Transcript Reuse of Data Coded with High

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 Presentation
The 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 80
Urinalysis showed protein of 1+ and glucose of 0
A blood culture was positive for methicillin-resistant Staphylococcus aureus (MRSA)
ECG - Sinus Rhythm, 74BPM, Axis -30 degrees, ST segment 2mm elevated and
T-waves down in leads I, L, V5 and V6
Chest X-ray Left upper lobe infiltrate, left ventricular hypertrophy
The 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 Presentation
The 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 80
Urinalysis showed protein of 1+ and glucose of 0
A blood culture was positive for methicillin-resistant Staphylococcus aureus (MRSA)
ECG - Sinus Rhythm, 74BPM, Axis -30 degrees, ST segment 2mm elevated and
T-waves down in leads I, L, V5 and V6
Chest X-ray Left upper lobe infiltrate, left ventricular hypertrophy
The 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…”
Electronic
Medical
Record
Admission
Discharge
Transfer
System
“Put the patient in
Room 5, Bed B…”
Automate the admission of the patient to a bed
But: how does the computer know that the
patient is female?
The record could say:
“female”
“Female”
“FEMALE”
“F”
“Woman”
“Girl”
Automate the admission of the patient to a bed
• 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
Automate the admission of the patient to a bed
Requirements for High-Quality Terminology
• Synonymy (not redundancy)
• Multiple levels of granularity
Information Form and Reuse
Information Form and Reuse
7
6
5
4
3
2
1
21 22 23 24 25 26 27 28 29
Summarize patient’s blood sugar tests, including
serum, plasma and fingerstick (but not urine)
Requirements for High-Quality Terminology
• Synonymy (not redundancy)
• Multiple levels of granularity
• Data model has terms too
New York Presbyterian Hospital
Clinical Information Systems Architecture
Medical Logic
Modules
Clinical Database
Alerts & Reminders
Database Monitor
Results Review
Database
Interface
Medical Entities
Dictionary (MED)
Administrative
Research
Reformatter
...
Radiology
Reformatter
Discharge
Summaries
Reformatter
Laboratory
...
MED Structure
Medical
Entity
Substance
Chemical
Laboratory
Specimen
Anatomic
Substance
Plasma
Carbohydrate
Bioactive
Substance
Glucose
Plasma
Specimen
Event
Diagnostic
Procedure
Laboratory
Test
Plasma
Glucose
Test
Laboratory
Procedure
CHEM-7
Part of
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
Lab Display
Lab Test
Intravascular Glucose Test
Fingerstick Glucose Test
Serum Glucose Test
Plasma Glucose Test
Chem20 Display
Summarize patient’s blood sugar tests, including
serum, plasma and fingerstick (but not urine)
DOP Summary
Summarize patient’s blood sugar tests, including
serum, plasma and fingerstick (but not urine)
WebCIS Summary
Summarize patient’s blood sugar tests, including
serum, plasma and fingerstick (but not urine)
Eclipsys Summary
Use patient history for automated reminders
489 Tuberculosis Codes in ICD9-CM
010.
010.0
010.00
010.01
010.02
010.03
010.04
010.05
010.06
010.1
010.8
010.9
PRIMARY TB INFECTION*
PRIMARY TB COMPLEX*
PRIM TB COMPLEX-UNSPEC
PRIM TB COMPLEX-NO EXAM
PRIM TB COMPLEX-EXM UNKN
PRIM TB COMPLEX-MICRO DX
PRIM TB COMPLEX-CULT DX
PRIM TB COMPLEX-HISTO DX
PRIM TB COMPLEX-OTH TEST
PRIMARY TB PLEURISY*
PRIM PROGRESSIVE TB NEC*
PRIMARY TB INFECTION NOS*
011.
012.
013.
014.
015.
016.
017.
018.
PULMONARY TUBERCULOSIS*
OTHER RESPIRATORY TB*
CNS TUBERCULOSIS*
INTESTINAL TB*
TB OF BONE AND JOINT*
GENITOURINARY TB*
TUBERCULOSIS NEC*
MILIARY TUBERCULOSIS*
Use patient history for automated reminders
More Tuberculosis in ICD9-CM
137.
137.0
137.1
137.2
137.3
137.4
647.
