Mining biomedical texts

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  • 1. Mining biomedical texts Lars Juhl Jensen >10 km
  • 2. exponential growth
  • 3.  
  • 4.  
  • 5. some things are constant
  • 6.  
  • 7. ~45 seconds per paper
  • 8. information retrieval
  • 9. find the relevant texts
  • 10. still too much to read
  • 11. computer
  • 12. as smart as a dog
  • 13. teach it specific tricks
  • 14.  
  • 15.  
  • 16. named entity recognition
  • 17. identify the concepts
  • 18. comprehensive lexicon
  • 19. small molecules
  • 20. proteins
  • 21. cellular components
  • 22. organisms
  • 23. diseases
  • 24. orthographic variation
  • 25. “ black list”
  • 26. Reflect.ws
  • 27. augmented browsing
  • 28. browser add-on
  • 29. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009 O’Donoghue et al., Journal of Web Semantics , 2010
  • 30. Firefox
  • 31. Internet Explorer
  • 32. Google Chrome
  • 33. Safari
  • 34. Utopia Documents
  • 35. web services
  • 36. ~150 years of publishing
  • 37.  
  • 38. dead wood
  • 39.  
  • 40. dead e-wood
  • 41. added value
  • 42. collaboration
  • 43.  
  • 44.  
  • 45. SciVerse application
  • 46.  
  • 47.  
  • 48.  
  • 49.  
  • 50.  
  • 51. STITCH
  • 52. Kuhn et al., Nucleic Acids Research , 2010
  • 53. curated knowledge
  • 54. drug targets
  • 55. pathways
  • 56. Letunic & Bork, Trends in Biochemical Sciences , 2008
  • 57. experimental data
  • 58. physical interactions
  • 59. Jensen & Bork, Science , 2008
  • 60. text mining
  • 61. co-mentioning
  • 62.  
  • 63. NLP Natural Language Processing
  • 64.  
  • 65. abstracts
  • 66. full text
  • 67. restricted access
  • 68.  
  • 69. collaboration
  • 70. electronic patient journals
  • 71. a hard problem
  • 72. in Danish
  • 73. no lexicon
  • 74. by busy doctors
  • 75. acronyms
  • 76. typos
  • 77. about psychiatric patients
  • 78. delusions
  • 79. domain specific system
  • 80. F20 F200 Negation Family
  • 81. diagnoses
  • 82. patient stratification
  • 83. Roque et al., PLoS Computational Biology , 2011
  • 84. disease comorbidity
  • 85. Roque et al., PLoS Computational Biology , 2011
  • 86. medication
  • 87. adverse drug events
  • 88. pharmacovigilance
  • 89. phenotype
  • 90. genotype
  • 91. Thank you!
      • Reflect.ws
      • Sune Frankild
      • Heiko Horn
      • Evangelos Pafilis
      • Michael Kuhn
      • Reinhardt Schneider
      • Sean O’Donoghue
      • SciVerse app
      • Juan-Carlos Silla-Castro
      • Sean O’Donoghue
      • EPJ-mining
      • Francisco S Roque
      • Peter B Jensen
      • Robert Eriksson
      • Henriette Schmock
      • Marlene Dalgaard
      • Massimo Andreatta
      • Thomas Hansen
      • Karen Søeby
      • Søren Bredkjær
      • Anders Juul
      • Thomas Werge
      • Søren Brunak
  • 92. larsjuhljensen