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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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Current Orthodoxy: Concept-Based Coding

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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

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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

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 wayExisting coding systems and technologies

can be used for the implementationThe use of Health Card technology will

make the assignment of IUIs very easy to implement

Use of randomly assigned alphanumeric IDs can also bring data security advantages

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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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