Advanced Library Services Advanced Library Services Developing a Biomedical Knowledge RepositoryDeveloping a Biomedical Knowledge Repository
to Support Advanced Information Management Applicationsto Support Advanced Information Management Applications
Olivier BodenreiderOlivier Bodenreider, M.D., Ph.D., M.D., Ph.D.Thomas C. RindfleschThomas C. Rindflesch, Ph.D., Ph.D.
Biomedical Information Science and Technology Initiativeand Roadmap Implementation Working Group
February 1, 2007
2Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
BKR as a KEBRBKR as a KEBR
Some characteristics of Some characteristics of KEBRsKEBRsInteroperability Interoperability –– permit integration across multiple data formspermit integration across multiple data formsAdaptability Adaptability –– adaptable in real time to new knowledgeadaptable in real time to new knowledge““EvolvabilityEvolvability”” –– biomedical research community needs exert the biomedical research community needs exert the prime selection pressure on the evolution of knowledge prime selection pressure on the evolution of knowledge environments environments SustainabilitySustainability
3Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
ContextContext
Provide biomedical informationProvide biomedical informationto health care professionals and consumersto health care professionals and consumers
Exploit NLM resourcesExploit NLM resourcesMaintain NLMMaintain NLM’’s cutting edges cutting edge
Proposal overviewAdvanced Library ServicesBiomedical Knowledge Repository
Pilot projects
Proposal overviewProposal overviewAdvanced Library ServicesAdvanced Library ServicesBiomedical Knowledge RepositoryBiomedical Knowledge Repository
Pilot projectsPilot projects
4Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Why additional services?Why additional services?
Biomedical information is growing at an Biomedical information is growing at an increasingly faster paceincreasingly faster pace
HighHigh--throughput approach to knowledge processingthroughput approach to knowledge processingInformation retrieval is the starting point, not the Information retrieval is the starting point, not the end of the journey for the researcherend of the journey for the researcher
Towards Towards ““computablecomputable”” knowledgeknowledgeIntegration between literature and other resources Integration between literature and other resources is insufficientis insufficient
Adequate for navigation purposesAdequate for navigation purposesInsufficient for knowledge processingInsufficient for knowledge processing
5Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
What additional services?What additional services?
Refined information retrievalRefined information retrievalIndexing on relations in addition to conceptsIndexing on relations in addition to conceptsFind articles asserting that Find articles asserting that ILIL--13 inhibits COX13 inhibits COX--22
MultiMulti--document summarizationdocument summarizationExtract and visualize facts from the literatureExtract and visualize facts from the literatureSummarize the top 300 papers on Summarize the top 300 papers on panic disorderpanic disorder
Question answeringQuestion answeringClinical and biological questionsClinical and biological questionsWhat drugs What drugs interactinteract with with imipramineimipramine??
Knowledge discoveryKnowledge discoveryReasoning with facts from heterogeneous resourcesReasoning with facts from heterogeneous resourcesFrom MEDLINE and UMLS togetherFrom MEDLINE and UMLS together
6Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Normalized and integrated knowledgeNormalized and integrated knowledge
Normalized knowledgeNormalized knowledgeCommon formatCommon formatCommon identification mechanismCommon identification mechanism
Integrated knowledgeIntegrated knowledgeSingle repositorySingle repositorySeamless environmentSeamless environmentPhenotype and genotype information togetherPhenotype and genotype information together
Biomedical Knowledge Repository
7Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Sources of knowledgeSources of knowledge
Biomedical literatureBiomedical literaturePredications extracted from Predications extracted from MEDLINEMEDLINE abstracts and fullabstracts and full--text text publicly available articles using text mining techniquespublicly available articles using text mining techniquesOther corpora (e.g., Other corpora (e.g., ClinicalTrials.govClinicalTrials.gov))
Terminological knowledgeTerminological knowledgeUMLSUMLS
Structured knowledge basesStructured knowledge basesNCBI resources (e.g., NCBI resources (e.g., Entrez GeneEntrez Gene))Functional annotations from model organism databasesFunctional annotations from model organism databases……
Contributed knowledgeContributed knowledgeThe repository is open to collaborators outside NLMThe repository is open to collaborators outside NLM
