Reflect and friends - Tools and resources for mining biomedical text

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Reflect and friends - Tools and resources for mining biomedical text

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

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