Title: Controlled Terminologies in Patient Care and Research: An Informatics Perspective
1Controlled Terminologies in Patient Care and
Research An Informatics Perspective
James J. Cimino, M.D.Department of Biomedical
InformaticsColumbia University
2Overview
- 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
3Problems 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
4Information Form and Reuse
5Information Form and Reuse
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7Research Data
Patient Care Data
Text
Images
Natural Language Processing
Feature Extraction
8Research Data
Patient Care Data
Text
Images
9Case Presentation
- The 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 100
- Chem7 (plasma) Glucose 150
- CBC Hgb 15, Hct 45, WBC 11,000
- A fingerstick blood sugar was 80
- Urinalysis 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.
10Reuse of Clinical Data
- To what bed should the patient be admitted?
- What were all the results of the patient's blood
glucose tests (including serum, plasma and
fingerstick)? - Does the patient have a history of tuberculosis?
- Is the patient allergic to any ordered
medications? - How often are patient with the diagnosis of
myocardial infarction started on beta blockers? - Can the patients data be used by an expert
system? - Can the patients data be used to search health
literature? - Does the patient represent an index case in an
epidemic? - Does the patient meet the criteria for a clinical
trial of patients over the age of 50 with
elevated blood pressure?
11To what bed should the patient be admitted?
- Patient is an 50 year old female
12To 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
13Coding the Data Gender
- Data element - gender
- Controlled terminology Male, Female, Unknown
- Representation M,F,U 0,1,2
- What about other values?
14Whats the Gender?
15What are the blood glucose test results?
16420 ICD9-CM Tuberculosis Codes (plus 69
hierarchical codes)
Does the patient have a history of tuberculosis?
011. PULMONARY TUBERCULOSIS 012. OTHER
RESPIRATORY TB 013. CNS TUBERCULOSIS 014. INTEST
INAL TB 015. TB OF BONE AND JOINT 016. GENITOURI
NARY TB 017. TUBERCULOSIS NEC 018. MILIARY
TUBERCULOSIS
- 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
17Thirteen TB codes not under 01x.
Does the patient have a history of tuberculosis?
- 137. LATE EFFECT TUBERCULOSIS
- 137.0 LATE EFFECT TB, RESP/NOS
- 137.1 LATE EFFECT CNS TB
- 137.2 LATE EFFECT GU TB
- 137.3 LATE EFF BONE JOINT TB
- 137.4 LATE EFFECT TB NEC
- 647. INFECTIVE DIS IN PREG
- 647.3 TUBERCULOSIS IN PREG
- 647.30 TB IN PREG-UNSPECIFIED
- 647.31 TUBERCULOSIS-DELIVERED
- 647.32 TUBERCULOSIS-DELIV W P/P
- 647.33 TUBERCULOSIS-ANTEPARTUM
- 647.34 TUBERCULOSIS-POSTPARTUM
18New York Presbyterian HospitalClinical
Information Systems Architecture
19Medical Entities Dictionary A Central
Terminology Repository
20Communicating Terminology Changes
21Research Data
Patient Care Data
Text
Images
22Terminology Desiderata
Cimino JJ. Desiderata for controlled medical
vocabularies in the Twenty-First Century.
Methods of Information in Medicine
199837(4-5)394-403.
- Concept orientation
- Concept permanence
- Nonsemantic identifiers
- Polyhierarchy
- Reject Not Elsewhere Classified
- Formal definitions
23Polyhierarchy
disease
infectious disease
lung disease
24Communication with Hierarchies
25Communication with Hierarchies
K1
K2
26Reject Not Elsewhere Classified
1995
1996
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
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
- The Will Rogers Phenomenon During the Great
Dust Bowl Era, when Oakies moved to California,
the IQ in both states increased.
27Formal Definitions in the MED
Medical Entity
CHEM-7
Plasma Glucose Test
28MED Data Model
MED 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
29Using the MED
MED
30The MED and Messaging
Ancillary System
31Using 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?
32Whats 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
33The MED Today
- Concept-based (102,071)
- Multiple hierarchy (152,508)
- Synonyms (883,095)
- Translations (436,005)
- Semantic links (395,854)
- Attributes (2,030,184)
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37What are the blood glucose test results?
38Using the MED for Summary Reporting
What are the blood glucose test results?
Chem20 Display
Serum Glucose Test
Fingerstick Glucose Test
Plasma Glucose Test
39DOP Summary
What are the blood glucose test results?
40WebCIS Summary
What are the blood glucose test results?
41Eclipsys Summary
What are the blood glucose test results?
42Adapting 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
43Lab Tests and Procedures in the MED
44Lab Tests and Procedures in the MED
Lab Procedures
Lab Tests
Chem7
SMAC
CBC
Orderable Tests
Hematocrit
Glucose
Sodium
45Is the patient allergic to any ordered
medications?
- Check the drugs allergy codes, or
- Infer the allergy codes from the MED, or
- Use formal definitions in the MED to check
ingredients
Allergy Bufferin Ordered Medications
Enteric-Coated Aspirin If ingredient of allergic
drug equals ingredient of ordered drug, then send
alert
Bufferin
Enteric-Coated Aspirin
46Does the patient have a history of tuberculosis?
Tuberculosis Infection
47How often are patient with the diagnosis of
myocardial infarction started on beta blockers?
48How often are patient with the diagnosis of
myocardial infarction started on beta blockers?
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
49Can the patients data be used by an expert
system?
Serum Potassium Test
50Can the patients data be used by an expert
system?
51Can the patients data be used by an expert
system?
52Can the patients data be used by an expert
system?
53Can the patients data be used to search health
literature?
Injectable Gentamicin
Serum Gentamicin Level
Gentamicin
Gentamicn Sensitivity Test
Gentamicin Toxicity
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61Reuse of Clinical Data
Research Data
Patient Care Data
Text
Images
62Reuse of Clinical Data
- To what bed should the patient be admitted?
- What were all the results of the patient's blood
glucose tests (including serum, plasma and
fingerstick)? - Does the patient have a history of tuberculosis?
- Is the patient allergic to any ordered
medications? - How often are patient with the diagnosis of
myocardial infarction started on beta blockers? - Can the patients data be used by an expert
system? - Can the patients data be used to search health
literature? - Does the patient represent an index case in an
epidemic? - Does the patient meet the criteria for a clinical
trial of patients over the age of 50 with
elevated blood pressure?
63Conclusions
- 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 Dictionary
- Serves as a repository for institutional and
standard terminologies - Uses multihierarchy semantic network
- Supports sophisticated data integration
- Supports sophisticated data reuse
64 Questions?