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Controlled Medical Terminologies:What can they do for me?
James J. Cimino, M.D.
Department of Medical InformaticsColumbia University
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Definition
Terminology:
A finite, enumerated set of terms intended to convey information unambiguously
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Some General Classes of Terms
Diagnostic Procedures Therapeutic Procedures Medications Diagnoses Findings Organisms Anatomy
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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
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ICD9-CM Examples
------Diseases-----003. @ OTHER SALMONELLA INFECTIONS003.0 SALMONELLA GASTROENTERITIS003.2 @ LOCALIZED SALMONELLA INFECTIONS003.20 LOCALIZED SALMONELLA INFECTION, UNSPECIFIED003.21 SALMONELLA MENINGITIS003.29 OTHER LOCALIZED SALMONELLA INFECTIONS
------Procedures-----01. @ INCISION AND EXCISION OF SKULL, BRAIN,...01.0 @ CRANIAL PUNCTURE01.01 CISTERNAL PUNCTURE01.09 OTHER CRANIAL PUNCTURE
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SNOMED
Systematized Nomenclature of Medicine College of American Pathologists Organized into axes Synonyms Assemble complex terms from axes SNOMED-RT (Reference Terminology)
under development
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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
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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"
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MeSH
Medical Subject Headings National Library of Medicine Indexing the medical literature Multiple hierarchy Synonyms
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MeSH ExampleD011014: 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
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UMLS
Unified Medical Language System National Library of Medicine Metathesaurus groups terms under
single concept id No new hierarchy Translation of terms
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Metathesaurus
80+ sources
1,358,891 strings
626,893 concepts
Strings have attributes
Concepts have attributes, including Relations
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Metathesaurus
String
String
Lexical groupConcept
String
String
Lexical group
String
String
Lexical groupConcept
String
String
Lexical group
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Metathesaurus - MRCONC0153957|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|HeartC0153957|GER|P|L1258174|PF|S1500120|Gutartige Neubildung: Herz
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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|
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Metathesaurus - MRSTY
C0153957|T191|Neoplastic Process|
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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||
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Uses of Terminology
Storing in database
Querying database
Transferring data
Billing
Monitoring data
Integration of systems
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MED
Medical Entities Dictionary CPMC Multiple hierarchy Synonyms Translations Semantic links Attributes 60,000 concepts
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MED StructureMedicalEntity
LaboratoryTest
PlasmaGlucose
LaboratorySpecimen
PlasmaSpecimen
AnatomicSubstance
Plasma Substance
Sampled
Part of
Has S
pecimen
Substance Measured
Event
LaboratoryProcedure
CHEM-7
DiagnosticProcedure
Substance
BioactiveSubstance
Glucose
Chemical
Carbo-hydrate
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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
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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?
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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.
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No Growth after ...
How We Outsmarted the Lab
No Growth
No Growth after 48 Hours
No Growth after 72 Hours
“No Growth” Results
No Growth after 24 Hours
No Growth to Date
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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
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LaboratoryTest
Medical Entities Dictionary
HasIngredient
Measures
Chemical
AminoglycosideAntibiotic
Gentamicin
Serum Gentamicin
Test
Drug
Injectable GentamicinTrade-Name: Garamycin"Has-Ingredient: GentamicinMeasures
Random Gentamicin Level
Main-MeSH:
Supplementary-MeSH: "Gentamicin/bl"
Measures: Gentamicin
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Linking Text Reports to On-line Information Sources
Natural Language Processing
Data representation to support reuse
Codification of information needs
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MED Browsers
www.cpmc.columbia.edu/resources/ med/browsers/
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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
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Questions?