An ontology-based methodology for the migration of biomedical terminologies to the EHR

1. An ontology-based methodology for the migration of biomedical terminologies to the EHR Barry Smith and Werner Ceusters http://ontologist.com

2. An ontology-based methodology for • migration • evidence-based quality control of • terminologies • the automatic generation of mappings between terminologies http://ontologist.com

3. Current Orthodoxy: The Concept Orientation • Jim Cimino • “Desiderata for Controlled Medical Vocabularies in the Twenty-First Century” • 1998 http://ontologist.com

4. How do concepts apply to clinical phenomena? The concept diabetes mellitus becomes ‘associated with a diabetic patient’ http://ontologist.com

5. The concept diabetes mellitus becomes ‘associated with a diabetic patient’ • concept patient concept diabetes http://ontologist.com

6. The concept diabetes mellitus becomes ‘associated with a diabetic patient’ • concept patient concept diabetes • what it is on the • side of the patient ? ? http://ontologist.com

7. The story of Jane Smith(with apologies to Alan Rector) http://ontologist.com

8. Jane’s favourite supermarket The freezer section of Jane’s favourite supermarket The only available warning sign used outside A very suspiciously shaped upper leg July 4th, 1990: Jane goes shopping: http://ontologist.com

9. A visit to the hospital • City Health Centre Dr. Peters • (City HC) Dr. Longley http://ontologist.com

10. Diagnosis: a severe spiral fracture of the femur http://ontologist.com

11. Standard EHRs • Specific codes for: patients, physicians, times, places, sometimes to X-ray images • General codes for everything else • The record tells us that there is some instance of the class the code refers to http://ontologist.com

12. Different patients. Same supermarket? Same freezer section? PtID Date ObsCode Narrative 5572 5572 5572 5572 5572 5572 2309 298 298 47804 5572 17/05/1993 01/04/1997 22/08/1993 04/07/1990 22/08/1993 04/07/1990 03/04/1993 12/07/1990 12/07/1990 21/03/1992 01/04/1997 9001224 26442006 81134009 26442006 58298795 9001224 79001 9001224 79001 2909872 26442006 Other lesion on other specified region closed fracture of shaft of femur Fracture, closed, spiral Essential hypertension Essential hypertension Accident in public building (supermarket) Accident in public building (supermarket) closed fracture of shaft of femur 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 Same patient, different dates, same fracture codes: same (numerically identical) fracture ? 2309 21/03/1992 26442006 closed fracture of shaft of femur Same patient, same date, 2 different fracture codes: same (numerically identical) fracture ? Same patient, different dates, Different codes. Same (numerically identical) polyp ? Different patients, same fracture codes: Same (numerically identical) fracture ? 0939 20/12/1998 255087006 malignant polyp of biliary tract Problems http://ontologist.com

13. Difficult to: • count the number of (numerically) different diseases (bad statistics on incidence, prevalence, cost ...) http://ontologist.com

14. Difficult to: • relate (numerically the same or different) causal factors to disorders: Dangerous public places (swimming pools) HIV contaminated blood food from unhygienic source, ... http://ontologist.com

15. The solutionunique numerical IDs for all concrete individual entities relevant to the diagnosis and therapy of each patient http://ontologist.com

16. Referent tracking already used as a matter of course for bank and credit card transactions legal documents (in court systems) Fedex / UPS parcels cargo conveyor belt manufacturing mp3 files (for Digital Rights Management) archeological specimens http://ontologist.com

17. http://ontologist.com

18. types • rabbit, headache, human being, salute, death • Mary’s rabbit, my current headache, me, Rumsfeld’s salute at 4pm on 6/22/04, Reagan’s death instances http://ontologist.com

19. Referent Tracking • Method: introduce an Instance Unique Identifier(IUI) for each relevant individual entity • Outcome: An ever growing map of clinical cases, and of their interrelations to other clinical cases http://ontologist.com

20. Services • IUI generator • IUI assignment (facility now in openEHR) • IUI repository • Referent Tracking Database (RTDB): statements relating instances to instances and types software now available will be tested in a clinical setting http://ontologist.com

21. Conclusion 1/4 • Referent tracking can solve a number of problems in an elegant way • Existing coding systems and technologies can be used for the implementation http://ontologist.com

22. Conclusion 2/4 • because the same patient often attends different hospitals using different coding systems the use of common IUI repositories will gradually lead to automatic mappings between terminologies http://ontologist.com

23. Conclusion 3/4 • as IUIs come to be associated with a plurality of codes from different coding systems • we can run statistical tests to find outliers – codes which were misapplied; or ill-defined • or to test and enhance rules for reasoning postulated by coding systems such as SNOMED-CT http://ontologist.com

24. Conclusion 4/4 • Over time, the IUI repository will come to serve as a benchmark of correctness for coding systems • allowing automatic step-by-step improvements • http://ontology.buffalo.edu/referent-tracking http://ontologist.com