biomedical knowledge repository and semantic …2007/06/25 · biomedical knowledge repository and...

Biomedical Knowledge RepositoryBiomedical Knowledge Repositoryand Semantic Medlineand Semantic Medline

Olivier BodenreiderOlivier Bodenreider, M.D., Ph.D., M.D., Ph.D.Thomas C. RindfleschThomas C. Rindflesch, Ph.D., Ph.D.

National Institute of AllergyNational Institute of Allergyand Infectious Diseasesand Infectious DiseasesJune 25, 2007June 25, 2007

2Lister 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


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


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


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


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


Formalism Formalism TriplesTriples

FactsFactsAssertionsAssertionsRelationsRelationsSemantic predicationsSemantic predicationsRDF triplesRDF triples

Imipramine Panic Disorder

treats

APP Alzheimer disease

has_associated_disease

concept1 concept2

relationship


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


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



QuestionAnswering

KnowledgeDiscovery



annotations)

UMLSTerminological

Knowledge

GO


Knowl. Bases



BiomedicalKnowledgeRepositoryStructured

Knowl. Bases

EntrezGene

Advanced Library Services Pilot projectsAdvanced Library Services Pilot projects


Populating the repository Exploiting the repository

Source selection(PubMed)

XSLT


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)


…


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


…

APP(GeneID: 351)

amyloid beta A4 protein

has_protein_name


APP (geneid-351) amyloid beta A4 protein

eg:has_protein_reference_name_E

subject predicate object

RDF triple RDF triple Gene propertyGene property


RDF graph RDF graph Connecting several genesConnecting several genes

PARK1 Parkinson disease


MAPT Parkinson disease

MAPT Pick disease

TBP Parkinson disease

TBP Spinocerebellar ataxia


Parkinson diseaseMAPT

Pick disease

Parkinson diseaseTBP

Spinocerebellar ataxia


MAPT Pick disease

TBP Spinocerebellar ataxia


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



Alzheimer disease

Parkinson disease

Neurodegenerative diseases

isa


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.



QuestionAnswering

KnowledgeDiscovery



annotations)

UMLSTerminological

Knowledge

GO


Knowl. Bases




Advanced Library Services Pilot projectsAdvanced Library Services Pilot projects


Populating the repository Exploiting the repository

Source selection(PubMed)


SemRep


Managing retrieval resultsManaging retrieval results

Information retrieval

summarization

Semantic Medline

HIV

Network of relations

retrieval

500 citations


Managing retrieval resultsManaging retrieval results

HIV


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


StructuredBiomedical

DataUMLS

SemanticPredications

SemRep

InformativeGraph

Visualize

SalientSemantic

Predications

Summarize

Semantic Medline Semantic Medline OverviewOverview

Text

MEDLINEClinicalTrials.gov

PubMedEssieQuery



DataUMLS


SemRep

InformativeGraph

Visualize

SalientSemantic

Predications

Summarize

Document selectionDocument selection

Text


PubMedQuery “HIV”““HIVHIV””



DataUMLS


SemRep

InformativeGraph

Visualize

SalientSemantic

Predications

Summarize

MEDLINE citationsMEDLINE citations


PubMedEssieQuery

Text…… Tat activities, which play a Tat activities, which play a role in HIV disease development.role in HIV disease development.

……increased risk of invasive increased risk of invasive pneumococcalpneumococcal infection observed infection observed in HIVin HIV--1 infection.1 infection.



Data

InformativeGraph

Visualize

SalientSemantic

Predications

Summarize

Semantic Semantic intepretationintepretation


PubMedEssieQuery

UMLS


SemRep

Text


Semantic interpretationSemantic interpretation

…… TatTat activities, which activities, which play a role play a role in in HIV diseaseHIV diseasedevelopment.development.

tat genes HIV Infectionsassociated_with

……increased risk of invasive increased risk of invasive pneumococcalpneumococcal infectioninfectionobserved observed inin HIVHIV--1 infection1 infection..

Pneumococcal Infections HIV Infectionsco-exists_with



DataUMLS

SemRep

InformativeGraph

Visualize

SalientSemantic

Predications

Summarize

Semantic predicationsSemantic predications

Text


PubMedEssieQuery


tat genes Toxic effectcauses

Pneumococcal Infections HIV Infectionsco-exist_with


HIV Infections Personsprocess_of

Disease HIV Infectionsco-exist_with

… … …



DataUMLS

SemRep

InformativeGraph

Visualize

SummarizationSummarization

Text


PubMedEssieQuery

SalientSemantic

Predications

Summarize



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



DataUMLS

SemRep

InformativeGraph

VisualizeSummarize

Salient semantic predicationsSalient semantic predications

Text

MEDLINE

PubMedQuery


SalientSemantic

Predications

tat genes Toxic effectcauses

Pneumococcal Infections HIV Infectionsco-exist_with


HIV Infections Personsprocess_of

Disease HIV Infectionsco-exist_with

… … …



DataUMLS

SemRep Summarize

VisualizationVisualization

Text


PubMedEssieQuery


InformativeGraph

Visualize

SalientSemantic

Predications


SemRep Summarize

Informative graphInformative graph


PubMedEssieQuery


Visualize

SalientSemantic

Predications


DataUMLS

Text InformativeGraph

PneumococcalInfectionsToxic effect

HIV Infections

tat gene

causes

associated_with

co-exists_with


Semantic Medline Semantic Medline LiveLive


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


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


AcknowledgmentsAcknowledgments

Caroline AhlersCaroline AhlersMariana DimitrovMariana DimitrovMarcelo FiszmanMarcelo FiszmanHalil KilicogluHalil KilicogluFranFranççoisois--Michel LangMichel LangLee PetersLee PetersAnna RippleAnna RippleGraciela RosemblatGraciela RosemblatSatyaSatya SahooSahooKelly Kelly ZengZeng


ReferencesReferences

Bodenreider O, Bodenreider 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

http://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 BodenreiderOlivier Bodenreider [email protected]@nlm.nih.govThomas C. Thomas C. RindfleschRindflesch [email protected]@nlm.nih.gov

biomedical knowledge repository and semantic …2007/06/25 · biomedical knowledge repository and...

Documents