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UMLS

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UMLS

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  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. Metathesaurs:Concept structure Concept(CUI): Term1 String 1 (SUI)(preferred) (LUI) String 2 (SUI) String 3 (SUI) Term2 String 1 String 2 String 3

  10. Metathesaurus:example 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 <1> 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. 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)

  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 Addison’s disease(MesH term) Search MeSH indexed database

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