unified medical language system semantic navigator · 14-11-2006 · semantic type semantic...
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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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2Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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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3Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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
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UMLS Semantic Navigator SemNav
http://umlsks.nlm.nih.gov*
► SN Resources ► Semantic Navigator(* free UMLS registration required)
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5Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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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6Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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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7Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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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8Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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
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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
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[…]
[…]
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MeSHBrowser
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13Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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14Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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15Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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16Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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17Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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18Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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19Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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20Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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21Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
SemNavSemNav Visualization optionsVisualization options
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22Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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26Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
SemNavSemNav RelationshipsRelationships
Dystrophin
Concepts
Semantic Types
MuscularDystrophy,Duchenne
190
Amino Acid,Peptide or Protein
Disease orSyndrome
Biologically ActiveSubstance
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27Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
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)
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MedicalOntologyResearch
Olivier BodenreiderOlivier Bodenreider
Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical CommunicationsBethesda, Maryland Bethesda, Maryland -- USAUSA
Contact:Contact:Web:Web:
[email protected]@nlm.nih.govmor.nlm.nih.govmor.nlm.nih.gov