Transcript Slide 1

October 2, 2014
Department of Biomedical Informatics
BMIF 300
Clinical Terminologies
S. Trent Rosenbloom, MD MPH
Associate Professor and Vice Chair
Departments of Biomedical Informatics, Internal Medicine and Pediatrics
Vanderbilt University Medical Center
• Terminologies can provide formal and
machine-computable representations of
knowledge and data
• Such representation can facilitate
interoperability, dissemination, decision
support, research
• Terminologies are formal representations of
entities and their interrelationships.
– Embodied as concepts, terms, linkages
• Concepts are the cognitive representation of entities
or meanings
• Terms are evocative words or phrases
• Linkages are explicitly defined relationships
• Concept - ischemic injury and necrosis of heart
muscle cells resulting from absent or
diminished blood flow in a coronary artery
• Terms –
–Myocardial Infarction
–Heart Attack
• Linkage –
–is_a Disease of the Heart
–has_severity Severities
Morning Star
Evening Star
The second planet from the sun, having an average radius of 6,052 kilometers (3,761 miles), a
mass 0.815 times that of Earth, and a sidereal period of revolution about the sun of 224.7 days
at a mean distance of approximately 108.2 million kilometers (67.2 million miles).
Physical Entity
The second planet from the sun, having an average radius of 6,052 kilometers (3,761 miles), a
mass 0.815 times that of Earth, and a sidereal period of revolution about the sun of 224.7 days
at a mean distance of approximately 108.2 million kilometers (67.2 million miles).
Representative Terms
Morning Star
Conceptual Experience
Evening Star
Adapted from Campbell, ‘Representing thoughts, words, and things in the UMLS’, 1998.
Planets of the Solar System
Concept: Myocardial Infarction
CUI: C0027051
Semantic Type: Disease or Syndrome
Entity: Gross necrosis of the myocardium, as a result of interruption of the blood supply to the
area. (Dorland, 27th ed)
Representative Terms (synonyms):
• Myocardial Infarction
• Attack coronary
• Cardiac infarction
• Heart attack
• Infarction of heart
• MI
• MI - Myocardial infarction
• Myocardial Infarct
• Myocardial infarction (disorder)
• Myocardial infarction syndrome
• myocardium; infarction
Adapted from the UMLS Metathesaurus.
More Specific Concepts (children):
Acute myocardial infarction
Old myocardial infarction
Microinfarct of heart
True posterior wall infarction
Aborted myocardial infarction
Other specified anterior myocardial infarction
Silent myocardial infarction
Subsequent myocardial infarction
Postoperative myocardial infarction
First myocardial infarction
Myocardial infarction with complication
Non-Q wave myocardial infarction
• There are a lot of terminologies
• In 2003, the National Committee on Vital Health and
Statistics (NCVHS) recommended a subset of existing
terminologies as:
“uniform data standards for patient medical record
information (PMRI) and the electronic exchange of
such information”
• PMRI standards:
– SNOMED CT (as licensed by the National Library of
Medicine) - for the exchange, aggregating, and analysis of
patient medical information.
– Logical observation Identifiers Names and Codes - for the
representation of individual laboratory tests
– Federal Drug Terminologies:
• RxNorm;
• The representations of the mechanism of action and physiologic
effect of drugs from NDF-RT;
• Ingredient name, manufactured dosage form and package type form
the FDA
• What about the UMLS?
(Unified Medical Language System)
– The UMLS is a terminology collection
– Concepts are unique
– No formal relationships among concepts
present, per se
• Using the UMLS:
– Semantics and relationships from source
terminologies lost (or implied)
– May mix up different levels of detail from
different terminologies
– Can loose link with source terminology, which
can hinder maintenance
Terminology History
• Classification scheme for the London Bills of
Mortality - 16th century
• John Gaunt’s refinement - middle of the 17th
• International Classification of Diseases (ICD) - first
adopted in Paris in 1900
• Multi-axial Standardized Nomenclature of Diseases
(SND) – 1928
• Standardized Nomenclature of Diseases and
Operations (SNDO) - 1933
Terminology History
• “Modern era for clinical descriptions”
• With SND and SNDO
• Multiaxial: users could model complex concepts by
constructing them from more primitive building blocks
• Designed to classify diseases based on:
Relationships between them
Terminology Desiderata
Statement of purpose, scope, and comprehensiveness
Complete coverage of domain specific content
Use of concepts rather than terms, phrases and words (concept orientation)
Concepts do not change with time, view or use (concept consistency)
Concepts must evolve with change in knowledge
Concepts identified through nonsense identifiers (context-free identifier)
Representation of concept context consistently from multiple hierarchies
Concepts have single explicit formal definitions
Support for multiple levels of concept detail
Absence of or methods to identify duplication, ambiguity, and synonymy
Integration with other terminologies
Mapping to administrative terminologies
Adapted from Cimino, ‘Desiderata for controlled medical vocabularies in the twenty-first century’, 1998.
• Coverage achieved by one of two ways
• Post-coordination - complex concepts from different
levels of detail are composed as needed from
fundamental concepts
(e.g., ‘chest pain’ composed from the concepts ‘chest’ and
‘pain’ when needed)
• Pre-coordination - all levels of detail are modeled with
distinct concepts
(e.g., ‘chest pain’, ‘substernal chest pain’, and ‘crushing
substernal chest pain’ are all in the terminology)
• Completeness measured by Coverage:
• coverage calculated as the proportion of concepts
covered by a terminology
• multiple studies: post-coordinated terminologies
generally have better coverage than pre-coordinated
Post-coordination versus Pre-coordination
Select One Flavor
Select One Topping
Select One Cone
…or…Select One Favorite
Ice Cream
• Post-Coordination
Wide choice
Rules implied
Explicit relationships
Permits Inappropriate
• Pre-Coordination
No flexibility
Limited choice
Asserted knowledge
Implied relationships
Only appropriate
• Consequences of post-coordination:
G-A231 01 Acute
• Inefficient post-coordination:
01 Appendicitis,
01 Acute inflammation,
NOS entry” G-A231 01 Acute
G-CO06 01 In
M-40000 01 inflammation, NOS
D5-46210 01 Acute appendicitis, NOS
T-59200 01 Appendix, NOS
• Nonsensical Concepts
G-CO06 01 In
T-59200 01 Appendix, NOS
Table. Duplication due to compositionality: four ways to compose ‘Appendicitis’ in SNOMED, from the
• Concept duplication
• Rigorous development may produce terminologies
unusable by healthcare providers for routine clinical
• Rector: tension between clinical usability and
meticulous knowledge representation mirrors the
conflict • human users require flexible, expressive terminologies that model
common colloquial phrases
• computer programs are generally designed to process formally
defined concepts having rigidly defined interrelationships.
• Rector’s six tasks for terminologies:
support efficient data entry and query formulation
record and archive clinical information
support sharing and reuse of clinical information
infer and suggest knowledge according to decision
support algorithms
5) support terminology maintenance
6) create a natural language output from manual structured