From Terminology Integration to Interoperability2002/08/01 · Olivier Bodenreider Lister Hill...
Transcript of From Terminology Integration to Interoperability2002/08/01 · Olivier Bodenreider Lister Hill...
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Olivier BodenreiderOlivier Bodenreider
Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical CommunicationsBethesda, Maryland Bethesda, Maryland -- USAUSA
From Terminology Integrationto Interoperability
Information Technologies for HealthcareInformation Technologies for HealthcareBarriers to ImplementationBarriers to Implementation
NIST NIST -- August 1, 2002August 1, 2002
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2Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
The Problem The Problem Adrenal gland diseasesAdrenal gland diseases
Adrenal Gland Diseases
C0001621
Adrenal gland diseases MeSH D000307Adrenal disorder AOD 0000005418Disorder of adrenal gland Read C15z.Diseases of the adrenal glands SNOMED DB-70000
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3Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
OutlineOutline
◆◆ Case study:Case study:Unified Medical Language System (UMLS)Unified Medical Language System (UMLS)
◆◆ HistoryHistory
◆◆ OverviewOverview
◆◆ BenefitsBenefits
◆◆ LimitationsLimitations
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History
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5Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
MotivationMotivation
◆◆ Started in 1986Started in 1986
◆◆ National Library of MedicineNational Library of Medicine
◆◆ “Long“Long--term R&D project”term R&D project”
◆◆ Complementary to IAIMSComplementary to IAIMS
[Lindberg & al., Methods, 1993][Humphreys & al., JAMIA, 1998]
«[…] the UMLS project is an effort to overcome two significant barriers to effective retrieval of machine-readable information.
• The first is the variety of ways the same concepts are expressedin different machine-readable sources and by different people.
• The second is the distribution of useful information among many disparate databases and systems.»
(Integrated Academic(Integrated AcademicInformation Management Systems)Information Management Systems)
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6Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
UMLS research teamUMLS research team
◆◆ Bill HoleBill Hole
◆◆ L. Kingsland IIIL. Kingsland III
◆◆ Dan Dan MasysMasys
◆◆ Alexa Alexa McCrayMcCray
◆◆ Stuart NelsonStuart Nelson
◆◆ Roy Roy RadaRada
◆◆ Rick RodgersRick Rodgers
◆◆ Peri Peri SchuylerSchuyler
◆◆ Brigham & Women’s H.Brigham & Women’s H.
◆◆ CarnegieCarnegie--Mellon Univ.Mellon Univ.
◆◆ Columbia Univ.Columbia Univ.
◆◆ Lexical Technology, Inc.Lexical Technology, Inc.
◆◆ Massachusetts General H.Massachusetts General H.
◆◆ UCSFUCSF
◆◆ Univ. of PittsburghUniv. of Pittsburgh
◆◆ Univ. of UtahUniv. of Utah
◆◆ […][…]
[Humphreys & al., JAMIA, 1998]
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7Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
UMLS chronologyUMLS chronology
◆◆ Definition of 3 knowledge sources (1986Definition of 3 knowledge sources (1986--88)88)●● MetathesaurusMetathesaurus
●● Semantic NetworkSemantic Network
●● Information Sources MapInformation Sources Map
◆◆ Building, distributing, and testing (1989Building, distributing, and testing (1989--91)91)●● Integration vs. Integration vs. ad hocad hoc development development
●● First release in 1990First release in 1990
◆◆ Development of applications (1992Development of applications (1992--94)94)
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Overview
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9Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Biomedical terminologiesBiomedical terminologies
◆◆ Core vocabulariesCore vocabularies●● anatomy (UWDA,anatomy (UWDA, NeuronamesNeuronames))
●● drugs (Firstdrugs (First DataBankDataBank,, MicromedexMicromedex))
●● medical devices (UMD, SPN)medical devices (UMD, SPN)
◆◆ Several perspectivesSeveral perspectives●● clinical terms (SNOMED, CTV3)clinical terms (SNOMED, CTV3)
●● information sciences (MeSH, CRISP)information sciences (MeSH, CRISP)
●● administrative terminologies (ICDadministrative terminologies (ICD--99--CM, CPTCM, CPT--4)4)
●● standards (HL7, LOINC)standards (HL7, LOINC)
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10Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Biomedical terminologies Biomedical terminologies (cont’d)(cont’d)
◆◆ Specialized vocabulariesSpecialized vocabularies●● nursing (NIC, NOC, NANDA, Omaha, PCDS)nursing (NIC, NOC, NANDA, Omaha, PCDS)
●● dentistry (CDT)dentistry (CDT)
●● oncology (PDQ)oncology (PDQ)
●● psychiatry (DSM, APA)psychiatry (DSM, APA)
●● adverse reactions (COSTART, WHO ART)adverse reactions (COSTART, WHO ART)
●● primary care (ICPC)primary care (ICPC)
◆◆ Knowledge bases (AI/Rheum, Knowledge bases (AI/Rheum, DXplainDXplain, QMR), QMR)
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Adrenal Cortex Diseases
Hypoadrenalism
Adrenal Gland Hypofunction
Adrenal cortical hypofunction
Endocrine Diseases
Adrenal Gland Diseases
organize concepts
Addison’s Disease
UMLS
SNOMEDMeSHAODRead Codes
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Endocrine Diseases