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Formalism Formalism TriplesTriples
FactsFactsAssertionsAssertionsRelationsRelationsSemantic predicationsSemantic predicationsRDF triplesRDF triples
Imipramine Panic Disorder
treats
APP Alzheimer disease
has_associated_disease
concept1 concept2
relationship
9Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Annotated knowledgeAnnotated knowledge
Provenance informationProvenance informationSource (e.g., PMID)Source (e.g., PMID)Extraction mechanismExtraction mechanismTimestampTimestamp
Frequency informationFrequency informationRedundancyRedundancy
Collaborative annotationCollaborative annotation““Was this information useful?Was this information useful?””Context of use/usefulnessContext of use/usefulness
10Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Semantic Web perspectiveSemantic Web perspective
Common format for knowledgeCommon format for knowledgeResource Description Format (RDF)Resource Description Format (RDF)
Common identification schemeCommon identification schemeUnified Resource Identifier (URI)Unified Resource Identifier (URI)
Standard toolsStandard toolsRDF browsersRDF browsersRDF RDF ““reasonersreasoners””
High level of interest for biomedicine in the SW High level of interest for biomedicine in the SW communitycommunity
Health Care and Life Sciences Interest GroupHealth Care and Life Sciences Interest Group
BiomedicalKnowledgeRepository
InformationRetrieval
QuestionAnswering
KnowledgeDiscovery
DocumentSummarization
Sourceselection(PubMed,
annotations)
UMLSTerminological
Knowledge
GO
EntrezGene Structured
Knowl. Bases
ContributedKnowledge
Advanced Library Services SummaryAdvanced Library Services Summary
MEDLINE BiomedicalLiteratureCT.gov
BiomedicalKnowledgeRepository
InformationRetrieval
QuestionAnswering
KnowledgeDiscovery
DocumentSummarization
Sourceselection(PubMed,
annotations)
UMLSTerminological
Knowledge
GO
EntrezGene Structured
Knowl. Bases
ContributedKnowledge
MEDLINE BiomedicalLiteratureCT.gov
BiomedicalKnowledgeRepositoryStructured
Knowl. Bases
EntrezGene
Advanced Library Services Pilot projectsAdvanced Library Services Pilot projects
DocumentSummarization
Populating the repository Exploiting the repository
Source selection(PubMed)
XSLT
MEDLINE BiomedicalLiteratureCT.gov
SemRep
Pilot #1Pilot #1
Populating and exploiting thePopulating and exploiting theBiomedical Knowledge RepositoryBiomedical Knowledge Repository
Converting Entrez Gene into RDFConverting Entrez Gene into RDF
With With SatyaSatya SahooSahoo (U. Georgia)(U. Georgia)and and Kelly Kelly ZengZeng (LHC)(LHC)
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…
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OverviewOverview
XML(file)XML(file)
RDF(file)RDF(file)
RDF(Oracle)
RDF(Oracle)
JAPX Jena
XSLTStylesheet
XSLTStylesheet
124 element tags2M genes
106 properties410M triples
Names has_name
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…
APP(GeneID: 351)
amyloid beta A4 protein
has_protein_name
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APP (geneid-351) amyloid beta A4 protein
eg:has_protein_reference_name_E
subject predicate object
RDF triple RDF triple Gene propertyGene property
18Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
RDF graph RDF graph Connecting several genesConnecting several genes
PARK1 Parkinson disease
has_associated_disease
MAPT Parkinson disease
MAPT Pick disease
TBP Parkinson disease
TBP Spinocerebellar ataxia
PARK1 Parkinson disease
Parkinson diseaseMAPT
Pick disease
Parkinson diseaseTBP
Spinocerebellar ataxia
PARK1 Parkinson disease
MAPT Pick disease
TBP Spinocerebellar ataxia
19Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Future workFuture work
Transform additional resources into RDFTransform additional resources into RDFUMLS MetathesaurusUMLS MetathesaurusOther NCBI databasesOther NCBI databasesDrug knowledge basesDrug knowledge bases……
Integrate resourcesIntegrate resourcesQuery across resourcesQuery across resources
APP Alzheimer disease
PARK1 Parkinson disease
has_associated_disease
Alzheimer disease
Parkinson disease
Neurodegenerative diseases
isa
20Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
From From glycosyltransferaseglycosyltransferaseto to congenital muscular dystrophycongenital muscular dystrophy
MIM:608840 Muscular dystrophy, congenital, type 1D
GO:0008375
has_associated_phenotype
has_molecular_function
EG:9215LARGE
acetylglucosaminyl-transferase
GO:0016757glycosyltransferase
GO:0008194isa
GO:0008375 acetylglucosaminyl-transferase
GO:0016758
Pilot #2Pilot #2
Populating and exploiting thePopulating and exploiting theBiomedical Knowledge RepositoryBiomedical Knowledge Repository
Semantic Medline:Semantic Medline:MultiMulti--document summarizationdocument summarization
and visualizationand visualization
With With Marcelo Fiszman, Marcelo Fiszman, M.D., Ph.D.M.D., Ph.D.and and Halil Kilicoglu,Halil Kilicoglu, M.S.M.S.
