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Controlled Terminologies in Patient Care and Research: An Informatics Perspective
James J. Cimino, M.D.Department of Biomedical Informatics
Columbia University
Overview
• Motivation for data encoding: reuse
• Challenges to encoding with controlled terminologies
• Approach at Columbia/NY Presbyterian Hospital
• Desiderata for controlled terminologies
• Successful data reuse at Columbia/NYPH
Problems We Are Trying to Solve
• Collecting data from disparate sources
• Aggregating like data
• Sharing data
• Reusing data– Patient care– Administrative functions– Research– Automated decision support
Information Form and Reuse
21 22 23 24 25 26 27 28 29
7
6
5
4
3
2
1
Information Form and Reuse
Patient Care Data
Research Data
?
Finds what is mentioned but not what is discussed (ambiguity, redundancy,
false positives, false negatives)
Text Processing
Text Images
Patient Care Data
Research Data
Text Images
Natural Language Processing
Feature Extraction
Controlled terminology; distinguishes what is
discussed from what is mentioned (concept
oriented)
Patient Care Data
Research Data
Text Images
Encoded Data
Controlled Terminologies
Gender Causes of Death
ReuseSymbolic
Manipulation
Knowledge Networks
Data Mining
Knowledge
Patient Care
Case PresentationThe patient is a 50 year old female who presents 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 reports that she was treated in the past for tuberculosis while she was pregnant, and that she is allergic to Bufferin.
Physical examination reveals 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 101.3, and a blood pressure of 150/100. Examination reveals rales and rhonchi in the left upper chest.
Labs: Chem7 (serum): Glucose 100Chem7 (plasma): Glucose 150CBC: Hgb 15, Hct 45, WBC 11,000A fingerstick blood sugar was 80Urinalysis showed protein of 1+ and glucose of 0
Chest X-ray: Left upper lobe infiltrate, left ventricular hypertrophy
The patient is started on antibiotics and aspirin and is admitted to the hospital.
A medical student reviewing the case is concerned about patients with pneumonia and myocardial infarction. She decides to do a literature search.
The ER physician is wondering if this patient could be heralding an epidemic.
Reuse of Clinical Dataa) To what bed should the patient be admitted?
b) What were all the results of the patient's blood glucose tests (including serum, plasma and fingerstick)?
c) Does the patient have a history of tuberculosis?
d) Is the patient allergic to any ordered medications?
e) How often are patient with the diagnosis of myocardial infarction started on beta blockers?
f) Can the patient’s data be used by an expert system?
g) Can the patient’s data be used to search health literature?
h) Does the patient represent an index case in an epidemic?
i) Does the patient meet the criteria for a clinical trial of patients over the age of 50 with elevated blood pressure?
To what bed should the patient be admitted?
“Patient is an 50 year old female…”
Admission Discharge Transfer System
“Put the patient in Room 5, Bed B…”
Electronic Medical Record
To what bed should the patient be admitted?
But: how does the computer know the patient is female?
The record could say:
“female”
“Female”
“FEMALE”
“F”
“Woman”
“Girl”
Coding the Data: Gender
• Data element - gender
• Controlled terminology: Male, Female, Unknown
• Representation: M,F,U; 0,1,2
• What about other values?
What’s the Gender?
What are the blood glucose test results?
420 ICD9-CM Tuberculosis Codes (plus 69 hierarchical codes)
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
010.1 PRIMARY TB PLEURISY*
010.8 PRIM PROGRESSIVE TB NEC*
010.9 PRIMARY TB INFECTION NOS*
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*
Does the patient have a history of tuberculosis?
Thirteen TB codes not under 01x.137. 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
Does the patient have a history of tuberculosis?
New York Presbyterian HospitalClinical Information Systems Architecture
Clinical Database
Medical Entities Dictionary
Database Monitor
Medical Logic Modules
DatabaseInterface
Research
Administrative
Alerts & Reminders
Results Review
. . .. . .Radiology LaboratoryDischarge
Summaries
Reformatter Reformatter Reformatter
Medical Entities Dictionary: A Central Terminology Repository
K#1 = 4.2K#1 = 3.3
K#2 = 3.2
K#1 = 3.0
Communicating Terminology Changes
K#1
K#2
K#3 = 2.6
K#3
Patient Care Data
Research Data
Text Images
Encoded Data
Controlled Terminologies
Gender Causes of Death
ReuseSymbolic
Manipulation
Quality Control
Desiderata
Knowledge Networks
Data Mining
Knowledge
Patient Care
Terminology Desiderata
• Concept orientation• Concept permanence• Nonsemantic identifiers• Polyhierarchy• Reject “Not Elsewhere Classified”• Formal definitions
Cimino JJ. Desiderata for controlled medical vocabularies in the Twenty-First Century. Methods of Information in Medicine; 1998;37(4-5):394-403.
Polyhierarchy
disease
cholera meningitis
infectious disease lung disease
tuberculosis
tuberculosis in pregnancy
infectious diseasein pregnancy
K#1 = 4.2K#1 = 3.3
K#2 = 3.2
K#1 = 3.0
Communication with Hierarchies
K#1
K#2
K#3 = 2.6
K#3
K#1 = 4.2K#1 = 3.3
K#2 = 3.2
K#1 = 3.0
Communication with Hierarchies
K#1
K#2
K
K#3
K#3 = 2.6
Reject “Not Elsewhere Classified”
The “Will Rogers Phenomenon”: During the Great Dust Bowl Era, when Oakies moved to California, the IQ in both states increased.
