Olivier BodenreiderOlivier Bodenreider

Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical CommunicationsBethesda, Maryland Bethesda, Maryland -- USAUSA

Unified Medical Language SystemSemantic Navigator

DemosNovember 14, 2006

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IssuesIssues

SizeSizeLarge number of concepts (>1 million)Large number of concepts (>1 million)

ComplexityComplexityPolyhierarchicalPolyhierarchical structuresstructuresMultiple information sourcesMultiple information sourcesMultiple propertiesMultiple properties

Lack of formalityLack of formalityRedundant relationsRedundant relationsHierarchies vs. hierarchical relationsHierarchies vs. hierarchical relations

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ChallengesChallenges

Restrict information space to selected information Restrict information space to selected information sourcessourcesReduce Reduce complexitycomplexity

Group concepts by semantic groupsGroup concepts by semantic groupsTransitive reduction on hierarchical relationsTransitive reduction on hierarchical relationsSelect coSelect co--occurring conceptsoccurring concepts

Reduce the cognitive burden on the userReduce the cognitive burden on the userUse graphUse graph--based rather than treebased rather than tree--based representationsbased representations

UMLS Semantic Navigator SemNav

http://umlsks.nlm.nih.gov*

► SN Resources ► Semantic Navigator(* free UMLS registration required)

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UUnified nified MMedical edical LLanguage anguage SSystemystem®®

Developed at NLM since 1990Developed at NLM since 1990139 source vocabularies139 source vocabularies

17 languages17 languagesBroad coverage of biomedicineBroad coverage of biomedicine

5.1M names5.1M names1.3M concepts1.3M concepts16M relations16M relations

IntegrationIntegrationSynonymous terms are clustered in a conceptSynonymous terms are clustered in a conceptHierarchies (trees) are combined in a graph structureHierarchies (trees) are combined in a graph structure

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Terminology integration Terminology integration TermsTerms

Duchenne muscular dystrophy

MeSH, SNOMEDCTV3, Jablonski,CRISP, DxPlain,MedDRA, LOINC

pseudohypertrophic muscular dystrophy MeSH, CTV3SNOMED

X-liked recessive muscular dystrophy Jablonski

Duchenne de Boulogne muscular dystrophy Jablonski

Duchenne’s muscular dystrophy COSTAR

severe generalized familial muscular dystrophy SNOMED

Duchenne type progressive muscular dystrophy SNOMED

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Terminology integration Terminology integration RelationshipsRelationships

InterInter--concept concept relationships: hierarchies relationships: hierarchies from the source from the source vocabulariesvocabulariesRedundancy: multiple Redundancy: multiple pathspathsOne One graphgraph instead of instead of multiple multiple treestrees(multiple inheritance)(multiple inheritance)

A

B D E H D E

B

G H

E F H

C

B C

A

E FD

G H

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UMLS UMLS A twoA two--level structurelevel structure

TwoTwo--level structurelevel structureSemantic NetworkSemantic Network

135 Semantic Types (135 Semantic Types (STsSTs))54 types of relationships54 types of relationshipsamong among STsSTs

MetathesaurusMetathesaurus>1M concepts>1M concepts~12 M inter~12 M inter--conceptconceptrelationshipsrelationships

Link = categorizationLink = categorizationConcept

Metathesaurus

SemanticType

Semantic Network

categorization

Heart

Concepts

Metathesaurus

22

225

97

4

12

9 31

Esophagus

Left PhrenicNerve

HeartValves

FetalHeart

Medias-tinum

SaccularViscus

AnginaPectoris

CardiotonicAgents

TissueDonors

AnatomicalStructure

Fully FormedAnatomical

StructureEmbryonicStructure

Body Part, Organ orOrgan Component Pharmacologic

Substance

Disease orSyndrome

PopulationGroup

Semantic Types

SemanticNetwork

[…]

[…]

MeSHBrowser

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SemNavSemNav Visualization optionsVisualization options

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SemNavSemNav RelationshipsRelationships

Dystrophin

Concepts

Semantic Types

MuscularDystrophy,Duchenne

190

Amino Acid,Peptide or Protein

Disease orSyndrome

Biologically ActiveSubstance

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Technical detailsTechnical details

Simple web/Simple web/cgicgi technology (apache, Perl)technology (apache, Perl)dot (dot (GraphVizGraphViz))

PNG file (PNG file (--TpngTpng))ClientClient--side map (side map (--TcmapTcmap))

PrecomputePrecompute the transitive closure on hierarchical the transitive closure on hierarchical relations to perform the transitive closure fastrelations to perform the transitive closure fastRemove cycles (UMLS)Remove cycles (UMLS)

MedicalOntologyResearch

Olivier BodenreiderOlivier Bodenreider

Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical CommunicationsBethesda, Maryland Bethesda, Maryland -- USAUSA

Contact:Contact:Web:Web:

olivier@nlm.nih.govolivier@nlm.nih.govmor.nlm.nih.govmor.nlm.nih.gov