Mining molecules from text and data

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  • This is a conservative estimate based only on what is in PubMed Too much to read! Text mining used to extract relations Similar methods used to mine medical records and link diseases

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  • 1. Mining molecules from text and data Lars Juhl Jensen
  • 2. Reflect
  • 3. augmented browsing
  • 4. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009 O’Donoghue et al., Journal of Web Semantics , 2010
  • 5. web services
  • 6.  
  • 7. STITCH
  • 8. Kuhn et al., Nucleic Acids Research , 2010
  • 9. >74,000 small molecules
  • 10. >2.5 million proteins
  • 11. 630 genomes
  • 12. Gleevec
  • 13.  
  • 14. evidence types
  • 15. primary experimental data
  • 16. physical interactions
  • 17.  
  • 18. curated knowledge
  • 19. drug targets
  • 20. pathways
  • 21. >10 km
  • 22. literature mining
  • 23. co-mentioning
  • 24.  
  • 25. NLP Natural Language Processing
  • 26.  
  • 27. integration
  • 28. incomparable data
  • 29. quality scores
  • 30. calibrate vs. gold standard
  • 31. Acknowledgments
      • Reflect
      • Sune Frankild
      • Heiko Horn
      • Evangelos Pafilis
      • Michael Kuhn
      • Reinhardt Schneider
      • Sean O’Donoghue
      • STITCH
      • Michael Kuhn
      • Damian Szklarczyk
      • Andrea Franceschini
      • Monica Campillos
      • Christian von Mering
      • Andreas Beyer
      • Peer Bork
  • 32. larsjuhljensen