Clinical Terminologies for Research

1. Clinical Terminologies for Research S. Trent Rosenbloom, MD MPH Assistant Professor, Department of Biomedical Informatics Assistant Professor in Clinical Nursing, School of Nursing Adjunct Faculty, Departments of Internal Medicine & Pediatrics Vanderbilt University Medical Center, Nashville, TN, USA

2. Pithy Quote Water, water, everywhere, and all the boards did shrink; Water, water, everywhere, nor any drop to drink. Samuel Taylor Coleridge, The Rime of the Ancient Mariner, 1798

3. Significance • There is a lot of patient data in clinical documents (i.e., Water, water, everywhere) • Most data is difficult to extract for research or automation of routine operational tasks (i.e., nor any drop to drink) • Terminologies may improve the accessibility of clinical data.

4. What is a Terminology? • In my research database: • “Myocardial Infarction” • “Heart Attack” • In another researcher’s database • “Myocardial Infarct” This leads to problems of ambiguity and with interoperability

5. What is a Terminology? • The problem is not just theoretical: • At our institution, weight is stored in at least ten formats within the same EHR system • WizOrder (>3) • StarPanel • StarNotes • StarForms (?n) • Quill (can reuse data, user does not always opt for this) • Dictations • Research intake forms (?n) • Others? • How do I perform efficient HSR and QA?

6. What is a Terminology? Morning Star Evening Star The second planet from the sun, having an average radius of 6,052 kilometers (3,761 miles), a mass 0.815 times that of Earth, and a sidereal period of revolution about the sun of 224.7 days at a mean distance of approximately 108.2 million kilometers (67.2 million miles).

7. What is a Terminology? Physical Entity The second planet from the sun, having an average radius of 6,052 kilometers (3,761 miles), a mass 0.815 times that of Earth, and a sidereal period of revolution about the sun of 224.7 days at a mean distance of approximately 108.2 million kilometers (67.2 million miles). Representative Terms Conceptual Experience Morning Star Evening Star Venus Adapted from Campbell, ‘Representing thoughts, words, and things in the UMLS’, 1998.

8. What is a Terminology? Planets of the Solar System inside outside Mercury Jupiter Venus Saturn Earth Neptune

9. What is a Terminology? • Terminologies are formal representations of entities and their interrelationships. • Embodied as concepts and terms • Concepts are universal definitional meanings • Terms are evocative words or phrases.

10. What is a Terminology? Concept: Myocardial Infarction CUI: C0027051 Semantic Type: Disease or Syndrome Entity: Gross necrosis of the myocardium, as a result of interruption of the blood supply to the area. (Dorland, 27th ed) Representative Terms (synonyms): • Myocardial Infarction • Attack coronary • Cardiac infarction • Heart attack • Infarction of heart • MI • MI - Myocardial infarction • Myocardial Infarct • Myocardial infarction (disorder) • Myocardial infarction syndrome • myocardium; infarction • More Specific Concepts (children): • Acute myocardial infarction • Old myocardial infarction • Microinfarct of heart • True posterior wall infarction • Aborted myocardial infarction • Other specified anterior myocardial infarction • Silent myocardial infarction • Subsequent myocardial infarction • Postoperative myocardial infarction • First myocardial infarction • Myocardial infarction with complication • Non-Q wave myocardial infarction Adapted from the UMLS Metathesaurus.

11. What is a Terminology? • Best terminology practices can help improve research data in terms of: • Interoperability • Clarity • Consistency • Query-ability (accuracy and precision) • Manipulability

12. What is a Terminology? • Terminology Desiderata • Statement of purpose, scope, and comprehensiveness • Complete coverage of domain specific content • Use of concepts rather than terms, phrases and words (concept orientation) • Concepts do not change with time, view or use (concept consistency) • Concepts must evolve with change in knowledge • Concepts identified through nonsense identifiers (context-free identifier) • Representation of concept context consistently from multiple hierarchies • Concepts have single explicit formal definitions • Support for multiple levels of concept detail • Absence of or methods to identify duplication, ambiguity, and synonymy • Integration with other terminologies • Mapping to administrative terminologies • Bottom line: comprehensively represents a medical domain with all the concepts it contains, called Completeness Adapted from Cimino, ‘Desiderata for controlled medical vocabularies in the twenty-first century’, 1998.

13. What is a Terminology? • Completeness achieved by one of two ways • Post-coordination - complex concepts from different levels of detail are composed as needed from fundamental concepts (e.g., ‘chest pain’ composed from the concepts ‘chest’ and ‘pain’ when needed) • Pre-coordination - all levels of detail are modeled with distinct concepts (e.g., ‘chest pain’, ‘substernal chest pain’, and ‘crushing substernal chest pain’ are all in the terminology)

14. What is a Terminology?

15. What is a Terminology? • Completeness measured by Coverage: • coverage calculated as the proportion of concepts covered by a terminology • multiple studies: post-coordinated terminologies generally have better coverage than pre-coordinated terminologies

16. What is a Terminology? • Consequences of post-coordination: • Inefficient post-coordination: “too cumbersome for complex problem entry” • Nonsensical Concepts • Concept duplication

17. What is a Terminology? • Terminologies come in different flavors Interface Terminology Adapted from Chute, Layers of Terminology Processing, in ‘Desiderata for a Clinical Terminology Server’, 1999.

