Reuse of Data Coded with High-Quality Terminologies: Practical Examples from Patient Care Settings James J. Cimino, M.D. Department of Biomedical Informatics

Reuse of Data Coded with High-Quality Terminologies:

Practical Examples from Patient Care Settings

James J. Cimino, M.D.Department of Biomedical Informatics

Columbia University College of Physicians and Surgeons

Case PresentationThe patient is a 50 year old, Native American female who present to the emergency room with the chief complaint of cough and chest pain. The patient reports that she has had a productive cough for three days but that chest pain developed one hour ago.She gives a history of hypertension and states that she was getting a "capsule, half green, half blue-green" from her private doctor. She also reports that she was treated in the past for tuberculosis while she was pregnant, but doesn't remember what she was treated with or for how long. She reports that she was at another hospital on the other side of town, where she had a liver biopsy. She reports that she thinks the diagnosis was Hepatitis C.The patient reports an allergy to Bufferin.Physical examination revealed a well-developed, well-nourished female in moderate respiratory distress. Vital signs showed a pulse of 90, a respiratory rate of 22, an oral temperature of 100.3, and a blood pressure of 150/100. Examination revealed rales and rhonchi in the left upper chest. Abdominal exam revealed a tender, palpable liver edge.Labs:Chem7 (serum): Glucose 100 (70-105) Chem7 (plasma): Glucose 150 (75-110)CBC: Hgb 15 (12.0-15.8), Hct 45 (42.4-48.0), WBC 11,000 (3,540-9,060), Plate. 145K (165-415K)A fingerstick blood sugar was 80Urinalysis showed protein of 1+ and glucose of 0A blood culture was positive for methicillin-resistant Staphylococcus aureus (MRSA)ECG - Sinus Rhythm, 74BPM, Axis -30 degrees, ST segment 2mm elevated andT-waves down in leads I, L, V5 and V6Chest X-ray Left upper lobe infiltrate, left ventricular hypertrophyThe patient was admitted to the hospital, started on antibiotics and aspirin.A medical student reviewing the case is concerned about the risk of MRSA in patients with pneumonia and a recent myocardial infarction. She decides to do a literature search.

Case PresentationThe patient is a 50 year old, Native American female who present to the emergency room with the chief complaint of cough and chest pain. The patient reports that she has had a productive cough for three days but that chest pain developed one hour ago.She gives a history of hypertension and states that she was getting a "capsule, half green, half blue-green" from her private doctor. She also reports that she was treated in the past for tuberculosis while she was pregnant, but doesn't remember what she was treated with or for how long. She reports that she was at another hospital on the other side of town, where she had a liver biopsy. She reports that she thinks the diagnosis was Hepatitis C.The patient reports an allergy to Bufferin.Physical examination revealed a well-developed, well-nourished female in moderate respiratory distress. Vital signs showed a pulse of 90, a respiratory rate of 22, an oral temperature of 100.3, and a blood pressure of 150/100. Examination revealed rales and rhonchi in the left upper chest. Abdominal exam revealed a tender, palpable liver edge.Labs:Chem7 (serum): Glucose 100 (70-105) Chem7 (plasma): Glucose 150 (75-110)CBC: Hgb 15 (12.0-15.8), Hct 45 (42.4-48.0), WBC 11,000 (3,540-9,060), Plate. 145K (165-415K)A fingerstick blood sugar was 80Urinalysis showed protein of 1+ and glucose of 0A blood culture was positive for methicillin-resistant Staphylococcus aureus (MRSA)ECG - Sinus Rhythm, 74BPM, Axis -30 degrees, ST segment 2mm elevated andT-waves down in leads I, L, V5 and V6Chest X-ray Left upper lobe infiltrate, left ventricular hypertrophyThe patient was admitted to the hospital, started on antibiotics and aspirin.A medical student reviewing the case is concerned about the risk of MRSA in patients with pneumonia and a recent myocardial infarction. She decides to do a literature search.