647.3
647.30
647.31
647.32
647.33
647.34
LATE EFFECT TUBERCULOSIS*
LATE EFFECT TB, RESP/NOS
LATE EFFECT CNS TB
LATE EFFECT GU TB
LATE EFF BONE & JOINT TB
LATE EFFECT TB NEC
INFECTIVE DIS IN PREG*
TUBERCULOSIS IN PREG*
TB IN PREG-UNSPECIFIED
TUBERCULOSIS-DELIVERED
TUBERCULOSIS-DELIV W P/P
TUBERCULOSIS-ANTEPARTUM
TUBERCULOSIS-POSTPARTUM
Use patient history for automated reminders
Tuberculosis
Infection
Primary
TB (010)
Primary TB
Complex 010.0
Primary TB
Complex
Uspec
010.00
Pulmonary
TB (011)
Other Resp
TB (012)
Infective Disease
in Pregnancy (647)
Late Effect
TB (137)
Primary TB
Pleurisy 010.1
Primary TB
Complex
No Exam
010.01
Primary TB
Pleurisy
Uspec
010.10
Primary TB
Pleurisy
No Exam
010.11
TB in
Preg (647.3)
Requirements for High-Quality Terminology
• Synonymy (not redundancy)
• Multiple levels of granularity
• Data model has terms too
• Multiple hierarchies
Reuse the patient’s data for quality assurance
Reuse the patient’s data for quality assurance
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
MI
MI+Beta
2000
2001
2002
2003
2004
Use patient history to prevent drug reactions
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
Aspirin Preparations
Bufferin
has-ingredient
Aspirin
Enteric-Coated Aspirin
IF allergic drug [X] has ingredient [Y]
AND ordered drug [Z] has ingredient [Y]
THEN send alert
Requirements for High-Quality Terminology
• Synonymy (not redundancy)
• Multiple levels of granularity
• Data model has terms too
• Multiple hierarchies
• Include definitional knowledge
Use test results for automated diagnosis
Serum Potassium Test
Serum Specimen
Abnormalities of
Serum Potassium
Serum
Potassium
Hypokalemia
Use test results for automated diagnosis
Use test results for automated diagnosis
Use test results for automated diagnosis
Requirements for High-Quality Terminology
• Synonymy (not redundancy)
• Multiple levels of granularity
• Data model has terms too
• Multiple hierarchies
• Include definitional knowledge
• Support automated translation
Use data for automated information retrieval
Clinical Data
Injectable
Gentamicin
Serum
Gentamicin
Level
Gentamicin
Gentamicn
Sensitivity
Test
Decision
Rule
Gentamicin
Toxicity
Drug
Information
Expert
System
Reuse the patient’s data for epidemiologic studies
1995
Diagnosis ICD9-CM
Code
1996
ICD9-CM
Name
Diagnosis ICD9-CM
Code
ICD9-CM
Name
Hepatitis A
070.1
Hepatitis A
Hepatitis A
070.1
Hepatitis A
Hepatitis B
070.3
Hepatitis B
Hepatitis B
070.3
Hepatitis B
Hepatitis C
070.5
Hepatitis NEC
Hepatitis C
070.4
Hepatitis C
Hepatitis E
070.5
Hepatitis NEC
Hepatitis E
070.5
Hepatitis NEC
Viral Hepatitis Mortality
070.1
070.3
070.5
1994
1995
1996
Requirements for High-Quality Terminology
• Synonymy (not redundancy)
• Multiple levels of granularity
• Data model has terms too
• Multiple hierarchies
• Include definitional knowledge
• Support automated translation
• Avoid “Not Elsewhere Classified” (NEC)
Reuse the patient’s data for epidemiologic studies
NEC
• 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 B
Hepatitis C
Hepatitis, NEC
Hepatitis E
Accommodating NEC
Viral Hepatitis
Hepatitis A
Hepatitis B
Hepatitis C
Hepatitis, NEC
Hepatitis, NEC
Hepatitis E
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
Requirements for High-Quality Terminology
• Synonymy (not redundancy)
• Multiple levels of granularity
• Data model has terms too
• Multiple hierarchies
• Include definitional knowledge
• Support automated translation
• Avoid “Not Elsewhere Classified” (NEC)
Requirements for High-Quality Terminology
• 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?