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Principles of Referent Tracking: Application in Biomedical Informatics

This seminar explores the principles of Referent Tracking and its application in biomedical informatics, including the use of Basic Formal Ontology and the importance of accurate representation of reality. The seminar also discusses past and ongoing projects in translational data warehousing.

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Principles of Referent Tracking: Application in Biomedical Informatics

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  1. Principles of Referent Tracking and its Application in Biomedical InformaticsOctober 20, 2009Rochester Clinical & Translational Research Curriculum Seminar Series Werner CEUSTERS Center of Excellence in Bioinformatics and Life Sciences Ontology Research Group University at Buffalo, NY, USA

  2. Seminar overview • Setting the scene: a rough description of what Referent Tracking is and why it is important • Review the basics of Basic Formal Ontology relevant to Referent Tracking • The crucial distinction between representations and what they represent • How to apply this • past and ongoing projects • translational data warehousing at UB

  3. Part 1:Setting the sceneReferent Tracking:What and Why ?

  4. What is Referent Tracking ? • A paradigm under development since 2005, • based on Basic Formal Ontology, • designed to keep track of relevant portions of reality and what is believed and communicated about them, • enabling adequate use of realism-based ontologies, terminologies, thesauri, and vocabularies, • originally conceived to track particulars on the side of the patient and his environment denoted in his EHR, • but since then studied in and applied to a variety of domains, • and now evolving towards tracking absolutely everything, not only particulars, but also universals.

  5. ‘Principles for Success’ • Evolutionary change • Radical change: • Principle 6: Architect Information and Workflow Systems to Accommodate Disruptive Change • Organizations should architect health care IT for flexibility to support disruptive change rather than to optimize today’s ideas about health care. • Principle 7: Archive Data for Subsequent Re-interpretation • Vendors of health care IT should provide the capability of recording any data collected in their measured, uninterpreted, original form, archiving them as long as possible to enable subsequent retrospective views and analyses of those data.NOTE NOTE: ‘See, for example, Werner Ceusters and Barry Smith, “Strategies for Referent Tracking in Electronic Health Records” Journal of Biomedical Informatics 39(3):362-378, June 2006.’ Willam W. Stead and Herbert S. Lin, editors; Committee on Engaging the Computer Science Research Community in Health Care Informatics; National Research Council. Computational Technology for Effective Health Care: Immediate Steps and Strategic Directions (2009)

  6. Source of all data Reality !

  7. A digital copy of the world Ultimate goal of Referent Tracking

  8. Requirements for this digital copy • R1: A faithful representation of reality • R2 … of everything that is digitally registered, what is generic scientific theories what is specific what individual entities exist and how they relate • R3: … throughout reality’s entire history, • R4 … which is computable in order to … … allow queries over the world’s past and present, … make predictions, … fill in gaps, … identify mistakes, ...

  9. In fact … the ultimate crystal ball

  10. The ‘binding’ wall How to do it right ? I don’t want a cartoon of the world

  11. PtID Date ObsCode Narrative 5572 5572 5572 298 5572 5572 298 2309 47804 5572 5572 12/07/1990 01/04/1997 12/07/1990 17/05/1993 22/08/1993 21/03/1992 22/08/1993 04/07/1990 01/04/1997 04/07/1990 03/04/1993 81134009 9001224 26442006 9001224 79001 79001 9001224 26442006 2909872 58298795 26442006 Essential hypertension Accident in public building (supermarket) Closed fracture of radial head closed fracture of shaft of femur Essential hypertension Accident in public building (supermarket) Other lesion on other specified region closed fracture of shaft of femur Fracture, closed, spiral closed fracture of shaft of femur Accident in public building (supermarket) 5572 04/07/1990 79001 Essential hypertension 0939 24/12/1991 255174002 benign polyp of biliary tract 2309 21/03/1992 26442006 closed fracture of shaft of femur 0939 20/12/1998 255087006 malignant polyp of biliary tract Terminologies for ‘unambiguous representation’ ???

