reuse of data coded with high-quality terminologies: practical examples from patient care settings...
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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”
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
Requirements for High-Quality Terminology
• Synonymy (not redundancy)
• Multiple levels of granularity
• 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
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
Summarize patient’s blood sugar tests, including serum, plasma and fingerstick (but not urine)
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
Use patient history for automated reminders
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
Use patient history for automated reminders
Requirements for High-Quality Terminology
• Synonymy (not redundancy)
• Multiple levels of granularity
• Data model has terms too
• Multiple hierarchies
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
Requirements for High-Quality Terminology
• Synonymy (not redundancy)
• Multiple levels of granularity
• Data model has terms too
• Multiple hierarchies• Include definitional knowledge
Potassium
Hypokalemia
Serum Potassium Test
Serum Specimen
Serum
Abnormalities ofSerum Potassium
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
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
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)
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, 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
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)