Adrenal Gland Diseases
Adrenal Cortex Diseases
Adrenal Cortex Dysfunction
Hypoadrenalism
Adrenal Gland Hypofunction
Adrenal cortical hypofunction
Addison’s Disease
Addison’s disease due to autoimmunity
Adrenal DysfunctionAdrenal Glands
Adrenal Cortex
Secondary hypocortisolism
Endocrine System
Endocrine Glands
Abdominal organ
Other disorders ofadrenal gland
Disorders of otherendocrine gland
Diseases
C0494313
C0014133
C0001625
C0014136 C0446633 C0012674
C0014130
C0549609
C0001621
C0348453
C0001614
C0235454
C0549149C0001613
C0001623
C0405580
C0271738 C0001403
C0271737Metathesaurus
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13Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
UMLSUMLS
◆◆ TwoTwo--level structurelevel structure●● Semantic NetworkSemantic Network
■■ 134 Semantic Types (134 Semantic Types (STsSTs))
■■ 54 types of relationships54 types of relationshipsamong among STsSTs
●● MetathesaurusMetathesaurus■■ 800,000 concepts800,000 concepts
■■ ~10 M inter~10 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 FormedAnatomicalStructure
EmbryonicStructure
Body Part, Organ orOrgan Component Pharmacologic
Substance
Disease orSyndrome
PopulationGroup
Semantic Types
SemanticNetwork
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Benefits
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16Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
UMLS compared to individual vocabulariesUMLS compared to individual vocabularies
◆◆ Broader scopeBroader scope
◆◆ Extended coverageExtended coverage
◆◆ Finer granularityFiner granularity
◆◆ Unique identifierUnique identifier
◆◆ Synonym terms clustered into conceptsSynonym terms clustered into concepts
◆◆ Additional synonymsAdditional synonyms
◆◆ Additional hierarchical relationshipsAdditional hierarchical relationships
◆◆ Semantic categorizationSemantic categorization
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Limitations
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18Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
LimitationsLimitations
◆◆ Licensing mechanismLicensing mechanism
◆◆ Too much informationToo much information
◆◆ Not enough informationNot enough information
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19Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Licensing mechanismLicensing mechanism
◆◆ Free UMLS registrationFree UMLS registration
◆◆ 4 levels of restriction4 levels of restriction●● L0 (~55%)L0 (~55%) must acknowledge NLM, no redistributionmust acknowledge NLM, no redistribution
●● L1 (~6%)L1 (~6%) must negotiate for translationmust negotiate for translation
●● L2 (~.1%)L2 (~.1%) must negotiate for creating health datamust negotiate for creating health data
●● L3 (~39%)L3 (~39%) must negotiate for must negotiate for anyany production useproduction use
◆◆ Possible license fees for certain vocabulariesPossible license fees for certain vocabularies
◆◆ MetamorphoSysMetamorphoSys helps subset by sourcehelps subset by source
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20Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Too much informationToo much information
◆◆ HugeHuge●● 1.5 M unique English strings1.5 M unique English strings
●● 775,000 concepts775,000 concepts
●● Over 10 M interconcept relationshipsOver 10 M interconcept relationships
◆◆ Complex twoComplex two--level structurelevel structure●● MetathesaurusMetathesaurus
●● Semantic NetworkSemantic Network
◆◆ Steep learning curveSteep learning curve
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21Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Not enough informationNot enough information
◆◆ UpdateUpdate●● FrequencyFrequency
●● MechanismMechanism
◆◆ Lack of coverageLack of coverage●● Major sourcesMajor sources
●● Major Major subdomainssubdomains
◆◆ Terminology vs. OntologyTerminology vs. Ontology
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Conclusions
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23Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Conclusions Conclusions The up sideThe up side
◆◆ Terminology integration is a step towards Terminology integration is a step towards interoperabilityinteroperability●● Clusters of synonyms from different sourcesClusters of synonyms from different sources
●● Paths between terms from different sourcesPaths between terms from different sources
Px
Py
Cy
Cz
Px
Py, Cy
Cz
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24Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Conclusions Conclusions The down sideThe down side
◆◆ However, interoperability requires more than However, interoperability requires more than loosely aligned terminologiesloosely aligned terminologies
◆◆ The UMLS does not claim to be an ontologyThe UMLS does not claim to be an ontology
◆◆ The UMLS is, however, a resource for acquiring The UMLS is, however, a resource for acquiring biomedical ontologiesbiomedical ontologies
Medical Ontology Research Project
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Contact:Contact: olivierolivier@@nlmnlm..nihnih..govgov
Olivier BodenreiderOlivier Bodenreider
Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical CommunicationsBethesda, Maryland Bethesda, Maryland -- USAUSA