18. The Problem • My colleagues down the hall have a grant to pay for data extraction from clinical records: • “The patient has MR” • “LAD disease was noted by the referring doc” • Data extraction usually isolated from patient care episodes • Documentation often performed without considering subsequent data extraction

19. Clinical Documentation • Encounters between patients and healthcare providers are typically recorded in clinical documents. • clinic notes, • procedural narratives, • comprehensive history and physical reports, • periodic assessments, • progress notes, consultation notes, • hospital discharge summaries • Clinical documentation creates an objective record of physical findings, medical reasoning, and delivered care • Many additional demands are imposed on clinical documentation by third parties

20. The federal government and major stakeholders in healthcare emphasize the importance of rapidly deploying electronic health record systems to all sites of health care. increase patient safety reduce errors improve efficiency reduce costs Capturing structured information from clinical notes can improve healthcare and research, but remains a major challenge. Clinical Documentation

21. Clinical Documentation • Medical documents have long served as legal treatises, recounting the care and procedures that individual patients receive for the purposes of potential future arbitration. • Insurers use the quality and quantity of documentation to justify the level of reimbursement for given services. • Elements of medical records may be used as markers for the quality of care provided to patients. • Clinical documentation content may be used as a substrate for decision support systems. Each of these forces defines additional components that must be included in medical documents.

22. Clinical Documentation • Current state of the art • Paper based / Impermanent • Asynchronous • Redundant • Expensive • Illegible (or inefficient to transcribe) • Location-Bound • Limited functionality • Unchanged in 5000+ years

23. Clinical Documentation • Clinical Note circa 3000 BCE

24. Chief Complaint History of Present Illness Past Medical History Family History Social History Review of Systems Physical Exam Clinical Documentation • Clinical Note circa 2000 CE

25. Clinical Documentation • To date, most CNCTs described in the literature serve only isolated domains or single problems • Workup of febrile neonates, • Evaluation of providers who have had blood and body fluid exposures, • Generation of progress notes in the neonatal and medical intensive care units, • Enhancing compliance with standards of diabetes care, • Documenting pediatric care based on national guidelines, • Construction of obstetric databases • Documentation of endoscopy procedures • Only a few general purpose CNCT have been described, although they may be increasing

26. Clinical Documentation • Clinical Documentation – current

27. Real-time documentation using categorical information is called Structured Entry Structured Entry can improve patient care by generating data in real time Structured Entry can generate data to support clinical research Requires an “Interface Terminology” Clinical Documentation

28. Background • A Structured Entry tool

29. Clinical Documentation • Structured entry of clinical notes currently poorly adopted in healthcare • Reasons for poor adoption not well characterized • Inefficient to use • Complicated interfaces • Inflexible in face of unforeseen clinical problems • Difficulty finding what you want to say • The terminologies supporting structured entry tools may play a significant role

30. Terminologies • There currently exist many terminologies • In 2003, the National Committee on Vital Health and Statistics (NCVHS) recommended a subset of existing terminologies as: “uniform data standards for patient medical record information (PMRI) and the electronic exchange of such information”

31. Terminologies • PMRI standards: • SNOMED CT (as licensed by the National Library of Medicine) - for the exchange, aggregating, and analysis of patient medical information. • Logical observation Identifiers Names and Codes - for the representation of individual laboratory tests • Federal Drug Terminologies: • RxNorm; • The representations of the mechanism of action and physiologic effect of drugs from NDF-RT; • Ingredient name, manufactured dosage form and package type form the FDA

32. Terminologies • PMRI recommended mapping priorities: • Priority 1: Terminologies previously designated as HIPAA medical code sets: • CPT-4 (Current Procedural Terminology) • CDT (Current Dental Terminology) • ICD-9-CM (International Classification of Diseases – Clinical Modification) • NDC (National Drug Codes)

33. Terminologies • PMRI recommended mapping priorities: • Priority 2: Terminologies in common use as enablers of important healthcare functions. • DSM-IV (diagnosis codes for mental disorders) • ISBT 128 (coding system for describing blood products and tissues) • Medcin (codes for structured entry of clinical notes) • MedDRA (international code set for use by drug regulatory agencies) • Nursing terminologies not otherwise included in SNOMED CT

34. Terminologies • What about the UMLS? (Unified Medical Language System) • The UMLS is a terminology collection • Concepts are unique and may fit the best practices desiderata • No formal relationships among concepts present, per se

35. Terminologies • Using the UMLS: • Semantics and relationships from source terminologies lost (or worse, implied) • May mix up different levels of detail from different terminologies • Can loose link with source terminology, which can hinder maintenance.

36. Conclusion • Clinical terminologies • are formal arrangements of terms, concepts and their interrelationships • can represent knowledge and data if generated according to best practices • Challenges remain • Getting data from narratives • Creating flexible structured entry tools • Picking the right terminology to fit the intended use

37. Acknowledgement • Assistance in developing this work: • Steven H. Brown • Kevin B. Johnson • Peter L. Elkin • Ted Speroff • Randolph A. Miller • Judy G. Ozbolt • supported by NIH 1 K22 LM08576-01

38. Discussion • Questions? trent.rosenbloom@vanderbilt.edu Thank You!