Transcript Clinical Vocabulary - Columbia University

Controlled Terminology in
Clinical Practice
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
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
heart attack
arrhythmia
lung disease
pneumonia
Polyhierarchy
disease
heart disease
heart attack
lung disease
arrhythmia
infectious disease
pneumonia
Semantic Network
specimen
is_a
test
is_a
serum
has_specimen
substance
is_a
potassium
serum potassium test
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 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
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"
"D3-15000"
"D3-15000"
"D3-15000"
"D3-15010"
"C-C137A"
"C-C137B"
"M-54700"
“M-54700"
"M-54700"
"M-54701"
"M-54701"
"S-10120"
"01"
"02"
"02"
"02"
"01"
"01"
"01"
"01"
"02"
"05"
"01"
"02"
"01"
"Myocardial infarction, NOS"
"Infarction of heart, NOS"
"Cardiac infarction, NOS"
"Heart attack, NOS”
"Microinfarct of heart”
"Bufferin Analgesic Tablets"
"Bufferin Analgesic Caplets"
"Infarct, NOS"
"Infarction, NOS"
"Infarcted"
"Focal infarct"
"Microscopic infarct"
"Mother, NOS"
"(T-32020) (M-54700)"
"(T-32020) (M-54700)"
"(T-32020) (M-54700)”
"(T-32020) (M-54700)"
"(T-32000) (M-54701)”
MeSH
Medical Subject Headings
 National Library of Medicine
 Indexing the medical literature
 Multiple hierarchy
 Synonyms

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
Nursing Terminologies
Diagnoses Interventions Outcomes
NANDA
Goals
X
NIC
NOC
GHHCC
X
X
X
PCDS
X
X
Omaha
X
X
X
AORN
X
X
X
ICNP
X
X
X
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
Concept
Lexical group
String
String
Concept
Lexical group
String
String
Lexical group
String
String
Lexical group
String
String
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
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|D3F0100|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
Medical
Entity
Substance
Chemical
Laboratory
Specimen
Anatomic
Substance
Plasma
Carbohydrate
Bioactive
Substance
Plasma
Specimen
Event
Diagnostic
Procedure
Laboratory
Test
Plasma
Glucose
Glucose
Laboratory
Procedure
CHEM-7
Part of
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
Retrieving Results Individually
K#1 = 4.2
K#1 = 3.3
K#2 = 3.2
K#1 = 3.0
K#3 = 2.6
K#1
K#2 K#3
Retrieving Results by Class
K#1 = 4.2
K#1 = 3.3
K#2 = 3.2
K#1 = 3.0
K#3 = 2.6
K
K#1
K#2 K#3
Case Study:
Summaries in the MED
Lab Display
Lab Test
Intravascular Glucose Test
Fingerstick Glucose Test
Serum Glucose Test
Plasma Glucose Test
Chem20 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
Lab Test
Intravascular Glucose Test
Fingerstick Glucose Test
Serum Glucose Test
Plasma Glucose Test
Chem 7
Case Study:
Orderable Tests
Lab Procedure
Lab Test
Intravascular Glucose Test
Fingerstick Glucose Test
Orderable Test
Serum Glucose Test
Plasma Glucose Test
Chem 7
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)
Medical Logic
Module
No Growth
No Growth
to Date
How We Outsmarted the Lab
(After)
“No Growth”
Results
No Growth
No Growth
to Date
No Growth
after 48 Hours
Medical Logic
Module
No Growth
after 24 Hours
No Growth
after 72 Hours
No Growth
after ...
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
Medical Entities Dictionary
Laboratory
Test
Serum
Gentamicin
Test
Antibiotic
Random Gentamicin Level
Main-MeSH:
Supplementary-MeSH:
"Gentamicin/bl"
Measures: Gentamicin
Drug
Chemical
Aminoglycoside
Gentamicin
Injectable Gentamicin
Trade-Name: Garamycin"
Has-Ingredient: Gentamicin