Unified Medical Language System

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Unified Medical Language System (UMLS)

• NLM Presentation Theater
• MLA 2007
• National Library of Medicine
• National Institutes of Health
• U.S. Dept. of Health and Human Services

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The UMLS consists of
SPECIALIST Lexicon Tools
Semantic Network

Metathesaurus
135 broad categories and 54 relationships between
them
lexical information and programs for language
processing
1 million biomedical concepts from over 100
sources
3 Knowledge Sources used separately or together
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UMLS Objectives

• Began in 1986 as long-term RD project
• Designed for systems developers
• Develop multi-purpose tools to enhance
  understanding of medical meaning across systems
• Overcome barriers to effective retrieval of
  machine-readable information
• Overcome variety of ways the same concepts are
  expressed in machine readable and human language

Dr. Donald A. Lindberg Director
National Library of Medicine
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UMLS Uses

• Information retrieval
• Thesaurus construction
• Natural language processing
• Automated indexing
• Electronic health records (EHR)
• Distribution mechanism for
• HIPAA, CHI, PHIN regulatory standards
• SNOMED CT

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UMLS Releases

• 3-4 updates (releases) per year
• 3 Knowledge Sources in 3 sets of relational files
• Tools
• MetamorphoSys install and customize
• RRF Subset Browser
• Lexical tools including LVG
• Download from UMLSKS or on DVD

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UMLS Access

• UMLS Knowledge Source Server (UMLSKS)
• http//umlsks.nlm.nih.gov/
• Browse 3 Knowledge Sources
• Query with Java or XML-based APIs
• Download files and programs
• Access documentation and other resources
• Local installation
• Use MetamorphoSys to install Knowledge Sources,
  customize Metathesaurus
• View customized subset with browser
• Use load scripts to load into database

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UMLS License Agreements

• Terms and conditions of use online
• Semantic Network
• SPECIALIST Lexicon Lexical Tools
• Metathesaurus
• Sign formal license agreement
• Additional restrictions apply to use of some
  sources as noted in the Appendix to the License
  Agreement

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Metathesaurus

• 100 general and specialized biomedical
  vocabularies
• 17 languages (63 English)
• 1 million concepts 6 million names
• 100K relationships (hierarchical, semantic,
  statistical and mapping relationships)
• Distributed in a common electronic format

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Metathesaurus Source Vocabularies

• Vary in purpose, structure and properties
• Used in clinical, research, administrative,
  public health reporting
• All are sets of valid values
• Thesauri, e.g., MeSH, CRISP, NCI
• Statistical classifications, e.g., ICD-9-CM
• Billing codes, e.g., CPT, ABC Codes
• Clinical coding systems, e.g., SNOMED CT

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SNOMED CT

• Comprehensive clinical terminology
• Created by College of American Pathologists
• Ownership transferred to International Health
  Terminology Standards Development Organisation
  (IHTSDO) in April 2007
• 9 charter member countries includes U.S.
• NLM represents U.S.
• NLM distributes SNOMED CT to U.S. users in both
  native and UMLS formats

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Metathesaurus Concepts

• Synonymous terms clustered into a concept
• Unique identifier (CUI) is assigned
• Source information preserved

Addisons disease SNOMED CT
PT 363732003 Addisons Disease
MedlinePlus PT T1233 Addison Disease
MeSH PT D000224 Primary Adrenal
Insufficiency MeSH EN D000224 Primary
hypoadreanlism MedDRA LT 10036696
syndrome, Addison
Addisons disease
C0001403
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Humphreys, BL and PL Schuyler, The Unified
Medical Language System Moving beyond the
vocabulary of bibliographic retrieval. In
Broering NC, ed. High- Performance Medical
Libraries advanced information management for
the virtual era. Westport (CT) Meckler 1993,
p. 33.
The UMLS approach
assumes continuing diversity in the formats and
vocabularies of different information sources and
in the language employed by different elements of
the biomedical community. It is not an attempt to
build a single standard biomedical vocabulary."
Betsy L. Humphreys, Deputy Director, National
Library of Medicine
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Semantic Network

• 135 Semantic Types
• Broad subject categories in 2 hierarchies
• Assigned to all Metathesaurus concepts
• 54 Semantic Relationships
• Useful, important links between Types
• Hierarchical isa and associative relations
• Categorize the Metathesaurus
• Enhance meaning of concepts

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Biologic Function hierarchy (isa)
Biologic Function 360
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Semantic Relations between types

• Disease or Syndrome associated_with Finding
• Disease or Syndrome result_of Pathologic Function
  
• Body Part, Organ, or Organ Component location_of
  Disease or Syndrome
• Hormone affects Disease or Syndrome Hormone
  causes Disease or Syndrome Hormone complicates
  Disease or Syndrome

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SPECIALIST Lexicon and Lexical Tools

• English lexicon of 300K common words and
  biomedical terms
• Lexical records encode information on
• Syntax
• Morphology
• Orthography
• Used with associated lexical tools
• in Metathesaurus production
• in natural language processing applications

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SPECIALIST Lexicon Lexical Entry

• basedisease entryE0023270    catnoun    var
  iantsreg    variantsuncount    complpphr(of,n
  pbone)    complpphr(of,npbreast)    complp
  phr(of,npliver)    complpphr(of,npovary)

Base form Unique identifier Part of
speech Lexical variants Prepositional phrase
complements
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Lexical Tools

• Manage lexical variation in biomedical
  terminologies and text
• Used separately or with SPECIALIST Lexicon
• Perform transformations selected and ordered by
  users
• 3 primary programs normalizer, word index
  generator, lexical variant generator
• http//umlslex.nlm.nih.gov/lvg/current/

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Normalization 1
Hodgkins diseases, NOS
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Normalization 2
Hodgkin Disease HODGKINS DISEASE Hodgkin's
Disease Disease, Hodgkin's Hodgkin's,
disease HODGKIN'S DISEASE Hodgkin's
disease Hodgkins Disease Hodgkin's disease
NOS Hodgkin's disease, NOS Disease,
Hodgkins Diseases, Hodgkins Hodgkins
Diseases Hodgkins disease hodgkin's
disease Disease, Hodgkin
disease hodgkin
normalize
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UMLS Knowledge Source Server (UMLSKS) Home Page

• From top links or buttons
• Search 3 Knowledge Sources
• From sidebar
• Downloads
• Documentation
• Resources

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UMLS Documentation and Support

• UMLS Home Page
• http//umlsinfo.nlm.nih.gov/
• UMLSKS
• http//umlsks.nlm.nih.gov
• NLP and Lexical Tools
• http//lexsrv3.nlm.nih.gov/SPECIALIST/index.html
• NLM customer service
• Email custserv_at_nlm.nih.gov

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Summary

• 3 Knowledge Sources
• Metathesaurus
• Semantic Network
• Lexicon Lexical Tools
• MetamorphoSys install, customize,
  browse
• UMLSKS
• browse, query, download
• License Agreement

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Thank you