Semantic Medline

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Semantic MedlineMulti-Document
Summarizationand Visualization Thomas C.
Rindflesch, Ph.D.Marcelo Fiszman, M.D., Ph.D.
Halil Kilicoglu, M.S.
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Information management application

• Manipulate information in addition to documents
• Manage the results of PubMed searches
• Help users decide what to read
• Connect knowledge from various sources
• Integrate application interfaces

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Managing retrieval results
breast cancer
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Managing retrieval results
breast cancer
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Seamless integration of technologies

• Information retrieval
• PubMed - MEDLINE
• Natural language processing SemRep
• Represent content of text with semantic
  predications
• Abstraction summarization
• Informative Overview of most salient information
• Visualization
• Indicative Links to source text and additional
  information

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Semantic Medline Overview
SemanticPredications
InformativeGraph
SalientSemanticPredications
Text
SemRep
Visualize
Summarize
PubMed
Query
StructuredBiomedicalData
UMLS
MEDLINEClinicalTrials.gov
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Document selection
SemanticPredications
InformativeGraph
SalientSemanticPredications
SemRep
Visualize
Summarize
StructuredBiomedicalData
UMLS
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MEDLINE citations
SemanticPredications
InformativeGraph
SalientSemanticPredications
Text
SemRep
Visualize
Summarize
PubMed
Query
StructuredBiomedicalData
UMLS
MEDLINEClinicalTrials.gov
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Semantic intepretation
InformativeGraph
SalientSemanticPredications
Visualize
Summarize
PubMed
Query
StructuredBiomedicalData
MEDLINEClinicalTrials.gov
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Semantic interpretation

• ... aromatase inhibitor provides mortality
  benefit in early breast carcinoma

determined the spectrum and frequency of ATM
missense variants in 443 breast cancer patients
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Semantic predications
InformativeGraph
SalientSemanticPredications
Text
SemanticPredications
SemRep
Visualize
Summarize
PubMed
Query
StructuredBiomedicalData
UMLS
MEDLINEClinicalTrials.gov
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Summarization
InformativeGraph
Text
SemRep
Visualize
PubMed
Query
StructuredBiomedicalData
UMLS
MEDLINEClinicalTrials.gov
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Abstraction summarization

• Specify a topic
• Retain predications on the topic
• Eliminate uninformative predications
• Retain most frequent predications

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Salient semantic predications
InformativeGraph
Text
SemanticPredications
SalientSemanticPredications
SemRep
Visualize
Summarize
PubMed
Query
StructuredBiomedicalData
UMLS
MEDLINEClinicalTrials.gov
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Visualization
Text
SemanticPredications
SemRep
Summarize
PubMed
Query
StructuredBiomedicalData
UMLS
MEDLINEClinicalTrials.gov
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Informative graph
SemanticPredications
SalientSemanticPredications
SemRep
Summarize
PubMed
Visualize
Query
MEDLINEClinicalTrials.gov
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Semantic Medline Live
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Home page
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Search MEDLINE
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Summarization options
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Summarization results
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More detail
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Substance interactions
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Acknowledgments

• Caroline Ahlers
• Marcelo Fiszman
• Philip Goetz
• Halil Kilicoglu
• Anna Ripple
• Graciela Rosemblat