Reflect and friends - Tools and resources for mining biomedical text
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Reflect and friends - Tools and resources for mining biomedical text Presentation Transcript

  • 1. Reflect and friendsTools and resources for mining biomedical text>10 km Lars Juhl Jensen
  • 2. exponential growth
  • 3. some things are constant
  • 4. ~45 seconds per paper
  • 5. computer
  • 6. as smart as a dog
  • 7. teach it specific tricks
  • 8. named entity recognition
  • 9. identify the concepts
  • 10. comprehensive lexicon
  • 11. small molecules
  • 12. proteins
  • 13. cellular components
  • 14. tissues
  • 15. organisms
  • 16. phenotypes
  • 17. diseases
  • 18. orthographic variation
  • 19. singular vs. plural
  • 20. flexible matching
  • 21. spaces and hyphens
  • 22. conflict resolution
  • 23. “black list”
  • 24. scalable implementation
  • 25. >10 km<10 hours
  • 26. augmented browsing
  • 27. Reflect
  • 28. reflect.ws
  • 29. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009 O’Donoghue et al., Journal of Web Semantics, 2010
  • 30. browser add-on
  • 31. Firefox
  • 32. Google Chrome
  • 33. Safari
  • 34. Internet Explorer
  • 35. PDF viewer
  • 36. Utopia Documents
  • 37. collaborate with publishers
  • 38. SciVerse application
  • 39. corpora
  • 40. ~20 mio. abstracts
  • 41. 1.8 mio. full-text articles
  • 42. collaborate with publishers
  • 43. web-centric databases
  • 44. guilt by association
  • 45. information extraction
  • 46. co-mentioning
  • 47. STRING
  • 48. string-db.org
  • 49. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
  • 50. ~2.6 million proteins
  • 51. STITCH
  • 52. stitch-db.org
  • 53. Kuhn et al., Nucleic Acids Research, 2012
  • 54. ~300,000 small molecules
  • 55. COMPARTMENTS
  • 56. subcellular localization
  • 57. compartments.jensenlab.org
  • 58. search for proteins
  • 59. DISEASES
  • 60. >8,000 disease terms
  • 61. diseases.jensenlab.org
  • 62. search for diseases
  • 63. search for proteins
  • 64. evidence viewers
  • 65. disease behavior
  • 66. Thank you!Reflect STRING and STITCH COMPARTMENTSune Frankild Damian Szklarczyk S and DISEASESHeiko Horn Andrea Franceschini Sune FrankildEvangelos Pafilis Michael Kuhn Janos BinderJanos Binder Milan SimonovicReinhardt Schneider Alexander RothSean O’Donoghue Pablo Minguez Tobias Doerks Manuel Stark Jean Muller Peer Bork Christian von Mering