UMLS
Unified Medical Language System
What is UMLS?
A Unified knowledge representation
system
 Project of NLM

Large scale
 Distributed
 First launched in 1986

UMLS: the purpose

To reduce the fundamental barriers
to the computer application in
medicine:

Lack of standard languages
• The disparity of terminologies used in
different information resources and by
different users
UMLS: approach

Knowledge source for system
developers
Metathesaurus
 The Semantic Network
 SPECIALIST lexicon and associated
lexical tools

UMLS Knowledge source
UMLS knowledge source:

Core components:
 Metathesaurs
Semantic Network
 SPECIALIST lexicon and associated
lexical tools

Metathesaurus:


Database of concepts
Purpose:


link alternative names together
identify useful relationships between different
concepts.
Metathesaurus:

Organization
Basic principle:

group alternative names together by
concept
Metathesaurs:Concept structure
Concept(CUI):
Term1
String 1 (SUI)(preferred)
(LUI)
String 2 (SUI)
String 3 (SUI)
Term2
String 1
String 2
String 3
Metathesaurus:example
TERM
Zea mays
Zea mays
Zea mays
ZEA MAYS
Corn <1>
Corn
Corn
Corn
corn
corn
Indian Corn
Corn, Indian
Maize
Maize
maize
maize
SOURCE
MTH
SNMI98
CSP2000
NDDF00
MTH
MSH2000
SNMI98
LCH90
AOD99
CSP2000
MSH2000
MSH2000
MSH2000
SNMI98
AOD99
CSP2000
TERM TYPE
PN
PT
ET
IN
MM
MH
SY
PT
DE
PT
EP
PM
EP
SY
NP
ET
CODE
NOCODE
L-DB941
2340-8793
006695
U000077
D003313
L-DB941
U001161
0000013135
2340-8793
D003313
D003313
D003313
L-DB941
0000026523
2340-8793
Metathesaurs relationships

Hierarchical:






Broader(RB)
Narrower(RN)
Other related(RO)
Parent (PAR)
Child(CHD)
Non-hierarchical:




LIKE(RL)
Sibling(SIB)
AQ
QB
Metathesaurus:
other data elements
Semantic types
 Additional Attributes


Definitions (source: MeSH, ..)
Metathesaurus:current status

In 2002 edition:



Approximately 730,000 concepts
1.5 M concept names (terms)
covers 60+ vocabularies and classifications,
such as:
• MeSH(The medical subject heading)
• DxPlain(MGH expert system)
• UMDNS(Universal Medical Device Nomenclature
System)
• PDQ2001(Physician Data Query Online System)
• ICD2002(International Statistical Classification of
Disease)
UMLS Knowledge source:

Core components:

Metathesaurs
 Semantic

Lexical tools
Network
Semantic Network
Provides categorization of all
concepts in Metathesaurus
 Currently including:



134 semantic types
54 semantic links (relationships)
Semantic Types (134):
Sample Definition:
 tree structure
 Top notes:

“Entity”
 “Event”

Semantic relationships(54)

hierarchical (isa = is a kind of)

Among types:
• Plant isa organism
• Activity isa event

Among relations:
• Treats isa affects
• Affects isa related to

non-hierarchical:


Injuries or poisoning disrupts physiology
functions
Pharmacologic substance treats pathologic
functions
Hierarchical relations types:
Associative (non-isa) relatonships
Lexicon tools
SPECIALIST lexicon
 Lexical tools

SPECIALIST Lexicon

Content:
English lexicon
 100,000+ Biomedical terms


Provide lexical information for lexical
tools:
Syntactic category
 Inflectional variations

UMLS Knowledge source:

Core components:
Metathesaurs
 Semantic Network

 SPECIALIST
Lexical tools
Lexicon and
Lexical tools
To manage lexical variation in
medical terminologies
 Major tools

Normalization
 Indexed
 Lexical variation generation

Develop UMLS Applications
UMLS Distribution




Knowledge source and associated lexical
tools
Annual updates since 1990
Free, but requires a license agreement
Full UMLS available:




CD-ROM
ftp from the Knowledge Source Server
Application Programming Interface(API)
Knowledge Source Server
UMLS Application
PubMed
 NLM Gateway
 NCBI Entrez Taxonomy

Names of all organisms that are
represented in the genetic database
with at least one nucleotide or protein
substance.
 Will be mapped to UMLS

Example: PubMed
Bronzed disease
UMLS tools
Addison’s disease(MesH term)
Search MeSH indexed database
Others:
A UMLS-Based Knowledge
Acquisition Tools for RuleBased Clinical Decision
Support System Construction
 WizOrder

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UMLS - George Washington University