Controlled Terminology in Clinical Practice James J. Cimino, M.D. Department of Medical Informatics...
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Transcript of Controlled Terminology in Clinical Practice James J. Cimino, M.D. Department of Medical Informatics...
Controlled Terminology in Clinical Practice
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
Uses of Terminology
Storing in database
Querying database
Transfering data
Billing
Monitoring data
Term - Basic Features
Unique Identifier (Code) 12345
Official Name aspirin
Synonyms ASA
Translations NDC: 5502; UMLS: C0004057
Term - Advanced Features
Classes antipyretic, anti-inflammatory, analgesic
Semantic Links CAUSES: gastritis TREATS: arthritis
Attributes UNITS: mg
Desiderata for Terminology
Content
Concept Orientation Nonredundant Nonambiguous Permanent
Nonsemantic Concept Identifiers
Polyhierarchy
Semantic relationships
Strict Hierarchy
disease
heart disease lung disease
heart attack arrhythmia pneumonia
Polyhierarchy
disease
heart attack arrhythmia
heart disease lung disease infectious disease
pneumonia
Semantic Network
serum potassium test
testspecimen substance
is_a is_ais_a
serum potassium
has_specimen measures_substance
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
Nursing Terminologies
Diagnoses Interventions Outcomes Goals
NANDA X
NIC XNOC X
GHHCC X X X
PCDS X X X
Omaha X X X
AORN X X X
ICNP X X X
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||
MED
Medical Entities Dictionary CPMC Multiple hierarchy Synonyms Translations Semantic links Attributes 60,000 concepts
Central Controlled Vocabulary
MED Structure
MedicalEntity
LaboratoryProcedure
CHEM-7PlasmaGlucose
LaboratorySpecimen
PlasmaSpecimen
Substance
Sampled
Part of
Has S
pecimen
Substance Measured
Event
LaboratoryTest
DiagnosticProcedure
Plasma
AnatomicSubstance
Substance
BioactiveSubstance
Glucose
Chemical
Carbo-hydrate
What do we want to do with these data?
Primary use Other patient care reuse Financial Management Information transfer (messaging) Clinical research Expert systems Information retrieval Vocabulary discovery
Primary Use of Data
Spit back the reports
Other Patient Care Reuse
Summaries Comparability of data
Trending of data Time representation
K#1 = 4.2K#1 = 3.3
K#2 = 3.2
K#1 = 3.0
K#3 = 2.6
Retrieving Results Individually
K#1
K#2 K#3
K#1 = 4.2K#1 = 3.3
K#2 = 3.2
K#1 = 3.0
K#3 = 2.6
Retrieving Results by Class
K#1
K#2 K#3
K
Case Study:Summaries in the MED
Plasma Glucose Test
Serum Glucose TestFingerstick Glucose Test
Lab Test
Intravascular Glucose Test Chem20 Display
Lab Display
DOP Summary
WebCIS Summary
Financial
Reporting Accounting Inventory
Case Study:Orderable Tests
HCFA won’t pay for lab batteries Individual tests now treated as
orderable procedures Need to appear in database as
procedures and as tests
Case Study:Orderable Tests
Lab Procedure
Chem 7
Lab Test
Intravascular Glucose Test
Plasma Glucose Test
Serum Glucose TestFingerstick Glucose Test
Case Study:Orderable Tests
Lab Procedure
Chem 7
Lab Test
Intravascular Glucose Test
Plasma Glucose Test
Serum Glucose TestFingerstick Glucose Test
Orderable Test
Management
Quality assurance Case management
Information Transfer (messaging)
Transfer to repository State reporting
Clinical Research
Epidemiology - symptoms, incidence, history of disease
Outcomes - effectiveness of therapy, ideal length of stay
Expert systems
Knowledge base construction Case abstraction Automated decision support
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
Decision Support Example: TB
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.
How We Outsmarted the Lab(Before)
No Growth
Medical Logic Module
No Growth to Date
No Growth after ...
How We Outsmarted the Lab(After)
No Growth
No Growth after 48 Hours
No Growth after 72 Hours
“No Growth” Results
No Growth after 24 Hours
No Growth to Date
Medical Logic Module
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