  12. PtID Date ObsCode Narrative 5572 5572 47804 5572 2309 5572 298 298 5572 5572 5572 21/03/1992 04/07/1990 17/05/1993 12/07/1990 01/04/1997 12/07/1990 03/04/1993 22/08/1993 01/04/1997 22/08/1993 04/07/1990 79001 26442006 9001224 26442006 81134009 26442006 9001224 9001224 79001 58298795 2909872 closed fracture of shaft of femur closed fracture of shaft of femur Fracture, closed, spiral Essential hypertension closed fracture of shaft of femur Closed fracture of radial head Accident in public building (supermarket) Essential hypertension Other lesion on other specified region Accident in public building (supermarket) Accident in public building (supermarket) 5572 04/07/1990 79001 Essential hypertension 0939 24/12/1991 255174002 benign polyp of biliary tract 2309 21/03/1992 26442006 closed fracture of shaft of femur If two different fracture codes are used in relation to observations made on the same day for the same patient, do they denote the same fracture ? 0939 20/12/1998 255087006 malignant polyp of biliary tract Terminologies for ‘unambiguous representation’ ???

  13. PtID Date ObsCode Narrative 5572 5572 47804 5572 2309 5572 298 298 5572 5572 5572 21/03/1992 04/07/1990 17/05/1993 12/07/1990 01/04/1997 12/07/1990 03/04/1993 22/08/1993 01/04/1997 22/08/1993 04/07/1990 79001 26442006 9001224 26442006 81134009 26442006 9001224 9001224 79001 58298795 2909872 closed fracture of shaft of femur closed fracture of shaft of femur Fracture, closed, spiral Essential hypertension closed fracture of shaft of femur Closed fracture of radial head Accident in public building (supermarket) Essential hypertension Other lesion on other specified region Accident in public building (supermarket) Accident in public building (supermarket) 5572 04/07/1990 79001 Essential hypertension 0939 24/12/1991 255174002 benign polyp of biliary tract If the same fracture code is used for the same patient on different dates, can these codes denote the same fracture? 2309 21/03/1992 26442006 closed fracture of shaft of femur 0939 20/12/1998 255087006 malignant polyp of biliary tract Terminologies for ‘unambiguous representation’ ???

  14. PtID Date ObsCode Narrative 5572 5572 47804 5572 2309 5572 298 298 5572 5572 5572 21/03/1992 04/07/1990 17/05/1993 12/07/1990 01/04/1997 12/07/1990 03/04/1993 22/08/1993 01/04/1997 22/08/1993 04/07/1990 79001 26442006 9001224 26442006 81134009 26442006 9001224 9001224 79001 58298795 2909872 closed fracture of shaft of femur closed fracture of shaft of femur Fracture, closed, spiral Essential hypertension closed fracture of shaft of femur Closed fracture of radial head Accident in public building (supermarket) Essential hypertension Other lesion on other specified region Accident in public building (supermarket) Accident in public building (supermarket) 5572 04/07/1990 79001 Essential hypertension 0939 24/12/1991 255174002 benign polyp of biliary tract 2309 21/03/1992 26442006 closed fracture of shaft of femur Can the same fracture code used in relation to two different patients denote the same fracture? 0939 20/12/1998 255087006 malignant polyp of biliary tract Terminologies for ‘unambiguous representation’ ???

  15. PtID Date ObsCode Narrative 5572 5572 47804 5572 2309 5572 298 298 5572 5572 5572 21/03/1992 04/07/1990 17/05/1993 12/07/1990 01/04/1997 12/07/1990 03/04/1993 22/08/1993 01/04/1997 22/08/1993 04/07/1990 79001 26442006 9001224 26442006 81134009 26442006 9001224 9001224 79001 58298795 2909872 closed fracture of shaft of femur closed fracture of shaft of femur Fracture, closed, spiral Essential hypertension closed fracture of shaft of femur Closed fracture of radial head Accident in public building (supermarket) Essential hypertension Other lesion on other specified region Accident in public building (supermarket) Accident in public building (supermarket) 5572 04/07/1990 79001 Essential hypertension 0939 24/12/1991 255174002 benign polyp of biliary tract 2309 21/03/1992 26442006 closed fracture of shaft of femur Can two different tumor codes used in relation to observations made on different dates for the same patient, denote the same tumor ? 0939 20/12/1998 255087006 malignant polyp of biliary tract Terminologies for ‘unambiguous representation’ ???

