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Semantic Medline: Multi-Document Summarization and Visualization

Lister Hill National Center for Biomedical Communications. Semantic Medline: Multi-Document Summarization and Visualization Thomas C. Rindflesch, Ph.D. Marcelo Fiszman, M.D., Ph.D. Halil Kilicoglu, M.S. Information management application. Manipulate information in addition to documents

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Semantic Medline: Multi-Document Summarization and Visualization

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  1. Lister Hill National Center for Biomedical Communications Semantic Medline:Multi-Document Summarizationand Visualization Thomas C. Rindflesch, Ph.D.Marcelo Fiszman, M.D., Ph.D.Halil Kilicoglu, M.S.

  2. 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

  3. retrieval summarization 500 citations Network of relations Information retrieval Semantic Medline Managing retrieval results breast cancer

  4. Managing retrieval results breast cancer

  5. 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

  6. Semantic Medline Overview Text SemanticPredications SalientSemanticPredications InformativeGraph PubMed SemRep Summarize Visualize Query MEDLINEClinicalTrials.gov UMLS StructuredBiomedicalData

  7. Text “breast cancer” PubMed Query MEDLINEClinicalTrials.gov Document selection SemanticPredications SalientSemanticPredications InformativeGraph SemRep Summarize Visualize UMLS StructuredBiomedicalData

  8. … aromatase inhibitor provides mortality benefit in early breast carcinoma… …determined the spectrum and frequency of ATM missense variants in 443 breast cancer patients… MEDLINE citations Text SemanticPredications SalientSemanticPredications InformativeGraph PubMed SemRep Summarize Visualize Query MEDLINEClinicalTrials.gov UMLS StructuredBiomedicalData

  9. Text SemanticPredications SemRep UMLS Semantic intepretation SalientSemanticPredications InformativeGraph PubMed Summarize Visualize Query MEDLINEClinicalTrials.gov StructuredBiomedicalData

  10. treats Aromatase Inhibitors Breast Carcinoma associated_with ATM gene Breast Carcinoma 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 …

  11. treats Tamoxifen Breast Carcinoma treats Aromatase Inhibitors Breast Carcinoma associated_with ATM gene Breast Carcinoma … … … treats Tamoxifen Patients process_of Breast Carcinoma Individual Semantic predications Text SemanticPredications SalientSemanticPredications InformativeGraph PubMed SemRep Summarize Visualize Query MEDLINEClinicalTrials.gov UMLS StructuredBiomedicalData

  12. SemanticPredications SalientSemanticPredications Summarize Summarization Text InformativeGraph PubMed SemRep Visualize Query MEDLINEClinicalTrials.gov UMLS StructuredBiomedicalData

  13. Specify a topic Retain predications on the topic Eliminate uninformative predications Retain most frequent predications All Predications SalientPredications Reduction Abstraction summarization

  14. treats Tamoxifen Breast Carcinoma treats Aromatase Inhibitors Breast Carcinoma associated_with ATM gene Breast Carcinoma … … … treats Tamoxifen Patients process_of Breast Carcinoma Individual Salient semantic predications Text SemanticPredications SalientSemanticPredications InformativeGraph PubMed SemRep Summarize Visualize Query MEDLINEClinicalTrials.gov UMLS StructuredBiomedicalData

  15. SalientSemanticPredications InformativeGraph Visualize Visualization Text SemanticPredications PubMed SemRep Summarize Query MEDLINEClinicalTrials.gov UMLS StructuredBiomedicalData

  16. Text InformativeGraph Aromatase Inhibitors Tamoxifen treats treats Breast Carcinoma associated_with ATM gene UMLS StructuredBiomedicalData Informative graph SemanticPredications SalientSemanticPredications PubMed SemRep Summarize Visualize Query MEDLINEClinicalTrials.gov

  17. Semantic Medline Live

  18. Home page

  19. Search MEDLINE

  20. Summarization options

  21. Summarization results

  22. More detail

  23. Substance interactions

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

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