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

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 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

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: 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: PubMedBronzed disease

UMLS tools

Addison’s disease(MesH term)

Search MeSH indexed database

Others: A UMLS-Based Knowledge Ac

quisition Tools for Rule-Based Clinical Decision Support System Construction

WizOrder