UMLS Unified Medical Language System. What is UMLS? A Unified knowledge representation system Project of NLM Large scale Distributed First launched in.

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Presentation transcript:

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): Term1String 1 (SUI)(preferred) (LUI) String 2 (SUI) String 3 (SUI) Term2String 1 String 2 String 3

Metathesaurus: example TERM SOURCE TERM TYPE CODE Zea mays MTH PN NOCODE Zea mays SNMI98 PT L-DB941 Zea mays CSP2000 ET ZEA MAYS NDDF00 IN Corn MTH MM U Corn MSH2000 MH D Corn SNMI98 SY L-DB941 Corn LCH90 PT U corn AOD99 DE corn CSP2000 PT Indian Corn MSH2000 EP D Corn, Indian MSH2000 PM D Maize MSH2000 EP D Maize SNMI98 SY L-DB941 maize AOD99 NP maize CSP2000 ET

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 Network Lexical tools

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

Semantic Types (134): Sample Definition: 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 Lexicon and Lexical tools

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: PubMedPubMed Bronzed disease UMLS tools Addison’s disease(MesH term) Search MeSH indexed database

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