an ontology-based methodology for the migration of biomedical terminologies to the ehr
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An ontology-based methodology for the migration of biomedical terminologies to the EHR. Barry Smith and Werner Ceusters. An ontology-based methodology for. migration evidence-based quality control of terminologies the automatic generation of mappings between terminologies. - PowerPoint PPT PresentationTRANSCRIPT
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An ontology-based methodology for the migration of biomedical terminologies to the EHR
Barry Smith and Werner Ceusters
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An ontology-based methodology for
1. migration2. evidence-based quality control of terminologies 1. the automatic generation of mappings
between terminologies
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Current Orthodoxy: The Concept Orientation
Jim Cimino
“Desiderata for Controlled Medical Vocabularies in the Twenty-First Century”
1998
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How do concepts apply to clinical phenomena?
The concept diabetes mellitus becomes ‘associated with a diabetic patient’
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The concept diabetes mellitus becomes ‘associated with a diabetic patient’
concept patient concept diabetes
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?
The concept diabetes mellitus becomes ‘associated with a diabetic patient’
?
concept patient concept diabetes
what it is on the
side of the patient
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The story of Jane Smith
(with apologies to Alan Rector)
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Jane’s favourite supermarket
July 4th, 1990: Jane goes shopping:
The freezer section of Jane’s favourite supermarket
The only available warning sign used outside
A very suspiciously shaped upper leg
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A visit to the hospital City Health Centre Dr. Peters
(City HC) Dr. Longley
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Diagnosis: a severe spiral fracture of the femur
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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
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5572 04/07/1990 26442006 closed fracture of shaft of femur
5572 04/07/1990 81134009 Fracture, closed, spiral
5572 12/07/1990 26442006 closed fracture of shaft of femur
5572 12/07/1990 9001224 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
2309 21/03/1992 9001224 Accident in public building (supermarket)
47804 03/04/1993 58298795 Other lesion on other specified region
5572 17/05/1993 79001 Essential hypertension
298 22/08/1993 2909872 Closed fracture of radial head
298 22/08/1993 9001224 Accident in public building (supermarket)
5572 01/04/1997 26442006 closed fracture of shaft of femur
5572 01/04/1997 79001 Essential hypertension
PtID Date ObsCode Narrative
0939 20/12/1998 255087006 malignant polyp of biliary tract
Different patients, same fracture codes:Same (numerically identical) fracture ?
Same patient, different dates, same fracture
codes: same (numerically identical)
fracture ?
Same patient, same date,2 different fracture codes:
same (numerically identical) fracture ?
ProblemsDifferent patients. Same supermarket? Same freezer section?
Same patient, different dates, Different codes. Same (numericallyidentical) polyp ?
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Difficult to:
count the number of (numerically) different diseases (bad statistics on incidence, prevalence, cost ...)
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Difficult to:relate (numerically the same or different) causal factors to disorders:
Dangerous public places (swimming pools)
HIV contaminated blood
food from unhygienic source, ...
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The solution
unique numerical IDs for all concrete individual entities relevant to the
diagnosis and therapy of each patient
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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
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types / concepts instances / particulars
scientific texts, dictionariesdiaries, biographies, histories, journalism
medical ontologies, terminologies
clinical records
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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
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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
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Services
– IUI generator– IUI assignment (facility now in openEHR)– IUI repository– Referent Tracking Database (RTDB):
statements relating instances to instances and types
software now availablewill be tested in a clinical setting
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Conclusion 1/4Referent tracking can solve a number of
problems in an elegant way
Existing coding systems and technologies can be used for the implementation
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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
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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-definedor to test and enhance rules for reasoning postulated by coding systems such as SNOMED-CT
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Conclusion 4/4Over time, the IUI repository will come to serve as a benchmark of correctness for coding systems
allowing automatic step-by-step improvements
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