Controlled Medical Terminologies:What can they do for me?

James J. Cimino, M.D.

Department of Medical InformaticsColumbia University

Definition

Terminology:

A finite, enumerated set of terms intended to convey information unambiguously

Some General Classes of Terms

Diagnostic Procedures Therapeutic Procedures Medications Diagnoses Findings Organisms Anatomy

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

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

SNOMED

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

under development

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

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"

MeSH

Medical Subject Headings National Library of Medicine Indexing the medical literature Multiple hierarchy Synonyms

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

UMLS

Unified Medical Language System National Library of Medicine Metathesaurus groups terms under

single concept id No new hierarchy Translation of terms

Metathesaurus

80+ sources

1,358,891 strings

626,893 concepts

Strings have attributes

Concepts have attributes, including Relations

Metathesaurus

String

String

Lexical groupConcept

String

String

Lexical group

String

String

Lexical groupConcept

String

String

Lexical group

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

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|

Metathesaurus - MRSTY

C0153957|T191|Neoplastic Process|

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||

Uses of Terminology

Storing in database

Querying database

Transferring data

Billing

Monitoring data

Integration of systems

MED

Medical Entities Dictionary CPMC Multiple hierarchy Synonyms Translations Semantic links Attributes 60,000 concepts

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

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

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?

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.

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

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

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

Linking Text Reports to On-line Information Sources

Natural Language Processing

Data representation to support reuse

Codification of information needs

MED Browsers

www.cpmc.columbia.edu/resources/ med/browsers/

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

Questions?