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Controlled Medical Terminologies: What can they do for me?

Controlled Medical Terminologies: What can they do for me?. James J. Cimino, M.D. Department of Medical Informatics Columbia University. Definition. Terminology: A finite, enumerated set of terms intended to convey information unambiguously. Some General Classes of Terms.

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Controlled Medical Terminologies: What can they do for me?

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  1. Controlled Medical Terminologies:What can they do for me? James J. Cimino, M.D. Department of Medical InformaticsColumbia University

  2. Definition Terminology: A finite, enumerated set of terms intended to convey information unambiguously

  3. Some General Classes of Terms • Diagnostic Procedures • Therapeutic Procedures • Medications • Diagnoses • Findings • Organisms • Anatomy

  4. ICD-9/10 and -CM • 9th International Classification of Diseases • WHO for collecting health statistics • Clinical Modifications added • 10th edition • Clinical modifications under construction • Strict hierarchy • Synonyms and “index” terms • Code determines place in hierarchy

  5. ICD9-CM Examples ------Diseases----- 003. @ OTHER SALMONELLA INFECTIONS 003.0 SALMONELLA GASTROENTERITIS 003.2 @ LOCALIZED SALMONELLA INFECTIONS 003.20 LOCALIZED SALMONELLA INFECTION, UNSPECIFIED 003.21 SALMONELLA MENINGITIS 003.29 OTHER LOCALIZED SALMONELLA INFECTIONS ------Procedures----- 01. @ INCISION AND EXCISION OF SKULL, BRAIN,... 01.0 @ CRANIAL PUNCTURE 01.01 CISTERNAL PUNCTURE 01.09 OTHER CRANIAL PUNCTURE

  6. SNOMED • Systematized Nomenclature of Medicine • College of American Pathologists • Organized into axes • Synonyms • Assemble complex terms from axes • SNOMED-RT (Reference Terminology) under development

  7. SNOMED - Axes • D - Diseases • C - Drugs • F - Function • L - Living Organisms • X - Manufacturers • G - Modifiers • M - Morphology • J - Occupations • A - Physical Agents • P - Procedures • S - Social Context • T - Topography

  8. SNOMED - Examples "D3-15000" "01" "Myocardial infarction, NOS" "(T-32020) (M-54700)" "D3-15000" "02" "Infarction of heart, NOS" "(T-32020) (M-54700)" "D3-15000" "02" "Cardiac infarction, NOS" "(T-32020) (M-54700)” "D3-15000" "02" "Heart attack, NOS” "(T-32020) (M-54700)" "D3-15010" "01" "Microinfarct of heart” "(T-32000) (M-54701)” "C-C137A" "01" "Bufferin Analgesic Tablets" "C-C137B" "01" "Bufferin Analgesic Caplets" "M-54700" "01" "Infarct, NOS" “M-54700" "02" "Infarction, NOS" "M-54700" "05" "Infarcted" "M-54701" "01" "Focal infarct" "M-54701" "02" "Microscopic infarct" "S-10120" "01" "Mother, NOS"

  9. MeSH • Medical Subject Headings • National Library of Medicine • Indexing the medical literature • Multiple hierarchy • Synonyms

  10. MeSH Example D011014: Pneumonia D018410: Pneumonia, Bacterial D007877: Legionnaires' Disease D011018: Pneumonia, Pneumococcal D011019: Pneumonia, Mycoplasma D009175: Mycoplasma Infections D011002: Pleuropneumonia, Contagious D011022: Pneumonia, Rickettsial D011023: Pneumonia, Staphylococcal D001996: Bronchopneumonia D009956: Ornithosis D011001: Pleuropneumonia D011015: Pneumonia, Aspiration D011017: Pneumonia, Lipid D011020: Pneumonia, Pneumocystis carinii D011024: Pneumonia, Viral

  11. UMLS • Unified Medical Language System • National Library of Medicine • Metathesaurus groups terms under single concept id • No new hierarchy • Translation of terms

  12. Metathesaurus • 80+ sources • 1,358,891 strings • 626,893 concepts • Strings have attributes • Concepts have attributes, including Relations

