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Semantic Medline:Semantic Medline:Multi-Document SummarizationMulti-Document Summarization
and Visualizationand Visualization
Thomas C. Rindflesch,Thomas C. Rindflesch, Ph.D. Ph.D.Marcelo Fiszman, Marcelo Fiszman, M.D., Ph.D.M.D., Ph.D.
Halil Kilicoglu,Halil Kilicoglu, M.S. M.S.
Lister Hill National Center for Lister Hill National Center for Biomedical CommunicationsBiomedical Communications
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 2
Information management applicationInformation management application
Manipulate information in addition to documentsManipulate information in addition to documents Manage the results of PubMed searchesManage the results of PubMed searches
Help users decide what to readHelp users decide what to read
Connect knowledge from various sourcesConnect knowledge from various sources Integrate application interfaces Integrate application interfaces
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 3
Managing retrieval resultsManaging retrieval results
Information retrieval
summarization
Semantic Medline
breast cancer
Network of relations
retrieval
500 citations
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 4
Managing retrieval resultsManaging retrieval results
breast cancer
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 5
Seamless integration of technologiesSeamless integration of technologies
Information retrievalInformation retrieval PubMed - MEDLINEPubMed - MEDLINE
Natural language processing: Natural language processing: SemRepSemRep Represent content of text with semantic predicationsRepresent content of text with semantic predications
Abstraction summarizationAbstraction summarization Informative: Overview of most salient informationInformative: Overview of most salient information
VisualizationVisualization Indicative: Links to source text and additional informationIndicative: Links to source text and additional information
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 6
StructuredBiomedical
DataUMLS
SemanticPredications
SemRep
InformativeGraph
Visualize
SalientSemanticPredications
Summarize
Semantic Medline Semantic Medline OverviewOverview
Text
MEDLINEClinicalTrials.gov
PubMedQuery
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 7
StructuredBiomedical
DataUMLS
SemanticPredications
SemRep
InformativeGraph
Visualize
SalientSemanticPredications
Summarize
Document selectionDocument selection
Text
MEDLINEClinicalTrials.gov
PubMedQuery ““breast cancer”breast cancer”““breast cancer”breast cancer”
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 8
StructuredBiomedical
DataUMLS
SemanticPredications
SemRep
InformativeGraph
Visualize
SalientSemanticPredications
Summarize
MEDLINE citationsMEDLINE citations
MEDLINEClinicalTrials.gov
PubMedQuery
Text
… … aromatase inhibitor provides aromatase inhibitor provides mortality benefit in early breast mortality benefit in early breast carcinomacarcinoma ……
……determined the spectrum and determined the spectrum and frequency of ATM missense frequency of ATM missense variants in 443 breast cancer variants in 443 breast cancer patientspatients ……
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 9
StructuredBiomedical
Data
InformativeGraph
Visualize
SalientSemanticPredications
Summarize
Semantic intepretationSemantic intepretation
MEDLINEClinicalTrials.gov
PubMedQuery
UMLS
SemanticPredications
SemRep
Text
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 10
Semantic interpretationSemantic interpretation
... ... aromatase inhibitor provides mortality benefit in early breast carcinoma … …
Aromatase Inhibitors Breast Carcinomatreats
… … determined the spectrum and frequency of ATM missense variants in 443 breast cancer patients … …
ATM gene Breast Carcinomaassociated_with
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 11
StructuredBiomedical
DataUMLS
SemRep
InformativeGraph
Visualize
SalientSemanticPredications
Summarize
Semantic predicationsSemantic predications
Text
MEDLINEClinicalTrials.gov
PubMedQuery
SemanticPredications
Aromatase Inhibitors Breast Carcinomatreats
ATM gene Breast Carcinomaassociated_with
Tamoxifen Breast Carcinomatreats
Tamoxifen Patientstreats
Breast Carcinoma Individualprocess_of
… … …
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 12
StructuredBiomedical
DataUMLS
SemRep
InformativeGraph
Visualize
SummarizationSummarization
Text
MEDLINEClinicalTrials.gov
PubMedQuery
SalientSemanticPredications
Summarize
SemanticPredications
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 13
Abstraction summarizationAbstraction summarization
AllPredications
Reduction SalientPredications
Specify a topicSpecify a topic Retain predications on the topicRetain predications on the topic Eliminate uninformative predicationsEliminate uninformative predications Retain most frequent predicationsRetain most frequent predications
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 14
StructuredBiomedical
DataUMLS
SemRep
InformativeGraph
VisualizeSummarize
Salient semantic predicationsSalient semantic predications
Text
MEDLINEClinicalTrials.gov
PubMedQuery
SemanticPredications
SalientSemanticPredications
Aromatase Inhibitors Breast Carcinomatreats
ATM gene Breast Carcinomaassociated_with
Tamoxifen Breast Carcinomatreats
Tamoxifen Patientstreats
Breast Carcinoma Individualprocess_of
… … …
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 15
StructuredBiomedical
DataUMLS
SemRep Summarize
VisualizationVisualization
Text
MEDLINEClinicalTrials.gov
PubMedQuery
SemanticPredications
InformativeGraph
Visualize
SalientSemanticPredications
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 16
SemRep Summarize
Informative graphInformative graph
MEDLINEClinicalTrials.gov
PubMedQuery
SemanticPredications
Visualize
SalientSemanticPredications
StructuredBiomedical
DataUMLS
Text InformativeGraph
treats
associated_with
treats
Aromatase InhibitorsTamoxifen
ATM gene
Breast Carcinoma
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Semantic Medline Semantic Medline LiveLive
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 18
Home pageHome page
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 19
Search MEDLINESearch MEDLINE
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 20
Summarization optionsSummarization options
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Summarization resultsSummarization results
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More detailMore detail
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Substance interactionsSubstance interactions
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Lister Hill National Center for Biomedical CommunicationsLister Hill National Center for Biomedical Communications 24
AcknowledgmentsAcknowledgments
Caroline AhlersCaroline Ahlers Marcelo FiszmanMarcelo Fiszman Philip GoetzPhilip Goetz Halil KilicogluHalil Kilicoglu Anna RippleAnna Ripple Graciela RosemblatGraciela Rosemblat