biomedical ontology and drug information · 11/05/2006 · lister hill national center for...
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Biomedical OntologyAnd Drug Information
Olivier BodenreiderOlivier Bodenreider
Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical CommunicationsBethesda, Maryland Bethesda, Maryland -- USAUSA
Bethesda, MarylandMay 11, 2006
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2Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
OutlineOutline
Drug vocabulariesDrug vocabularies
Drug vocabulary integration: Drug vocabulary integration: UMLSUMLS
Drug vocabulary standardization: Drug vocabulary standardization: RxNormRxNorm
Visualization and processingVisualization and processingof drug information: of drug information: RxNavRxNav
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Drug Vocabularies
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Drug vocabulariesDrug vocabularies
Master Drug Data BaseMaster Drug Data Base((MediMedi--Span, Span, WoltersWolters KluwerKluwer Health)Health)
MultumMultum MediSourceMediSource LexiconLexicon
MicromedexMicromedex DRUGDEXDRUGDEX
FDA National Drug Code DirectoryFDA National Drug Code Directory
NatNat’’l Drug Data File Plus Source Vocabulary l Drug Data File Plus Source Vocabulary (First (First DataBankDataBank Inc.)Inc.)
Veterans Health Administration National Drug Veterans Health Administration National Drug FileFile
9
43
9
21
54
21
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Drugs in SNOMED CTDrugs in SNOMED CT
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Drugs in SNOMED CTDrugs in SNOMED CT
18,735 drug concepts in SNOMED CT (<10%)
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Drugs in Drugs in MeSHMeSH
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Drugs in Drugs in MeSHMeSH
8,140 drug descriptors in MeSH (~30%)
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Drug vocabulary integration
Unified Medical Language System
UMLS
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Source VocabulariesSource Vocabularies
140 source vocabularies140 source vocabularies17 languages17 languages
Broad coverage of biomedicineBroad coverage of biomedicine5M names5M names
1.3M concepts1.3M concepts
16M relations16M relations
Common presentationCommon presentation
(2006AA)
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Integrating Integrating subdomainssubdomains
Biomedicalliterature
Biomedicalliterature
MeSH
GenomeannotationsGenome
annotations
GOModelorganisms
Modelorganisms
NCBITaxonomy
Geneticknowledge bases
Geneticknowledge bases
OMIM
Clinicalrepositories
Clinicalrepositories
SNOMEDOthersubdomains
Othersubdomains
…
AnatomyAnatomy
UWDA
UMLS
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MetathesaurusMetathesaurus conceptconcept
Acetaminophen
C0000970
AcetaminophenAcetamide, N-(4-hydroxyphenyl)-AcetamidophenolAcetominophenACMPAPAPHydroxyacetanilideN-(4-Hydroxyphenyl)acetanilideN-Acetyl-p-aminophenolp-AcetamidophenolParacetamolp-Hydroxyacetanilide
Paracétamol - FrenchAzetaminophen - GermanAcetaminofene - ItalianHidroxiacetanilida - PortugueseПАРАЦЕТАМОЛ - RussianAcetaminofeno - Spanish
Analgesic antipyretic derivative of acetanilide. It has weak anti-inflammatory properties and is used as a common analgesic, but may cause liver, blood cell, and kidney damage.
SNOMED CT MeSHMultumNDDF…
PharmacologicSubstance
OrganicChemical
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MetathesaurusMetathesaurus drug conceptsdrug concepts
Semantic typesSemantic typesPharmacologic SubstancePharmacologic Substance 101,801101,801
AntiparkinsonAntiparkinson AgentsAgents
VidarabineVidarabine PhosphatePhosphate
AntibioticAntibiotic 3,5923,592KanamycinKanamycin
Clinical DrugClinical Drug 165,378165,378Afrin Nose Drops 0.05%Afrin Nose Drops 0.05%
VerapamilVerapamil Oral Tablet [Oral Tablet [CalanCalan]]
270,000 concepts
(~21% of allMetathesaurus
concepts)
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Organize conceptsOrganize concepts
InterInter--concept concept relationships: hierarchies relationships: hierarchies from the source from the source vocabulariesvocabularies
Redundancy: multiple Redundancy: multiple pathspaths
One 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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MetathesaurusMetathesaurus relationsrelations
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Drug vocabulary standardization
RxNorm
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MotivationMotivation
Exchange of information requires standardized Exchange of information requires standardized namesnames
Ordering drugsOrdering drugs
Checking interactionsChecking interactions
Inventory managementInventory management
No standard naming conventions for drugsNo standard naming conventions for drugs
Integrating drug vocabulariesIntegrating drug vocabularies
Unique identifiers for drugsUnique identifiers for drugs
Specify relations among drug entitiesSpecify relations among drug entities
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Normalized formNormalized form
Ingredient
Dose form
Strength
Ingredient
IngredientStrength Dose form
Strength
4mg/ml
Ingredient
Fluoxetine
Dose form
Oral Solution
Semantic clinical drug component
Semantic clinical drug
Semantic clinical drug form
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Generic Generic vs.vs. BrandBrand
GenericGenericIngredientIngredient(IN)(IN)
Clinical drug formClinical drug form(SCDF)(SCDF)
Clinical drug componentClinical drug component(SCDC)(SCDC)
Clinical drugClinical drug(SCD)(SCD)
BrandBrandBrand nameBrand name(BN)(BN)
Branded drug formBranded drug form(SBDF)(SBDF)
Branded drug componentBranded drug component(SBDC)(SBDC)
Branded drugBranded drug(SBD)(SBD)
tradename_of
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Relations among drug entitiesRelations among drug entities
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RxNormRxNorm databasedatabase
Data sourcesData sourcesMaster Drug Data Base
MultumMultum MediSourceMediSource LexLex..