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
Formal Definitions in the MED
MedicalEntity
LaboratoryProcedure
CHEM-7PlasmaGlucose
Test
LaboratorySpecimen
PlasmaSpecimen
Substance
Sampled
Part of
Has S
pecimen
Event
LaboratoryTest
DiagnosticProcedure
Substance MeasuredGlucose
Plasma
AnatomicSubstance
Substance
BioactiveSubstance
Chemical
Carbo-hydrate
MED Data ModelMED Code Slot Code Value 1600 4 32703, 50000 1600 6 "Serum Glucose Measurement" 1600 8 1724 1600 16 31987 1600 18 "mg/dl" 1600 39 "50" 1600 40 "110" 1600 212 "2345-7" 1724 6 "SMAC" 31987 6 "Glucose" 32703 6 "Serum Glucose Tests“ 50000 6 "CPMC Lab Test "
Slot Slot Name 4 SUBCLASS-OF 6 PRINT-NAME 8 PART-OF 16 SUBSTANCE-
MEASURED 18 UNITS 39 LOW-NORMAL-VALUE 40 HIGH-NORMAL-VALUE 212 LOINC-CODE
Concept OrientedConcept Permanence
NonsemanticIdentifier
Polyhier- archy
FormalDefinitions
Using the MED
MED QueryMEDTranslation
TableInterfaceEngine
WebCIS
DecisionSupport
The MED and Messaging
AncillarySystem
LocalCodes
MEDCodes
ClinicalData
Repository
OtherSubscribers
Interface EngineTranslation
Table
Using the MED• Translation
– What is the display name for …?– What is the ICD9 Code for …?– What is the aggregation class for …?
• Translation Tables
• Class-based questions– Is Piroxicam a nonsteroidal antiinflammatory drug?– What are all the antibiotics?
• Knowledge queries– What are the pharmaceutic ingredients of…?
What’s in the MED?• Sunquest lab terms
• Cerner lab terms
• Digimedix drugs
• Cerner Drugs
• Sunquest Radiology
• ICD9-based problem list terms
• Eclipsys order catalogue
• Other applications
• Knowledge terms
The MED Today
• “Concept”-based (102,071)
• Multiple hierarchy (152,508)
• Synonyms (883,095)
• Translations (436,005)
• Semantic links (395,854)
• Attributes (2,030,184)
What are the blood glucose test results?
Using the MED for Summary Reporting
Plasma Glucose Test
Serum Glucose TestFingerstick Glucose Test
Lab Test
Intravascular Glucose Test Chem20 Display
Lab Display
What are the blood glucose test results?
DOP Summary
What are the blood glucose test results?
WebCIS Summary
What are the blood glucose test results?
Eclipsys Summary
What are the blood glucose test results?
Adapting to Changing Requirements
• Labs ordered as panels of tests
• HCFA will only reimburse for tests
• Clinicians have to order tests separately
• But: they want to review them as panels
• Changing the architecture:– Order tests separately– Group them for display– 2 FTEs– 4 months of work
• Solution: 5 minute change in the MED
Lab Tests and Procedures in the MED
Chem7 SMAC
Lab Procedures
CBC
Lab Tests
GlucoseSodium Hematocrit
Lab Tests and Procedures in the MED
Lab Tests
GlucoseSodium
Chem7 SMAC
Lab Procedures
CBC
Hematocrit
OrderableTests
1) Check the drugs’ allergy codes, or…
2) Infer the allergy codes from the MED, or…
3) Use formal definitions in the MED to check ingredients
Bufferin Enteric-Coated Aspirin
Aspirin PreparationsAspirin
has-ingredient
Allergy: Bufferin
Ordered Medications: Enteric-Coated Aspirin
If ingredient of allergic drug equals ingredient of ordered drug, then send alert
Is the patient allergic to any ordered medications?
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
Does the patient have a history of tuberculosis?
How often are patient with the diagnosis of myocardial infarction started on beta blockers?
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
How often are patient with the diagnosis of myocardial infarction started on beta blockers?
Potassium
Hypokalemia
Serum Potassium Test
Serum Specimen
Serum
Abnormalities ofSerum Potassium
Can the patient’s data be used by an expert system?
Can the patient’s data be used by an expert system?
Can the patient’s data be used by an expert system?
Can the patient’s data be used by an expert system?
Gentamicin
InjectableGentamicin
Gentamicn Sensitivity
Test
SerumGentamicin
Level
GentamicinToxicity
EtiologyMeasures
Sensitivity
Substance Measured Has ingredient
DrugInformation
ExpertSystem
PubMed
Can the patient’s data be used to search health literature?
LabManual
Patient Care Data
Research Data
Text Images
Encoded Data
Controlled Terminologies
Gender Causes of Death
ReuseSymbolic
Manipulation
Quality Control
Desiderata
Knowledge Networks
Data Mining
Knowledge
Patient Care
Reuse of Clinical Data
Reuse of Clinical Dataa) To what bed should the patient be admitted?
b) What were all the results of the patient's blood glucose tests (including serum, plasma and fingerstick)?
c) Does the patient have a history of tuberculosis?
d) Is the patient allergic to any ordered medications?
e) How often are patient with the diagnosis of myocardial infarction started on beta blockers?
f) Can the patient’s data be used by an expert system?
g) Can the patient’s data be used to search health literature?
h) Does the patient represent an index case in an epidemic?
i) Does the patient meet the criteria for a clinical trial of patients over the age of 50 with elevated blood pressure?
Terminology is key to data integration and reuse
High-quality terminology supports high-quality data integration and reuse
“Desiderata” facilitate high quality
Columbia/NYPH Medical Entities DictionaryServes as a repository for institutional and standard
terminologiesUses multihierarchy semantic networkSupports sophisticated data integrationSupports sophisticated data reuse
Conclusions
Questions?