Use and Reuse of Clinical Data

a) Automate the admission of the patient to a bed

b) Summarize the patient’s blood sugar tests, including serum, plasma and fingerstick (but not urine)

c) Use patient history to help with automated reminders

d) Aggregate the patient’s data for quality assurance

e) Use patient history to prevent adverse drug reactions

f) Use the laboratory test results for automated diagnosis

g) Use the patient’s data to automate information retrieval

h) Aggregate the patient’s data for epidemiologic studies

Automate the admission of the patient to a bed

“Patient is an 50 year old, Native American female…”

Admission Discharge Transfer System

“Put the patient in Room 5, Bed B…”

Electronic Medical Record

But: how does the computer know that the patient is female?

The record could say:

“female”

“Female”

“FEMALE”

“F”

“Woman”

“Girl”


• Data element - gender• Controlled terminology:

– Male– Female– Unknown (don’t know)– Unknown (can’t tell)

• Representation:– M,F,U1,U2– 0,1,2,3

• What about other values?– Genotypic– Phenotypic– Administrative



Requirements for High-Quality Terminology

• Synonymy (not redundancy)

• Multiple levels of granularity

Information Form and Reuse

Information Form and Reuse

21 22 23 24 25 26 27 28 29

7

6

5

4

3

2

1

Summarize patient’s blood sugar tests, including serum, plasma and fingerstick (but not urine)




• Data model has terms too

New York Presbyterian HospitalClinical Information Systems Architecture

Clinical Database

Medical Entities Dictionary (MED)

Database Monitor

Medical Logic Modules

DatabaseInterface

Research

Administrative

Alerts & Reminders

Results Review

. . .. . .Radiology LaboratoryDischarge

Summaries

Reformatter Reformatter Reformatter

MED Structure

MedicalEntity

LaboratoryProcedure

CHEM-7PlasmaGlucose

Test

LaboratorySpecimen

PlasmaSpecimen

Substance

Sampled

Part of

Has S

pecimen

Event

LaboratoryTest

DiagnosticProcedure

Substance MeasuredGlucose

Plasma

AnatomicSubstance

Substance

BioactiveSubstance

Chemical

Carbohydrate

The MED Today

• Concept-based (101,130)

• Multiple hierarchy (150,480)

• Synonyms (250,000)

• Translations (180,000)

• Semantic links (180,000)

• Attributes (240,000)

Using the MED for Summary Reporting

Plasma Glucose Test

Serum Glucose TestFingerstick Glucose Test

Lab Test

Intravascular Glucose Test

Lab Display

Chem20 Display

DOP Summary


WebCIS Summary


Eclipsys Summary


489 Tuberculosis Codes in ICD9-CM

010. PRIMARY TB INFECTION*

010.0 PRIMARY TB COMPLEX*

010.00 PRIM TB COMPLEX-UNSPEC

010.01 PRIM TB COMPLEX-NO EXAM

010.02 PRIM TB COMPLEX-EXM UNKN

010.03 PRIM TB COMPLEX-MICRO DX

010.04 PRIM TB COMPLEX-CULT DX

010.05 PRIM TB COMPLEX-HISTO DX

010.06 PRIM TB COMPLEX-OTH TEST

011. PULMONARY TUBERCULOSIS*

012. OTHER RESPIRATORY TB*013. CNS TUBERCULOSIS*014. INTESTINAL TB*015. TB OF BONE AND JOINT*016. GENITOURINARY TB*017. TUBERCULOSIS NEC*018. MILIARY TUBERCULOSIS*

Use patient history for automated reminders

010.1 PRIMARY TB PLEURISY*

010.8 PRIM PROGRESSIVE TB NEC*

010.9 PRIMARY TB INFECTION NOS*

More Tuberculosis in ICD9-CM137. LATE EFFECT TUBERCULOSIS*137.0 LATE EFFECT TB, RESP/NOS137.1 LATE EFFECT CNS TB137.2 LATE EFFECT GU TB137.3 LATE EFF BONE & JOINT TB137.4 LATE EFFECT TB NEC647. INFECTIVE DIS IN PREG*647.3 TUBERCULOSIS IN PREG*647.30 TB IN PREG-UNSPECIFIED647.31 TUBERCULOSIS-DELIVERED647.32 TUBERCULOSIS-DELIV W P/P647.33 TUBERCULOSIS-ANTEPARTUM647.34 TUBERCULOSIS-POSTPARTUM


