i in in Bi Bioi Bi Bioi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces Ontological Realism and EHRs W. Ceusters (20 min.) 13

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Ce Center of of E of E Exce Exce celle celle llence llence ce i ce i in in Bioi Bi Bi Bioi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces The ultimate goal of Healthcare IT Everything collected wherever, whenever and about whomever which is relevant to a medical problem in whomever, whenever and wherever, should be accessible without loss of relevant detail. Ceusters W. - MIE 2011

R T U New Y New Y Yor Yor ork St ork St Stat Stat ate ate R T U Center of Ce Ce Center of of E of E Exce Exce celle celle llence llence ce i ce i in in Bioi Bi Bioi Bi oinfor oinfor ormat ormat atics atics cs & L cs & L & Life Sci & Life Sci Science Science ces ces If it is possible outside healthcare … received confirmation call Note in ‘EHR’ about calories purchased (or card blocked?) Ceusters W. - MIE 2011