BiomedicalKnowledgeRepository
InformationRetrieval
QuestionAnswering
KnowledgeDiscovery
DocumentSummarization
Sourceselection(PubMed,
annotations)
UMLSTerminological
Knowledge
GO
EntrezGene Structured
Knowl. Bases
ContributedKnowledge
MEDLINE BiomedicalLiteratureCT.gov
BiomedicalKnowledgeRepository
Advanced Library Services Pilot projectsAdvanced Library Services Pilot projects
DocumentSummarization
Populating the repository Exploiting the repository
Source selection(PubMed)
MEDLINE BiomedicalLiteratureCT.gov
SemRep
23Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Managing retrieval resultsManaging retrieval results
Information retrieval
summarization
Semantic Medline
panic disorder
Network of relations
retrieval
300 citations
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Managing retrieval resultsManaging retrieval results
panic disorder
25Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Guiding principlesGuiding principles
VisualizationVisualizationOverview firstOverview firstDetails on demandDetails on demand
Integration of knowledge contentIntegration of knowledge contentAutomated management of knowledge from textAutomated management of knowledge from textSeamless application interfaces Seamless application interfaces
[Shneiderman 1996]
[BoSC, April, 2006]
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Seamless integration of technologiesSeamless integration of technologies
Information retrievalInformation retrievalPubMed PubMed -- MEDLINEMEDLINEEssie Essie -- ClinicalTrials.govClinicalTrials.gov
Natural language processing: Natural language processing: SemRepSemRepRepresent content of text with semantic predicationsRepresent content of text with semantic predications
Abstraction summarizationAbstraction summarizationInformative: Overview of most salient informationInformative: Overview of most salient information
VisualizationVisualizationIndicative: Links to source text and additional informationIndicative: Links to source text and additional information
27Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
StructuredBiomedical
DataUMLS
SemanticPredications
SemRep
InformativeGraph
Visualize
SalientSemantic
Predications
Summarize
Semantic Medline Semantic Medline OverviewOverview
Text
MEDLINEClinicalTrials.gov
PubMedEssieQuery
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StructuredBiomedical
DataUMLS
SemanticPredications
SemRep
InformativeGraph
Visualize
SalientSemantic
Predications
Summarize
Document selectionDocument selection
Text
MEDLINEClinicalTrials.gov
PubMedEssieQuery “panic disorder”““panic disorderpanic disorder””
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StructuredBiomedical
DataUMLS
SemanticPredications
SemRep
InformativeGraph
Visualize
SalientSemantic
Predications
Summarize
MEDLINE citationsMEDLINE citations
MEDLINEClinicalTrials.gov
PubMedEssieQuery
Text…… characterization of the characterization of the specific effects of specific effects of imipramineimipramine in in the treatment of panic disorderthe treatment of panic disorder……
……evidence that evidence that pharmacopharmaco--therapy leads to significant therapy leads to significant reductions in anxiety symptoms reductions in anxiety symptoms ……
30Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
StructuredBiomedical
Data
InformativeGraph
Visualize
SalientSemantic
Predications
Summarize
Semantic Semantic intepretationintepretation
MEDLINEClinicalTrials.gov
PubMedEssieQuery
UMLS
SemanticPredications
SemRep
Text
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Semantic interpretationSemantic interpretation
... ... characterization of the specific effects of imipramine in the treatment of panic disorder ……
Imipramine Panic Disordertreats
……evidence that pharmacotherapy leads to significant reductions in anxiety symptoms ……
Pharmacotherapy Anxiety symptomstreats
32Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
StructuredBiomedical
DataUMLS
SemRep
InformativeGraph
Visualize
SalientSemantic
Predications
Summarize
Semantic predicationsSemantic predications
Text
MEDLINEClinicalTrials.gov
PubMedEssieQuery
SemanticPredications
Imipramine Panic Disordertreats
Panic Disorder Agoraphobiacoexists_with
Alprazolam Panic Disordertreats
Pharmacotherapy Anxiety symptomstreats
Panic Disorder Patientsprocess_of
… … …
33Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
StructuredBiomedical
DataUMLS
SemRep
InformativeGraph
Visualize
SummarizationSummarization
Text
MEDLINEClinicalTrials.gov
PubMedEssieQuery
SalientSemantic
Predications
Summarize
SemanticPredications
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Abstraction summarizationAbstraction summarization
AllPredications
Reduction SalientPredications
Specify a topicSpecify a topicRetain predications on the topicRetain predications on the topicEliminate uninformative predicationsEliminate uninformative predicationsRetain most frequent predicationsRetain most frequent predications
35Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
StructuredBiomedical
DataUMLS
SemRep
InformativeGraph
VisualizeSummarize
Salient semantic predicationsSalient semantic predications
Text
MEDLINEClinicalTrials.gov
PubMedEssieQuery
SemanticPredications
SalientSemantic
Predications
Imipramine Panic Disordertreats
Panic Disorder Agoraphobiacoexists_with
Alprazolam Panic Disordertreats
Pharmacotherapy Anxiety symptomstreats
Panic Disorder Patientsprocess_of
… … …
36Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
StructuredBiomedical
DataUMLS
SemRep Summarize
VisualizationVisualization
Text
MEDLINEClinicalTrials.gov
PubMedEssieQuery
SemanticPredications
InformativeGraph
Visualize
SalientSemantic
Predications
37Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
SemRep Summarize
Informative graphInformative graph
MEDLINEClinicalTrials.gov
PubMedEssieQuery
SemanticPredications
Visualize
SalientSemantic
Predications
StructuredBiomedical
DataUMLS
Text InformativeGraph
AlprazolamImipramine
Panic Disorder
Agoraphobia
treats
coexists_with
treats
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Semantic Medline Semantic Medline LiveLive
39Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Related research Related research Visualizing relationsVisualizing relations
Maps of linked concepts among documentMaps of linked concepts among document
Literature network of coLiterature network of co--occurring genesoccurring genes
Associative concept space for discoveryAssociative concept space for discovery
Genomic information across structured and textual Genomic information across structured and textual databasesdatabases
[Fuller et al. 2004]
[Jensen et al. 2001]
[van der Eijk et al. 2004]
[Tao et al. 2005]
40Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Future workFuture work
Process all of MEDLINE/PubMedProcess all of MEDLINE/PubMedWith SemRepWith SemRep
Incrementally integrate structured knowledge sourcesIncrementally integrate structured knowledge sourcesEntrez databasesEntrez databasesUMLSUMLSGenetics Home ReferenceGenetics Home Reference
Implementation Implementation EfficiencyEfficiencyLarge amount of dataLarge amount of data
41Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
Applications / CollaborationsApplications / Collaborations
NHLBINHLBIHelp for the elaboration of clinical guidelinesHelp for the elaboration of clinical guidelines
Center for the Application of Research DiscoveriesCenter for the Application of Research DiscoveriesDr. Gregory J. Dr. Gregory J. MoroscoMoroscoCenter for Research Informatics and Information TechnologyCenter for Research Informatics and Information TechnologyDr. Charles FriedmanDr. Charles Friedman
Collaboration with other ICs welcomeCollaboration with other ICs welcome
42Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
SummarySummary
Deliver health informationDeliver health informationBiomedical Knowledge RepositoryBiomedical Knowledge RepositoryAdvanced Library ServicesAdvanced Library Services
ExploitExploitCurrent Library resourcesCurrent Library resourcesAdvanced information technologyAdvanced information technology
Support timely translationSupport timely translationOf biomedical researchOf biomedical researchInto improvements in patient careInto improvements in patient careand public healthand public health
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AcknowledgmentsAcknowledgments
Caroline AhlersCaroline AhlersMariana DimitrovMariana DimitrovMarcelo FiszmanMarcelo FiszmanHalil KilicogluHalil KilicogluFranFranççoisois--Michel LangMichel LangLee PetersLee PetersAnna RippleAnna RippleGraciela RosemblatGraciela RosemblatSatyaSatya SahooSahooKelly Kelly ZengZeng
44Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications
ReferencesReferences
BodenreiderBodenreider O, O, RindfleschRindflesch TC. TC. Advanced library Advanced library services: Developing a biomedical knowledge services: Developing a biomedical knowledge repository to support advanced information repository to support advanced information management applications.management applications. Technical report. Technical report. Bethesda, Maryland: Lister Hill National Center Bethesda, Maryland: Lister Hill National Center for Biomedical Communications, National Library for Biomedical Communications, National Library of Medicine; September 14, 2006.of Medicine; September 14, 2006.http://lhncbc.nlm.nih.gov/lhc/docs/reports/2006/tr2006001.pdfhttp://lhncbc.nlm.nih.gov/lhc/docs/reports/2006/tr2006001.pdf
Lister Hill National CenterLister Hill National Centerfor Biomedical Communicationsfor Biomedical CommunicationsBethesda, Maryland Bethesda, Maryland -- USAUSA
AdvancedLibraryServices
Olivier Olivier BodenreiderBodenreider [email protected]@nlm.nih.govThomas C. Thomas C. RindfleschRindflesch [email protected]@nlm.nih.gov