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

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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.

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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.

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Use and Reuse of Clinical Data

• a) Automate the admission of the patient to a bed
• b) Summarize the patients blood sugar tests,
  including serum, plasma and fingerstick (but not
  urine)
• c) Use patient history to help with automated
  reminders
• d) Aggregate the patients 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 patients data to automate information
  retrieval
• h) Aggregate the patients data for epidemiologic
  studies

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Automate the admission of the patient to a bed

• Patient is an 50 year old, Native American
  female

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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

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Automate the admission of the patient to a bed

• Data element - gender
• Controlled terminology
• Male
• Female
• Unknown (dont know)
• Unknown (cant tell)
• Representation
• M,F,U1,U2
• 0,1,2,3
• What about other values?
• Genotypic
• Phenotypic
• Administrative

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Automate the admission of the patient to a bed
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Requirements for High-Quality Terminology

• Synonymy (not redundancy)
• Multiple levels of granularity

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Information Form and Reuse
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Information Form and Reuse
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Summarize patients blood sugar tests, including
serum, plasma and fingerstick (but not urine)
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Requirements for High-Quality Terminology

• Synonymy (not redundancy)
• Multiple levels of granularity

• Data model has terms too

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New York Presbyterian HospitalClinical
Information Systems Architecture
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MED Structure
Medical Entity
CHEM-7
Plasma Glucose Test
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The MED Today

• Concept-based (101,130)
• Multiple hierarchy (150,480)
• Synonyms (250,000)
• Translations (180,000)
• Semantic links (180,000)
• Attributes (240,000)

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Using the MED for Summary Reporting
Lab Display
Serum Glucose Test
Fingerstick Glucose Test
Plasma Glucose Test
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DOP Summary
Summarize patients blood sugar tests, including
serum, plasma and fingerstick (but not urine)
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WebCIS Summary
Summarize patients blood sugar tests, including
serum, plasma and fingerstick (but not urine)
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Eclipsys Summary
Summarize patients blood sugar tests, including
serum, plasma and fingerstick (but not urine)
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489 Tuberculosis Codes in ICD9-CM
Use patient history for automated reminders
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
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More Tuberculosis in ICD9-CM
Use patient history for automated reminders

• 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

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Use patient history for automated reminders
Tuberculosis Infection
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Requirements for High-Quality Terminology

• Synonymy (not redundancy)
• Multiple levels of granularity
• Data model has terms too

• Multiple hierarchies

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Reuse the patients data for quality assurance
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Reuse the patients 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
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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
Bufferin
Enteric-Coated Aspirin
IF allergic drug X has ingredient Y AND
ordered drug Z has ingredient Y THEN send
alert
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Requirements for High-Quality Terminology

• Synonymy (not redundancy)
• Multiple levels of granularity
• Data model has terms too
• Multiple hierarchies

• Include definitional knowledge

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Use test results for automated diagnosis
Serum Potassium Test
Hypokalemia
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Use test results for automated diagnosis
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Use test results for automated diagnosis
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Use test results for automated diagnosis
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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

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Use data for automated information retrieval
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Reuse the patients data for epidemiologic studies
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
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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)

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Reuse the patients data for epidemiologic studies
NEC

• Can never have a formal definition
• Terminology changes induce semantic drift

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Accommodating NEC
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Accommodating NEC
Viral Hepatitis
Hepatitis A
Hepatitis, NEC
Hepatitis B
Hepatitis E
Hepatitis C
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Accommodating NEC
Viral Hepatitis
Hepatitis A
Retired
Hepatitis B
Hepatitis C
Hepatitis E
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Use and Reuse of Clinical Data

• a) Automate the admission of the patient to a bed
• b) Summarize the patients blood sugar tests,
  including serum, plasma and fingerstick (but not
  urine)
• c) Use patient history to help with automated
  reminders
• d) Aggregate the patients 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 patients data to automate information
  retrieval
• h) Aggregate the patients data for epidemiologic
  studies

52
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)

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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?