  16. PtID Date ObsCode Narrative Do three references of ‘hypertension’ for the same patient denote three times the same disease? 5572 5572 47804 2309 5572 5572 298 5572 5572 5572 298 21/03/1992 22/08/1993 04/07/1990 17/05/1993 12/07/1990 01/04/1997 03/04/1993 01/04/1997 22/08/1993 12/07/1990 04/07/1990 79001 9001224 9001224 26442006 26442006 81134009 9001224 2909872 26442006 79001 58298795 closed fracture of shaft of femur Fracture, closed, spiral Essential hypertension closed fracture of shaft of femur Accident in public building (supermarket) Essential hypertension Other lesion on other specified region Accident in public building (supermarket) closed fracture of shaft of femur Accident in public building (supermarket) Closed fracture of radial head 5572 04/07/1990 79001 Essential hypertension 0939 24/12/1991 255174002 benign polyp of biliary tract 2309 21/03/1992 26442006 closed fracture of shaft of femur 0939 20/12/1998 255087006 malignant polyp of biliary tract Terminologies for ‘unambiguous representation’ ???

  17. Can the same type of location code used in relation to three different events denote the same location? PtID Date ObsCode Narrative 5572 5572 298 5572 5572 5572 298 2309 47804 5572 5572 12/07/1990 01/04/1997 22/08/1993 12/07/1990 01/04/1997 04/07/1990 21/03/1992 04/07/1990 03/04/1993 17/05/1993 22/08/1993 81134009 9001224 2909872 58298795 26442006 9001224 79001 26442006 26442006 79001 9001224 Closed fracture of radial head Accident in public building (supermarket) Essential hypertension closed fracture of shaft of femur Accident in public building (supermarket) Other lesion on other specified region closed fracture of shaft of femur Fracture, closed, spiral closed fracture of shaft of femur Accident in public building (supermarket) Essential hypertension 5572 04/07/1990 79001 Essential hypertension 0939 24/12/1991 255174002 benign polyp of biliary tract 2309 21/03/1992 26442006 closed fracture of shaft of femur 0939 20/12/1998 255087006 malignant polyp of biliary tract Terminologies for ‘unambiguous representation’ ???

  18. PtID Date ObsCode Narrative 5572 5572 47804 5572 2309 5572 298 298 5572 5572 5572 01/04/1997 04/07/1990 01/04/1997 04/07/1990 03/04/1993 12/07/1990 22/08/1993 17/05/1993 21/03/1992 12/07/1990 22/08/1993 79001 9001224 26442006 9001224 26442006 81134009 2909872 26442006 9001224 58298795 79001 closed fracture of shaft of femur Accident in public building (supermarket) Accident in public building (supermarket) Essential hypertension Fracture, closed, spiral closed fracture of shaft of femur Closed fracture of radial head Accident in public building (supermarket) Essential hypertension closed fracture of shaft of femur Other lesion on other specified region 5572 04/07/1990 79001 Essential hypertension 0939 24/12/1991 255174002 benign polyp of biliary tract 2309 21/03/1992 26442006 closed fracture of shaft of femur 0939 20/12/1998 255087006 malignant polyp of biliary tract How will we ever know ?

  19. The problem in a nutshell • Generic terms used to denote specific entities do not have enough referential capacity • Usually enough to convey that some specific entity is denoted, • Not enough to be clear about which one in particular. • For many ‘important’ entities, unique identifiers are used: • UPS parcels • Patients in hospitals • VINs on cars • …

  20. Fundamental goals of ‘our’ Referent Tracking • explicitreference to the concrete individual entities relevant to the accurate description of some portion of reality, ... Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records. J Biomed Inform. 2006 Jun;39(3):362-78.

  21. 78 235 5678 321 322 666 427 Method: numbers instead of words • Introduce an Instance Unique Identifier(IUI) for each relevant particular (individual) entity Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records. J Biomed Inform. 2006 Jun;39(3):362-78.

