Network integration of data and text

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Network integration of data and text

  1. 1. Network integration of data and text Lars Juhl Jensen
  2. 2. Part 1 text mining
  3. 3. >10 km
  4. 4. exponential growth
  5. 7. law of diminishing returns
  6. 8. some things are constant
  7. 10. ~45 seconds per paper
  8. 11. computer
  9. 12. as smart as a dog
  10. 13. teach it specific tricks
  11. 16. named entity recognition
  12. 17. Reflect
  13. 18. augmented browsing
  14. 19. browser add-on
  15. 20. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
  16. 21. collaborations
  17. 23. web services
  18. 25. Utopia Documents
  19. 26. information extraction
  20. 27. co-mentioning
  21. 29. <10 hours
  22. 30. no access
  23. 31. Part 2 protein networks
  24. 32. STRING
  25. 33. Szklarczyk, Franceschini et al., Nucleic Acids Research , 2011
  26. 34. 630 genomes
  27. 35. many databases
  28. 36. genomic context
  29. 37. gene fusion
  30. 38. Korbel et al., Nature Biotechnology , 2004
  31. 39. conserved neighborhood
  32. 40. operons
  33. 41. Korbel et al., Nature Biotechnology , 2004
  34. 42. bidirectional promoters
  35. 43. Korbel et al., Nature Biotechnology , 2004
  36. 44. phylogenetic profiles
  37. 45. Korbel et al., Nature Biotechnology , 2004
  38. 46. experimental data
  39. 47. physical interactions
  40. 48. Jensen & Bork, Science , 2008
  41. 49. gene coexpression
  42. 51. curated knowledge
  43. 52. pathways
  44. 53. Letunic & Bork, Trends in Biochemical Sciences , 2008
  45. 54. text mining
  46. 56. many data types
  47. 57. many databases
  48. 58. different formats
  49. 59. different identifiers
  50. 60. variable quality
  51. 61. quality scores
  52. 62. calibrate vs. gold standard
  53. 63. von Mering et al., Nucleic Acids Research , 2005
  54. 64. orthology transfer
  55. 65. Frishman et al., Modern Genome Annotation , 2009
  56. 66. Part 3 small molecule networks
  57. 67. STITCH
  58. 68. Kuhn et al., Nucleic Acids Research , 2010
  59. 69. in vitro binding assays
  60. 70. text mining
  61. 71. chemical similarity
  62. 72. Campillos & Kuhn et al., Science , 2008
  63. 73. similar drugs share targets
  64. 74. Campillos & Kuhn et al., Science , 2008
  65. 75. only trivial predictions
  66. 76. phenotypic similarity
  67. 77. chemical perturbations
  68. 78. phenotypic readouts
  69. 79. drug treatment
  70. 80. side effects
  71. 81. no database
  72. 82. package inserts
  73. 83. Campillos & Kuhn et al., Science , 2008
  74. 84. text mining
  75. 85. manual validation
  76. 86. side-effect correlations
  77. 87. Campillos & Kuhn et al., Science , 2008
  78. 88. side-effect frequencies
  79. 89. Campillos & Kuhn et al., Science , 2008
  80. 90. raw similarity score
  81. 91. Campillos & Kuhn et al., Science , 2008
  82. 92. p-values
  83. 93. Campillos & Kuhn et al., Science , 2008
  84. 94. side-effect similarity
  85. 95. chemical similarity
  86. 96. Campillos & Kuhn et al., Science , 2008
  87. 97. drug–drug network
  88. 98. Campillos & Kuhn et al., Science , 2008
  89. 99. categorization
  90. 100. Campillos & Kuhn et al., Science , 2008
  91. 101. 20 drug–drug pairs
  92. 102. in vitro binding assays
  93. 103. K i <10 µM for 11 of 20
  94. 104. cell assays
  95. 105. 9 of 9 showed activity
  96. 106. Acknowledgments <ul><ul><li>Reflect </li></ul></ul><ul><ul><li>Sune Frankild </li></ul></ul><ul><ul><li>Heiko Horn </li></ul></ul><ul><ul><li>Evangelos Pafilis </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Reinhardt Schneider </li></ul></ul><ul><ul><li>Sean O’Donoghue </li></ul></ul><ul><ul><li>Side effects </li></ul></ul><ul><ul><li>Monica Campillos </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Anne-Claude Gavin </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>STRING/STITCH </li></ul></ul><ul><ul><li>Damian Szklarczyk </li></ul></ul><ul><ul><li>Andrea Franceschini </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Milan Simonovic </li></ul></ul><ul><ul><li>Alexander Roth </li></ul></ul><ul><ul><li>Pablo Minguez </li></ul></ul><ul><ul><li>Tobias Doerks </li></ul></ul><ul><ul><li>Manuel Stark </li></ul></ul><ul><ul><li>Jean Muller </li></ul></ul><ul><ul><li>Andreas Beyer </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>Christian von Mering </li></ul></ul>
  97. 107. larsjuhljensen

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