Literature mining: what is it, and should I care?

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EMBL Lab Day, European Molecular Biology Laboratory, Heidelberg, Germany, June 10, 2008

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Literature mining: what is it, and should I care?

  1. 1. Literature mining
  2. 2. Explosion
  3. 3. exponential increase
  4. 6. some things never change
  5. 8. “ graph calculus”
  6. 9. =
  7. 10. ~50 seconds per paper
  8. 11. Information retrieval
  9. 12. find the relevant papers
  10. 13. ad hoc retrieval
  11. 14. user-specified query
  12. 15. “ yeast AND cell cycle”
  13. 16. stemming
  14. 17. yeast / yeasts
  15. 18. dynamic query expansion
  16. 19. yeast / S. cerevisiae
  17. 20. ranking
  18. 29. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation
  19. 30. no tool will find it
  20. 31. Entity recognition
  21. 32. identify the substance(s)
  22. 33. Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation
  23. 34. good synonyms list
  24. 35. orthographic variation
  25. 36. CDC28
  26. 37. Cdc28p
  27. 38. disambiguation
  28. 39. Cdc2
  29. 40. APC
  30. 45. still too much to read
  31. 46. Information extraction
  32. 47. formalize the facts
  33. 48. co-mentioning
  34. 49. NLP Natural Language Processing
  35. 50. Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation
  36. 51. database
  37. 53. integration
  38. 58. STRING & STITCH
  39. 60. Acknowledgments <ul><li>STRING & STITCH </li></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Manuel Stark </li></ul></ul><ul><ul><li>Samuel Chaffron </li></ul></ul><ul><ul><li>Philippe Julien </li></ul></ul><ul><ul><li>Tobias Doerks </li></ul></ul><ul><ul><li>Jan Korbel </li></ul></ul><ul><ul><li>Berend Snel </li></ul></ul><ul><ul><li>Martijn Huynen </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>The movie “Brazil” </li></ul></ul><ul><li>Reflect </li></ul><ul><ul><li>Evangelos Pafilis </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Heiko Horn </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>Sean O’Donoghue </li></ul></ul><ul><ul><li>Reinhardt Schneider </li></ul></ul><ul><li>NLP pipeline </li></ul><ul><ul><li>Jasmin Saric </li></ul></ul><ul><ul><li>Rossitza Ouzounova </li></ul></ul><ul><ul><li>Isabel Rojas </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul>

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