  22. PtID Date ObsCode Narrative IUI-001 5572 5572 5572 298 2309 47804 5572 298 5572 5572 5572 03/04/1993 04/07/1990 04/07/1990 01/04/1997 12/07/1990 01/04/1997 22/08/1993 22/08/1993 21/03/1992 17/05/1993 12/07/1990 9001224 9001224 26442006 9001224 26442006 26442006 79001 79001 2909872 81134009 58298795 closed fracture of shaft of femur Essential hypertension Accident in public building (supermarket) closed fracture of shaft of femur Essential hypertension Accident in public building (supermarket) Accident in public building (supermarket) closed fracture of shaft of femur Closed fracture of radial head Fracture, closed, spiral Other lesion on other specified region IUI-001 IUI-001 IUI-007 5572 04/07/1990 79001 IUI-005 Essential hypertension 0939 24/12/1991 255174002 IUI-004 benign polyp of biliary tract 2309 21/03/1992 26442006 IUI-002 closed fracture of shaft of femur IUI-007 IUI-006 IUI-005 IUI-003 IUI-007 IUI-012 IUI-005 0939 20/12/1998 255087006 IUI-004 malignant polyp of biliary tract Codes for ‘types’ AND identifiers for instances 7 distinct disorders

  23. The shift envisioned • From: • ‘this human being is a 40 year old patient with a stomach tumor’ • To (something like): • ‘this-1 on which depend this-2 and this-3 has this-4’, where • this-1 instanceOf human being at t1 • this-2 instanceOf age-of-40-years at t2 • this-2 qualityOf this-1 at t2 • this-3 instanceOf patient-role at t3 • this-3 roleOf this-1 at t3 • this-4 instanceOf tumor at t4 • this-4 partOf this-5 at t6 • this-5 instanceOf stomach at t7 • this-5 partOf this-1 at t8 • …

  24. The shift envisioned • From: • ‘this human being is a 40 year old patient with a stomach tumor’ • To (something like): • ‘this-1 on which depend this-2 and this-3 has this-4’, where • this-1 instanceOf human being at t1 • this-2 instanceOf age-of-40-years at t2 • this-2 qualityOf this-1 at t2 • this-3 instanceOf patient-role at t3 • this-3 roleOf this-1 at t3 • this-4 instanceOf tumor at t4 • this-4 partOf this-5 at t6 • this-5 instanceOf stomach at t7 • this-5 partOf this-1 at t8 • … denotators for particulars

  25. The shift envisioned • From: • ‘this human being is a 40 year old patient with a stomach tumor’ • To (something like): • ‘this-1 on which depend this-2 and this-3 has this-4’, where • this-1instanceOf human being at t1 • this-2instanceOf age-of-40-years at t2 • this-2qualityOf this-1 at t2 • this-3instanceOf patient-role at t3 • this-3roleOf this-1 at t3 • this-4instanceOf tumor at t4 • this-4partOf this-5 at t6 • this-5instanceOf stomach at t7 • this-5partOf this-1 at t8 • … denotators for appropriaterelations

  26. The shift envisioned • From: • ‘this human being is a 40 year old patient with a stomach tumor’ • To (something like): • ‘this-1 on which depend this-2 and this-3 has this-4’, where • this-1instanceOfhuman being at t1 • this-2instanceOfage-of-40-years at t2 • this-2qualityOfthis-1 at t2 • this-3instanceOfpatient-role at t3 • this-3roleOfthis-1 at t3 • this-4instanceOftumor at t4 • this-4partOfthis-5 at t6 • this-5instanceOfstomach at t7 • this-5partOfthis-1 at t8 • … denotators foruniversalsor particulars

  27. The shift envisioned • From: • ‘this human being is a 40 year old patient with a stomach tumor’ • To (something like): • ‘this-1 on which depend this-2 and this-3 has this-4’, where • this-1instanceOfhuman beingat t1 • this-2instanceOfage-of-40-yearsat t2 • this-2qualityOfthis-1at t2 • this-3instanceOfpatient-roleat t3 • this-3roleOfthis-1at t3 • this-4instanceOftumorat t4 • this-4partOfthis-5at t6 • this-5instanceOfstomachat t7 • this-5partOfthis-1at t8 • … time periods (for continuants) when the relationships hold