  13. Concept Lexical group String String Concept Lexical group Lexical group String String String String Metathesaurus Lexical group String String

  14. Metathesaurus - MRCON C0153957|ENG|P|L0180790|PF|S1084242|benign neoplasm of heart C0153957|ENG|P|L0180790|VC|S0245316|Benign neoplasm of heart C0153957|ENG|P|L0180790|VO|S1446737|Benign neoplasm of heart, NOS C0153957|ENG|S|L0524277|PF|S0599118|Benign tumor of heart C0153957|ENG|S|L0524278|PF|S0599510|Benign tumour of heart C0153957|ENG|s|L0018787|PF|S0900815|Heart <3> C0153957|ENG|s|L0018787|VO|S0047194|Heart C0153957|GER|P|L1258174|PF|S1500120|Gutartige Neubildung: Herz

  15. Metathesaurus - MRSO C0153957|L0018787|S0047194|ICD10|PS|D15.1|3| C0153957|L0018787|S0900815|MTH|MM|U003158|0| C0153957|L0180790|S0245316|ICD10|PX|D15.1|3| C0153957|L0180790|S0245316|ICD99|PT|212.7|0| C0153957|L0180790|S0245316|RCD98|SY|B727.|3| C0153957|L0180790|S1084242|MTH|PN|U001287|0| C0153957|L0180790|S1446737|SNMI98|PT|D3-F0100|3| C0153957|L0524277|S0599118|RCDAE|PT|B727.|3| C0153957|L0524278|S0599510|RCD98|PT|B727.|3| C0153957|L1258174|S1500120|DMDICD|PT|D15.1|1|

  16. Metathesaurus - MRSTY C0153957|T191|Neoplastic Process|

  17. Metathesaurus - MRREL C0002871|CHD|C0002891|isa|MSH99|MTH|| C0002871|CHD|C0002892||CSP98||| C0002871|CHD|C0002893||RCD98||| C0002871|RB|C0221016||MTH|MTH|| C0002871|RL|C0002886|mapped_to|SNMI98|SNMI98||

  18. Uses of Terminology • Storing in database • Querying database • Transferring data • Billing • Monitoring data • Integration of systems

  19. MED • Medical Entities Dictionary • CPMC • Multiple hierarchy • Synonyms • Translations • Semantic links • Attributes • 60,000 concepts

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

  21. Terminology and Automated Decision Support • Data monitor checks for triggering conditions • Medical Logic Modules decide if warning conditions are present • Message sent to appropriate channel • Example: Tuberculosis culture result

  22. Caveats: TB Example • Monitors for delayed culture results • Sends message if result not equal to the code “No growth” • One day, dozens of alerts about positive results but no organism was reported • What happened?

  23. How the Lab Fooled the Alert • Alert looked for results = “No Growth” • Lab started reporting “No Growth to Date” • “No Growth to Date”<> “No Growth” • Solution: Use the controlled terminology to map all No-Growth-like lab terms into a single class, and have the alert logic refer to the class.

  24. “No Growth” Results No Growth after 24 Hours No Growth after 48 Hours No Growth after ... No Growth after 72 Hours How We Outsmarted the Lab No Growth to Date No Growth

  25. Linking to On-line Resources with Terminology • Clinician reviewing reports will have information needs • On-line information sources can satisfy that need • Data from report can be used to automate the query

  26. Laboratory Test Drug Serum Gentamicin Test Aminoglycoside Antibiotic Measures Measures Has Ingredient Medical Entities Dictionary Chemical Gentamicin Random Gentamicin Level Main-MeSH: Supplementary-MeSH: "Gentamicin/bl" Measures: Gentamicin Injectable Gentamicin Trade-Name: Garamycin" Has-Ingredient: Gentamicin

  27. Linking Text Reports to On-line Information Sources • Natural Language Processing • Data representation to support reuse • Codification of information needs

  28. MED Browsers www.cpmc.columbia.edu/resources/ med/browsers/

  29. Summary • Computers need controlled terminologies (CTs) • Different CTs for different needs (granularity) • Bridging between CTs facilitates bridging between applications • Consider use of/indexing with CTs in consumer applications

  30. Questions?

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