September 11 2013 Department of Biomedical Informatics BMIF

September 11, 2013 Department of Biomedical Informatics BMIF 300 Clinical Terminologies S. Trent Rosenbloom, MD MPH Associate Professor Departments of Biomedical Informatics, Internal Medicine and Pediatrics Vanderbilt University Medical Center

• Terminologies can provide formal and machine-computable representations of knowledge and data • Such representation can facilitate interoperability, dissemination, decision support, research

• Terminologies are formal representations of entities and their interrelationships. – Embodied as concepts, terms, linkages • Concepts are the cognitive representation of entities or meanings • Terms are evocative words or phrases • Linkages are explicitly defined relationships

• Concept - ischemic injury and necrosis of heart muscle cells resulting from absent or diminished blood flow in a coronary artery • Terms – – Myocardial Infarction – Heart Attack • Linkage – – is_a Disease of the Heart – has_severity Severities

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).

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 Morning Star Conceptual Experience Evening Star Venus Adapted from Campbell, ‘Representing thoughts, words, and things in the UMLS’, 1998.

Planets of the Solar System inside outside Mercury Jupiter Venus Saturn Earth Neptune

Concept: Myocardial Infarction CUI: C 0027051 Semantic Type: Disease or Syndrome Entity: Gross necrosis of the myocardium, as a result of interruption of the blood supply to the area. (Dorland, 27 th ed) Representative Terms (synonyms): • Myocardial Infarction • Attack coronary • Cardiac infarction • Heart attack • Infarction of heart • MI - Myocardial infarction • Myocardial Infarct • Myocardial infarction (disorder) • Myocardial infarction syndrome • myocardium; infarction Adapted from the UMLS Metathesaurus. 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

• There a lot of 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”

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: • Rx. Norm; • 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

• What about the UMLS? (Unified Medical Language System) – The UMLS is a terminology collection – Concepts are unique – No formal relationships among concepts present, per se

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

Terminology History • Classification scheme for the London Bills of Mortality - 16 th century • John Gaunt’s refinement - middle of the 17 th century • International Classification of Diseases (ICD) - first adopted in Paris in 1900 • Multi-axial Standardized Nomenclature of Diseases (SND) – 1928 • Standardized Nomenclature of Diseases and Operations (SNDO) - 1933

Terminology History • “Modern era for clinical descriptions” • With SND and SNDO • Multiaxial: users could model complex concepts by constructing them from more primitive building blocks • Designed to classify diseases based on: Etiology Manifestations Relationships between them

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 Adapted from Cimino, ‘Desiderata for controlled medical vocabularies in the twenty-first century’, 1998.

• Coverage 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)

• 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

Post-coordination versus Pre-coordination

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Ice Cream • Post-Coordination • • • Flexible Wide choice Rules implied Explicit relationships Inefficient Permits Inappropriate combinations • Pre-Coordination • • • No flexibility Limited choice Asserted knowledge Implied relationships Efficient Only appropriate combinations

• Consequences of post-coordination: G-A 231 01 Acute • Inefficient post-coordination: “too cumbersome for D 5 -46100 01 Appendicitis, NOS M-41000 complex 01 Acute inflammation, NOS entry” G-A 231 01 Acute problem G-CO 06 01 In M-40000 01 inflammation, NOS D 5 -46210 01 Acute appendicitis, NOS T-59200 01 Appendix, NOS • Nonsensical Concepts G-CO 06 01 In T-59200 01 Appendix, NOS Table. Duplication due to compositionality: four ways to compose ‘Appendicitis’ in SNOMED, from the CANON Group • Concept duplication

• Rigorous development may produce terminologies unusable by healthcare providers for routine clinical tasks. • Rector: tension between clinical usability and meticulous knowledge representation mirrors the conflict • human users require flexible, expressive terminologies that model common colloquial phrases • computer programs are generally designed to process formally defined concepts having rigidly defined interrelationships.

• Rector’s six tasks for terminologies: 1) 2) 3) 4) support efficient data entry and query formulation record and archive clinical information support sharing and reuse of clinical information infer and suggest knowledge according to decision support algorithms 5) support terminology maintenance 6) create a natural language output from manual structured input