  28. instance-of at t caused by #105 Relevance: the way RT-compatible systems ought to interact with representations of generic portions of reality

  29. Yes, but … • what are particulars ? • what are universals ? • what are denotators ? • … the answer is in …

  30. Part 2:Basic Formal OntologyNo (good) Referent Trackingwithout (good = realism-based) Ontology

  31. Ontology • In computer science: • a formal specification of a conceptualization

  32. Not the wrong sort

  33. No serious scholar should work with ‘concepts’

  34. Slow penetration of the idea …

  35. what is a concept description a description of? More serious scholars become convinced …

  36. The right sort of ontology can help … • In computer science: • a formal specification of a conceptualization • leads to bad ontologies • In philosophy: • a representation of reality • In the OBO Foundry: •  a representational artifact which is intended to represent universals and some defined classes. • foundation in philosophical realism

  37. Basic axioms underlying OBO Foundry ontologies • There is an external reality which is ‘objectively’ the way it is; • That reality is accessible to us; • We build in our brains cognitive representations of reality; • 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 Biomedical Domain. Proceedings of KR-MED 2006, Biomedical Ontology in Action, November 8, 2006, Baltimore MD, USA

  38. What is there ? The parts of BFO relevant for Referent Tracking some continuant universal some occurrent universal instanceOf at t instanceOf some continuant particular some occurrent particular

  39. The importance of temporal indexing malignant tumor benign tumor stomach instanceOf at t2 instanceOf at t1 instanceOf at t2 instanceOf at t1 partOf at t1 this-4 this-1’s stomach partOf at t2

  40. Sorts of relations UtoU: isa, partOf(UU), … U1 U2 PtoU: instanceOf, lacks, denotes(PU)… PtoP: partOf, denotes, … P2 P1

  41. The essential pieces dependent continuant material object spacetime region spatial region temporal region history instanceOf t t t participantOf at t occupies some temporal region some quality my 4D STR my life projectsOn me … at t projectsOn at t some spatial region located-in at t

  42. Three levels of reality of what is there L1 R L2 L3 symbolizations beliefs ‘about’

  43. Relation Defined … … … class Representations in ReferentTracking Portion of Reality Entity Configuration represents Universal Particular contains is about Non - referring Information content ent. particular corresponds - to denotes Representation RT - tuple class Representational unit Extension Denotator CUI IUI UUI RUI denotes denotes denotes

  44. Part 3:Applications of Referent Tracking

  45. (1) Making existing EHR systems RT compatible • In: Teich JM, Suermondt J, Hripcsak C. (eds.), AMIA 2007 Proceedings, Biomedical and Health Informatics: From Foundations to Applications to Policy, Chicago IL, 2007. • Rudnicki R, Ceusters W, Manzoor S, Smith B. What Particulars are Referred to in EHR Data? A Case Study in Integrating Referent Tracking into an Electronic Health Record Application. • Manzoor S, Ceusters W, Rudnicki R. A Middleware Approach to Integrate Referent Tracking in EHR Systems.

  46. Problems with prevailing EHR paradigms • Perfect ‘semantic’ tools are useless if data captured at the source is not of high quality • Prevailing HIT information models don’t allow data to be stored at acceptable quality level: • No formal distinction between disorders and diagnosis • Messy nature of the notions of ‘problem’ and ‘concern’ • No unique identification of the entities about which data is stored • Unique IDs for data-elements cannot serve as unique IDs for the entities denoted by these data-elements

  47. MedtuityEMR Patient’s Encounter Document

  48. (2) The ReMINE Project on Adverse Events • Ceusters W, Capolupo M, De Moor G, Devlies J. Introducing Realist Ontology for the Representation of Adverse Events. In: Eschenbach C, Gruninger M. (eds.) Formal Ontology in Information Systems, IOS Press, Amsterdam, 2008;:237-250 • Ceusters W, Capolupo M, Smith B, De Moor G. An Evolutionary Approach to the Representation of Adverse Events. In: Medical Informatics Europe 2009, Sarajevo, Bosnia and Herzegovina, August 31, 2009. Studies in health technology and informatics 150;:537-541

  49. ReMINE Taxonomy Annotated Events Risk Manager’s Event Administration System

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