http://ontologist.com 1/24

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

Barry Smith and Werner Ceusters

http://ontologist.com 2/24

An ontology-based methodology for

1. migration2. evidence-based quality control of terminologies 1. the automatic generation of mappings

between terminologies

http://ontologist.com 3/24

Current Orthodoxy: The Concept Orientation

Jim Cimino

“Desiderata for Controlled Medical Vocabularies in the Twenty-First Century”

1998

http://ontologist.com 4/24

How do concepts apply to clinical phenomena?

The concept diabetes mellitus becomes ‘associated with a diabetic patient’

http://ontologist.com 5/24

The concept diabetes mellitus becomes ‘associated with a diabetic patient’

concept patient concept diabetes

http://ontologist.com 6/24

?

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 7/24

The story of Jane Smith

(with apologies to Alan Rector)

http://ontologist.com 8/24

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

http://ontologist.com 9/24

A visit to the hospital City Health Centre Dr. Peters

(City HC) Dr. Longley

http://ontologist.com 10/24

Diagnosis: a severe spiral fracture of the femur

http://ontologist.com 11/24

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 12/24

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 ?

http://ontologist.com 13/24

Difficult to:

count the number of (numerically) different diseases (bad statistics on incidence, prevalence, cost ...)

http://ontologist.com 14/24

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 15/24

The solution

unique numerical IDs for all concrete individual entities relevant to the

diagnosis and therapy of each patient

http://ontologist.com 16/24

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 17/24

types / concepts instances / particulars

scientific texts, dictionariesdiaries, biographies, histories, journalism

medical ontologies, terminologies

clinical records

http://ontologist.com 18/24

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 19/24

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 20/24

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

http://ontologist.com 21/24

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

http://ontologist.com 22/24

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 23/24

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

http://ontologist.com 24/24

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

http://ontology.buffalo.edu/referent-tracking