Network biology: Large-scale data integration and text mining

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Network biology: Large-scale data integration and text mining

  1. 1. Network biology Large-scale data integration and text mining Lars Juhl Jensen
  2. 2. academic research center
  3. 3. contract research
  4. 4. association networks
  5. 5. guilt by association
  6. 6. STRING
  7. 7. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
  8. 8. computational predictions
  9. 9. gene fusion
  10. 10. Korbel et al., Nature Biotechnology, 2004
  11. 11. experimental data
  12. 12. physical interactions
  13. 13. Jensen & Bork, Science, 2008
  14. 14. curated knowledge
  15. 15. metabolic pathways
  16. 16. Letunic & Bork, Trends in Biochemical Sciences, 2008
  17. 17. many databases
  18. 18. different formats
  19. 19. different identifiers
  20. 20. variable quality
  21. 21. not comparable
  22. 22. hard work
  23. 23. quality scores
  24. 24. von Mering et al., Nucleic Acids Research, 2005
  25. 25. calibrate vs. gold standard
  26. 26. missing most of the data
  27. 27. >10 km
  28. 28. too much to read
  29. 29. computer
  30. 30. as smart as a dog
  31. 31. teach it specific tricks
  32. 32. named entity recognition
  33. 33. comprehensive lexicon
  34. 34. cyclin dependent kinase 1
  35. 35. CDC2
  36. 36. expansion rules
  37. 37. CDC2
  38. 38. hCdc2
  39. 39. flexible matching
  40. 40. cyclin dependent kinase 1
  41. 41. cyclin-dependent kinase 1
  42. 42. “black list”
  43. 43. SDS
  44. 44. count co-mentioning
  45. 45. general approach
  46. 46. species
  47. 47. Pafilis et al., PLOS ONE, 2013
  48. 48. environments
  49. 49. small molecules
  50. 50. Kuhn et al., Nucleic Acids Research, 2012
  51. 51. compartments
  52. 52. compartments.jensenlab.org
  53. 53. tissues
  54. 54. tissues.jensenlab.org
  55. 55. diseases
  56. 56. evidence viewers
  57. 57. web services
  58. 58. compartments.jensenlab.org
  59. 59. download files
  60. 60. Acknowledgments Protein networks Christian von Mering Damian Szklarczyk Michael Kuhn Manuel Stark Samuel Chaffron Chris Creevey Jean Muller Tobias Doerks Philippe Julien Alexander Roth Milan Simonovic Jan Korbel Berend Snel Martijn Huynen Literature mining Sune Frankild Evangelos Pafilis Heiko Horn Alberto Santos Kalliopi Tsafou Lucia Fanini Sarah Faulwetter Christina Pavloudi Aikaterini Vasileiadou Janos Binder Michael Kuhn Nigel Brown Christos Arvanitidis Reinhardt Schneider Sean O’Donoghue

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