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. association networks
  3. 3. guilt by association
  4. 4. STRING
  5. 5. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
  6. 6. computational predictions
  7. 7. gene fusion
  8. 8. Korbel et al., Nature Biotechnology, 2004
  9. 9. experimental data
  10. 10. physical interactions
  11. 11. Jensen & Bork, Science, 2008
  12. 12. curated knowledge
  13. 13. metabolic pathways
  14. 14. Letunic & Bork, Trends in Biochemical Sciences, 2008
  15. 15. many databases
  16. 16. different formats
  17. 17. different identifiers
  18. 18. variable quality
  19. 19. not comparable
  20. 20. hard work
  21. 21. quality scores
  22. 22. von Mering et al., Nucleic Acids Research, 2005
  23. 23. calibrate vs. gold standard
  24. 24. missing most of the data
  25. 25. >10 km
  26. 26. too much to read
  27. 27. computer
  28. 28. as smart as a dog
  29. 29. teach it specific tricks
  30. 30. named entity recognition
  31. 31. comprehensive lexicon
  32. 32. cyclin dependent kinase 1
  33. 33. CDC2
  34. 34. expansion rules
  35. 35. CDC2
  36. 36. hCdc2
  37. 37. flexible matching
  38. 38. cyclin dependent kinase 1
  39. 39. cyclin-dependent kinase 1
  40. 40. “black list”
  41. 41. SDS
  42. 42. count co-mentioning
  43. 43. general approach
  44. 44. small molecules
  45. 45. Kuhn et al., Nucleic Acids Research, 2012
  46. 46. compartments
  47. 47. compartments.jensenlab.org
  48. 48. tissues
  49. 49. tissues.jensenlab.org
  50. 50. diseases
  51. 51. evidence viewers
  52. 52. web services
  53. 53. compartments.jensenlab.org
  54. 54. download files
  55. 55. 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 Janos Binder Michael Kuhn Nigel Brown Reinhardt Schneider Sean O’Donoghue
  56. 56. Thanks Toruń! Janusz Bujnicki Wieslaw Nowak Arne Elofsson Wieslaw Nowak Witold Rudnicki Łukasz Pepłowski Karolina Mikulska Anna Gogolinská Rafał Jakubowski

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