UMLS

1
UMLS

• Unified Medical Language System

2
What is UMLS?

• A Unified knowledge representation system
• Project of NLM
• Large scale
• Distributed
• First launched in 1986

3
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

4
UMLS approach

• Knowledge source for system developers
• Metathesaurus
• The Semantic Network
• SPECIALIST lexicon and associated lexical tools

5
UMLS Knowledge source
6
UMLS knowledge source

• Core components
• Metathesaurs
• Semantic Network
• SPECIALIST lexicon and associated lexical tools

7
Metathesaurus

• Database of concepts
• Purpose
• link alternative names together
• identify useful relationships between different
  concepts.

8
Metathesaurus Organization

• Basic principle
• group alternative names together by concept

9
MetathesaursConcept structure

• Concept(CUI)

Term1 String 1 (SUI)(preferred) (LUI)
String 2 (SUI) String 3 (SUI)
Term2 String 1 String 2 String 3
10
Metathesaurusexample

• TERM SOURCE TERM TYPE CODE
• Zea mays MTH PN NOCODE
• Zea mays SNMI98 PT L-DB941
• Zea mays CSP2000 ET 2340-8793
• ZEA MAYS NDDF00 IN 006695
• Corn lt1gt MTH MM U000077
• Corn MSH2000 MH D003313
• Corn SNMI98 SY L-DB941
• Corn LCH90 PT U001161
• corn AOD99 DE 0000013135
• corn CSP2000 PT 2340-8793
• Indian Corn MSH2000 EP D003313
• Corn, Indian MSH2000 PM D003313
• Maize MSH2000 EP D003313
• Maize SNMI98 SY L-DB941
• maize AOD99 NP 0000026523
• maize CSP2000 ET 2340-8793

11
Metathesaurs relationships

• Hierarchical
• Broader(RB)
• Narrower(RN)
• Other related(RO)
• Parent (PAR)
• Child(CHD)
• Non-hierarchical
• LIKE(RL)
• Sibling(SIB)
• AQ
• QB

12
Metathesaurus other data elements

• Semantic types
• Additional Attributes
• Definitions (source MeSH, ..)

13
Metathesauruscurrent 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)

14
UMLS Knowledge source

• Core components
• Metathesaurs
• Semantic Network
• Lexical tools

15
Semantic Network

• Provides categorization of all concepts in
  Metathesaurus
• Currently including
• 134 semantic types
• 54 semantic links (relationships)

16
Semantic Types (134)

• Sample Definition
• tree structure
• Top notes
• Entity
• Event

17
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

18
Hierarchical relations types
19
Associative (non-isa) relatonships
20
Lexicon tools

• SPECIALIST lexicon
• Lexical tools

21
SPECIALIST Lexicon

• Content
• English lexicon
• 100,000 Biomedical terms
• Provide lexical information for lexical tools
• Syntactic category
• Inflectional variations

22
UMLS Knowledge source

• Core components
• Metathesaurs
• Semantic Network
• SPECIALIST Lexicon and Lexical tools

23
Lexical tools

• To manage lexical variation in medical
  terminologies
• Major tools
• Normalization
• Indexed
• Lexical variation generation

24
Develop UMLS Applications
25
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

26
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

27
Example PubMed
Bronzed disease
UMLS tools
Addisons disease(MesH term)
Search MeSH indexed database
28
Others

• A UMLS-Based Knowledge Acquisition Tools for
  Rule-Based Clinical Decision Support System
  Construction
• WizOrder