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Controlled Terminologies in Patient Care and Research: An Informatics Perspective

This informative text discusses the importance of controlled terminologies in encoding patient data for reuse in healthcare and research. It also explores the challenges and approaches to using controlled terminologies in data collection, aggregation, sharing, and automated decision support. The text provides examples of how controlled terminologies can improve data reuse in patient care, administrative functions, and research.

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Controlled Terminologies in Patient Care and Research: An Informatics Perspective

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  1. Controlled Terminologies in Patient Care and Research: An Informatics Perspective James J. Cimino, M.D.Department of Biomedical InformaticsColumbia University

  2. Overview • 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

  3. Problems 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

  4. Information Form and Reuse

  5. 7 6 5 4 3 2 1 21 22 23 24 25 26 27 28 29 Information Form and Reuse

  6. Research Data Patient Care Data Text Images Text Processing ? Finds what is mentioned but not what is discussed (ambiguity, redundancy, false positives, false negatives)

  7. Controlled terminology; distinguishes what is discussed from what is mentioned (concept oriented) Research Data Patient Care Data Text Images Natural Language Processing Feature Extraction

  8. Knowledge Data Mining Knowledge Networks Symbolic Manipulation Encoded Data Reuse Patient Care Controlled Terminologies Causes of Death Gender Research Data Patient Care Data Text Images

  9. Case 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.

  10. Reuse 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 patient’s data be used by an expert system? • Can the patient’s 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?

  11. Electronic Medical Record Admission Discharge Transfer System “Put the patient in Room 5, Bed B…” To what bed should the patient be admitted? “Patient is an 50 year old female…”

  12. To 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”

  13. Coding the Data: Gender • Data element - gender • Controlled terminology: Male, Female, Unknown • Representation: M,F,U; 0,1,2 • What about other values?

  14. What’s the Gender?

  15. What are the blood glucose test results?

  16. Does the patient have a history of tuberculosis? 420 ICD9-CM Tuberculosis Codes (plus 69 hierarchical codes) 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* 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*

  17. Does the patient have a history of tuberculosis? Thirteen TB codes not under 01x. 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

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

  19. Medical Entities Dictionary: A Central Terminology Repository

  20. K#1 = 4.2 K#1 = 3.3 K#2 = 3.2 K#1 = 3.0 K#3 = 2.6 K#1 K#2 K#3 Communicating Terminology Changes

  21. Knowledge Data Mining Knowledge Networks Symbolic Manipulation Encoded Data Reuse Patient Care Controlled Terminologies Quality Control Desiderata Causes of Death Gender Research Data Patient Care Data Text Images

  22. Terminology Desiderata Cimino JJ. Desiderata for controlled medical vocabularies in the Twenty-First Century. Methods of Information in Medicine; 1998;37(4-5):394-403. • Concept orientation • Concept permanence • Nonsemantic identifiers • Polyhierarchy • Reject “Not Elsewhere Classified” • Formal definitions

  23. cholera meningitis tuberculosis infectious disease in pregnancy tuberculosis in pregnancy Polyhierarchy disease infectious disease lung disease

  24. K#1 = 4.2 K#1 = 3.3 K#2 = 3.2 K#1 = 3.0 K#3 = 2.6 K#1 K#2 K#3 Communication with Hierarchies

  25. K#1 = 4.2 K#1 = 3.3 K#2 = 3.2 K#1 = 3.0 K#3 = 2.6 K K#3 Communication with Hierarchies K#1 K#2

  26. Reject “Not Elsewhere Classified” 1995 1996 The “Will Rogers Phenomenon”: During the Great Dust Bowl Era, when Oakies moved to California, the IQ in both states increased.

  27. Substance Laboratory Specimen Event Chemical Anatomic Substance Plasma Specimen Diagnostic Procedure Substance Sampled Plasma Laboratory Test Laboratory Procedure Has Specimen Carbo- hydrate Bioactive Substance Part of Glucose Substance Measured Formal Definitions in the MED Medical Entity CHEM-7 Plasma Glucose Test

  28. Polyhier- archy Formal Definitions Concept Oriented Concept Permanence Nonsemantic Identifier MED Data Model MED CodeSlot CodeValue 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 " SlotSlot 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

  29. WebCIS QueryMED Translation Table Interface Engine Decision Support Using the MED MED

  30. Clinical Data Repository Interface Engine Translation Table Local Codes MED Codes Other Subscribers The MED and Messaging Ancillary System

  31. Using 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…?

  32. What’s 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

  33. The MED Today • “Concept”-based (102,071) • Multiple hierarchy (152,508) • Synonyms (883,095) • Translations (436,005) • Semantic links (395,854) • Attributes (2,030,184)

  34. What are the blood glucose test results?

  35. Lab Display Lab Test Intravascular Glucose Test What are the blood glucose test results? Using the MED for Summary Reporting Chem20 Display Fingerstick Glucose Test Serum Glucose Test Plasma Glucose Test

  36. What are the blood glucose test results? DOP Summary

  37. What are the blood glucose test results? WebCIS Summary

  38. What are the blood glucose test results? Eclipsys Summary

  39. Adapting 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

  40. Lab Procedures Lab Tests Chem7 CBC SMAC Hematocrit Glucose Sodium Lab Tests and Procedures in the MED

  41. Lab Tests and Procedures in the MED Lab Procedures Lab Tests Chem7 CBC Orderable Tests SMAC Hematocrit Glucose Sodium

  42. has-ingredient Aspirin Preparations Aspirin Is 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

  43. Infective Disease in Pregnancy (647) Primary TB (010) Pulmonary TB (011) Other Resp TB (012) Late Effect TB (137) TB in Preg (647.3) Primary TB Complex 010.0 Primary TB Pleurisy 010.1 Primary TB Complex No Exam 010.01 Primary TB Pleurisy No Exam 010.11 Primary TB Pleurisy Uspec 010.10 Primary TB Complex Uspec 010.00 Does the patient have a history of tuberculosis? Tuberculosis Infection

  44. How often are patient with the diagnosis of myocardial infarction started on beta blockers?

  45. How 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

  46. Serum Specimen Abnormalities of Serum Potassium Potassium Serum Hypokalemia Can the patient’s data be used by an expert system? Serum Potassium Test

  47. Can the patient’s data be used by an expert system?

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