TuberculosisInfection

Primary TB Pleurisy 010.1

Primary TBComplex 010.0

PrimaryTB (010)

PulmonaryTB (011)

Other RespTB (012)

Primary TBPleurisyNo Exam 010.11

Primary TBPleurisyUspec010.10

Late EffectTB (137)

TB inPreg (647.3)

Infective Diseasein Pregnancy (647)

Primary TBComplex No Exam 010.01

Primary TBComplex

Uspec010.00






• Multiple hierarchies

Reuse the patient’s data for quality assurance

2000 2001 2002 2003 2004

MI

MI+Beta

select patient_id , time = primary_time

from visit2004_diagnosis

where diagnosis_code = 2618

and b.primary_time between '01/01/2000' and '01/01/2005'

and b.comp_code = 28144

Reuse the patient’s data for quality assurance

Method 1: Write a rule to check for each reaction

Method 2: Include allergy codes for each medication

Method 3: Include definitional information and infer

Bufferin Enteric-Coated Aspirin

Aspirin PreparationsAspirin

has-ingredient

IF allergic drug [X] has ingredient [Y]

AND ordered drug [Z] has ingredient [Y]

THEN send alert

Use patient history to prevent drug reactions





• Multiple hierarchies• Include definitional knowledge

Potassium

Hypokalemia

Serum Potassium Test

Serum Specimen

Serum

Abnormalities ofSerum Potassium

Use test results for automated diagnosis









• Include definitional knowledge• Support automated translation

Use data for automated information retrieval

InjectableGentamicin

Gentamicn Sensitivity

Test

SerumGentamicin

Level

GentamicinToxicity

Gentamicin

EtiologyMeasures

Sensitivity

Substance Measured Has ingredient

DecisionRule

ExpertSystem

DrugInformation

Clinical Data

1995

Viral Hepatitis Mortality

1994 1995 1996

070.1

070.3

070.5

Diagnosis ICD9-CM Code

ICD9-CM Name

Hepatitis A 070.1 Hepatitis A

Hepatitis B 070.3 Hepatitis B

Hepatitis C 070.5 Hepatitis NEC

Hepatitis E 070.5 Hepatitis NEC

1996

Diagnosis ICD9-CM Code

ICD9-CM Name

Hepatitis A 070.1 Hepatitis A

Hepatitis B 070.3 Hepatitis B

Hepatitis C 070.4 Hepatitis C

Hepatitis E 070.5 Hepatitis NEC

Reuse the patient’s data for epidemiologic studies






• Include definitional knowledge

• Support automated translation• Avoid “Not Elsewhere Classified” (NEC)

NECReuse the patient’s data for epidemiologic studies

• Can never have a formal definition

• Terminology changes induce semantic drift

Accommodating NEC

Viral Hepatitis

Hepatitis A Hepatitis B Hepatitis C Hepatitis E

Accommodating NEC

Viral Hepatitis

Hepatitis A Hepatitis, NECHepatitis B

Hepatitis C Hepatitis E

Accommodating NEC

Viral Hepatitis

Hepatitis A Hepatitis, NECRetired

Hepatitis B

Hepatitis C

Hepatitis E

Hepatitis, NEC

Use and Reuse of Clinical Data

a) Automate the admission of the patient to a bed

b) Summarize the patient’s blood sugar tests, including serum, plasma and fingerstick (but not urine)

c) Use patient history to help with automated reminders

d) Aggregate the patient’s data for quality assurance

e) Use patient history to prevent adverse drug reactions

f) Use the laboratory test results for automated diagnosis

g) Use the patient’s data to automate information retrieval

h) Aggregate the patient’s data for epidemiologic studies






• Include definitional knowledge

• Support automated translation

• Avoid “Not Elsewhere Classified” (NEC)


• MED has features of a high-quality terminology

• MED supports reuse of clinical data

• Try to find high-quality standards

• How do you determine terminology quality?

Documents

Reuse of Data Coded with High-Quality Terminologies: Practical Examples from Patient Care Settings James J. Cimino, M.D. Department of Biomedical Informatics