MicromedexMicromedex DRUGDEX DRUGDEX
FDA National Drug Code FDA National Drug Code Directory Directory
National Drug Data File National Drug Data File Plus Source Vocabulary Plus Source Vocabulary
VA National Drug File VA National Drug File
SNOMED Clinical Terms SNOMED Clinical Terms
ContentContent5,570 ingredients5,570 ingredients
10,788 brand names10,788 brand names
22,724 clinical drug comp.22,724 clinical drug comp.
29,734 clinical drugs29,734 clinical drugs
17,149 branded drugs17,149 branded drugs
16,447 branded drug comp.16,447 branded drug comp.
13,516 clinical drug forms13,516 clinical drug forms
13,035 branded drug forms 13,035 branded drug forms
140 dose forms 140 dose forms
(as of February 28, 2006)
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Visualization and processingof drug information
RxNav
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RxNavRxNav
Visualization and navigationVisualization and navigationRxNormRxNorm browserbrowser
Spelling correctionSpelling correction
Search on names and codesSearch on names and codes
Standalone applicationStandalone applicationRxNormRxNorm database at NLMdatabase at NLM
Local Local RxNormRxNorm databasedatabase
Drug information processingDrug information processingAPI to the API to the RxNormRxNorm databasedatabase
Web servicesWeb services
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RxNavRxNav demodemo
http://http://mor.nlm.nih.gov/download/rxnavmor.nlm.nih.gov/download/rxnav//
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Conclusions
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ConclusionsConclusions
Biomedical ontology and drug discoveryBiomedical ontology and drug discoveryOntologiesOntologies provideprovide
Terminology for entity recognition (text mining)Terminology for entity recognition (text mining)
Relations for reasoning about drugsRelations for reasoning about drugs
Terminology integration and standardization (Terminology integration and standardization (RxNormRxNorm) ) enables interoperability and mapping across enables interoperability and mapping across vocabulariesvocabularies
Entry point into knowledge basesEntry point into knowledge bases
Integration into broad Integration into broad ontologiesontologies (UMLS) enables (UMLS) enables information integration across information integration across subdomainssubdomains
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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
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ReferencesReferences
Drug vocabulariesMDDB http://www.medispan.com/Products/index.aspx?id=1
Multum http://www.multum.com/
DRUGDEXDRUGDEX http://http://www.micromedex.com/products/drugdexwww.micromedex.com/products/drugdex//
FDA NDC Dir.FDA NDC Dir. http://http://www.fda.gov/cder/ndcwww.fda.gov/cder/ndc//
NDDF PlusNDDF Plus http://http://www.firstdatabank.com/knowledge_bases/nddf_pluswww.firstdatabank.com/knowledge_bases/nddf_plus//
Other vocabulariesOther vocabulariesMeSH http://www.nlm.nih.gov/mesh/
SNOMED CT http://www.snomed.org/
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ReferencesReferences
Unified Medical Language System (UMLS)Unified Medical Language System (UMLS)http://www.nlm.nih.gov/research/umls/http://www.nlm.nih.gov/research/umls/Bodenreider O. (2004). Bodenreider O. (2004). The Unified Medical Language System The Unified Medical Language System (UMLS): Integrating biomedical terminology(UMLS): Integrating biomedical terminology. . Nucleic Acids Nucleic Acids ResearchResearch; D267; D267--D270.D270.
RxNormRxNormhttp://www.nlm.nih.gov/research/umls/rxnorm/index.htmlhttp://www.nlm.nih.gov/research/umls/rxnorm/index.html
RxNavRxNavhttp://http://mor.nlm.nih.gov/download/rxnavmor.nlm.nih.gov/download/rxnav//