1. 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

2. 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.

3. 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.

4. 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

5. 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

6. 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

7. 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

9. Requirements for High-Quality Terminology Synonymy (not redundancy) Multiple levels of granularity

10. Information Form and Reuse

11. 21 22 23 24 25 26 27 28 29 76543217654321

12. Summarize patient’s blood sugar tests, including serum, plasma and fingerstick (but not urine)

13. Requirements for High-Quality Terminology Synonymy (not redundancy) Multiple levels of granularity Data model has terms too

14. New York Presbyterian Hospital Clinical Information Systems Architecture Clinical Database Medical Entities Dictionary (MED) Database Monitor Medical Logic Modules Database Interface Research Administrative Alerts & Reminders Results Review... Radiology Laboratory Discharge Summaries Reformatter

15. MED Structure Medical Entity Laboratory Procedure CHEM-7 Plasma Glucose Test Laboratory Specimen Plasma Specimen Substance Sampled Part of Has Specimen Event Laboratory Test Diagnostic Procedure Substance Measured Glucose Plasma Anatomic Substance Bioactive Substance Chemical Carbohydrate

16. The MED Today Concept-based (101,130) Multiple hierarchy (150,480) Synonyms (250,000) Translations (180,000) Semantic links (180,000) Attributes (240,000)

17. Using the MED for Summary Reporting Plasma Glucose Test Serum Glucose TestFingerstick Glucose Test Lab Test Intravascular Glucose Test Lab Display Chem20 Display

21. DOP Summary Summarize patient’s blood sugar tests, including serum, plasma and fingerstick (but not urine)

22. WebCIS Summary Summarize patient’s blood sugar tests, including serum, plasma and fingerstick (but not urine)

23. Eclipsys Summary Summarize patient’s blood sugar tests, including serum, plasma and fingerstick (but not urine)

24. 489 Tuberculosis Codes in ICD9-CM 010.PRIMARY TB INFECTION* 010.0PRIMARY TB COMPLEX* 010.00PRIM TB COMPLEX-UNSPEC 010.01PRIM TB COMPLEX-NO EXAM 010.02PRIM TB COMPLEX-EXM UNKN 010.03PRIM TB COMPLEX-MICRO DX 010.04PRIM TB COMPLEX-CULT DX 010.05PRIM TB COMPLEX-HISTO DX 010.06PRIM 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 010.1PRIMARY TB PLEURISY* 010.8PRIM PROGRESSIVE TB NEC* 010.9PRIMARY TB INFECTION NOS*

25. More Tuberculosis in ICD9-CM 137.LATE EFFECT TUBERCULOSIS* 137.0LATE EFFECT TB, RESP/NOS 137.1LATE EFFECT CNS TB 137.2LATE EFFECT GU TB 137.3LATE EFF BONE & JOINT TB 137.4LATE EFFECT TB NEC 647.INFECTIVE DIS IN PREG* 647.3TUBERCULOSIS IN PREG* 647.30TB IN PREG-UNSPECIFIED 647.31TUBERCULOSIS-DELIVERED 647.32TUBERCULOSIS-DELIV W P/P 647.33TUBERCULOSIS-ANTEPARTUM 647.34TUBERCULOSIS-POSTPARTUM Use patient history for automated reminders

26. Tuberculosis Infection Primary TB Pleurisy 010.1 Primary TB Complex 010.0 Primary TB (010) Pulmonary TB (011) Other Resp TB (012) Primary TB Pleurisy No Exam 010.11 Primary TB Pleurisy Uspec 010.10 Late Effect TB (137) TB in Preg (647.3) Infective Disease in Pregnancy (647) Primary TB Complex No Exam 010.01 Primary TB Complex Uspec 010.00 Use patient history for automated reminders

27. Requirements for High-Quality Terminology Synonymy (not redundancy) Multiple levels of granularity Data model has terms too Multiple hierarchies

28. Reuse the patient’s data for quality assurance

29. 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

30. 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 Preparations Aspirin 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

31. Requirements for High-Quality Terminology Synonymy (not redundancy) Multiple levels of granularity Data model has terms too Multiple hierarchies Include definitional knowledge

32. Potassium Hypokalemia Serum Potassium Test Serum Specimen Serum Abnormalities of Serum Potassium Use test results for automated diagnosis

36. 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

37. Use data for automated information retrieval Injectable Gentamicin Gentamicn Sensitivity Test Serum Gentamicin Level Gentamicin Toxicity Gentamicin Etiology Measures Sensitivity Substance Measured Has ingredient Decision Rule Expert System Drug Information Clinical Data

45. 1995 DiagnosisICD9-CM Code ICD9-CM Name Hepatitis A070.1Hepatitis A Hepatitis B070.3Hepatitis B Hepatitis C070.5Hepatitis NEC Hepatitis E070.5Hepatitis NEC 1996 DiagnosisICD9-CM Code ICD9-CM Name Hepatitis A070.1Hepatitis A Hepatitis B070.3Hepatitis B Hepatitis C070.4Hepatitis C Hepatitis E070.5Hepatitis NEC Reuse the patient’s data for epidemiologic studies

46. 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)

47. NEC Reuse the patient’s data for epidemiologic studies Can never have a formal definition Terminology changes induce semantic drift

48. Accommodating NEC Viral Hepatitis Hepatitis A Hepatitis BHepatitis CHepatitis E

49. Accommodating NEC Viral Hepatitis Hepatitis A Hepatitis, NEC Hepatitis B Hepatitis C Hepatitis E

50. Accommodating NEC Viral Hepatitis Hepatitis A Hepatitis, NEC Retired Hepatitis B Hepatitis C Hepatitis E Hepatitis, NEC

51. 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

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)

53. 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?