Network biologyLarge-scale data integration and text mining               Lars Juhl Jensen
three parts
signaling networks
association networks
text mining
signaling networks
proteomics
in vivo PTMs
actors are unknown
sequence specificity
Miller, Jensen et al., Science Signaling, 2008
no context
complexes
NetworKIN
Linding, Jensen, Ostheimer et al., Cell, 2007
association network
STRING
Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
computational predictions
gene fusion
Korbel et al., Nature Biotechnology, 2004
experimental data
Jensen & Bork, Science, 2008
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences, 2008
many databases
different formats
different identifiers
variable quality
not comparable
hard work
quality scores
von Mering et al., Nucleic Acids Research, 2005
calibrate vs. gold standard
missing most of the data
text mining
>10 km
too much to read
computer
as smart as a dog
teach it specific tricks
named entity recognition
comprehensive lexicon
CDC2 = CDK1
orthographic variation
hCdc2
“black list”
SDS
information extraction
co-mentioning
quality scores
proteins
compartments
compartments.jensenlab.org
compartments.jensenlab.org
tissues
tissues.jensenlab.org
tissues.jensenlab.org
diseases
diseases.jensenlab.org
AcknowledgmentsNetPhorest                NetworKIN           STRING                 Text miningRune Linding              R...
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Network biology - Large-scale data integration and text mining
Network biology - Large-scale data integration and text mining
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 biologyLarge-scale data integration and text mining Lars Juhl Jensen
  2. 2. three parts
  3. 3. signaling networks
  4. 4. association networks
  5. 5. text mining
  6. 6. signaling networks
  7. 7. proteomics
  8. 8. in vivo PTMs
  9. 9. actors are unknown
  10. 10. sequence specificity
  11. 11. Miller, Jensen et al., Science Signaling, 2008
  12. 12. no context
  13. 13. complexes
  14. 14. NetworKIN
  15. 15. Linding, Jensen, Ostheimer et al., Cell, 2007
  16. 16. association network
  17. 17. STRING
  18. 18. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
  19. 19. computational predictions
  20. 20. gene fusion
  21. 21. Korbel et al., Nature Biotechnology, 2004
  22. 22. experimental data
  23. 23. Jensen & Bork, Science, 2008
  24. 24. curated knowledge
  25. 25. Letunic & Bork, Trends in Biochemical Sciences, 2008
  26. 26. many databases
  27. 27. different formats
  28. 28. different identifiers
  29. 29. variable quality
  30. 30. not comparable
  31. 31. hard work
  32. 32. quality scores
  33. 33. von Mering et al., Nucleic Acids Research, 2005
  34. 34. calibrate vs. gold standard
  35. 35. missing most of the data
  36. 36. text mining
  37. 37. >10 km
  38. 38. too much to read
  39. 39. computer
  40. 40. as smart as a dog
  41. 41. teach it specific tricks
  42. 42. named entity recognition
  43. 43. comprehensive lexicon
  44. 44. CDC2 = CDK1
  45. 45. orthographic variation
  46. 46. hCdc2
  47. 47. “black list”
  48. 48. SDS
  49. 49. information extraction
  50. 50. co-mentioning
  51. 51. quality scores
  52. 52. proteins
  53. 53. compartments
  54. 54. compartments.jensenlab.org
  55. 55. compartments.jensenlab.org
  56. 56. tissues
  57. 57. tissues.jensenlab.org
  58. 58. tissues.jensenlab.org
  59. 59. diseases
  60. 60. diseases.jensenlab.org
  61. 61. AcknowledgmentsNetPhorest NetworKIN STRING Text miningRune Linding Rune Linding Christian von Mering Sune FrankildMartin Lee Miller Heiko Horn Damian Szklarczyk Evangelos PafilisErwin Schoof Gerard Ostheimer Michael Kuhn Janos BinderFrancesca Diella Martin Lee Miller Manuel Stark Kalliopi TsafouClaus Jørgensen Francesca Diella Samuel Chaffron Heiko HornMichele Tinti Karen Colwill Chris Creevey Michael KuhnLei Li Jing Jin Jean Muller Nigel BrownMarilyn Hsiung Pavel Metalnikov Tobias Doerks Reinhardt SchneiderSirlester A. Parker Vivian Nguyen Philippe Julien Sean O’DonoghueJennifer Bordeaux Adrian Pasculescu Alexander RothThomas Sicheritz-Pontén Jin Gyoon Park Milan SimonovicMarina Olhovsky Leona D. Samson Jan KorbelAdrian Pasculescu Rob Russell Berend SnelJes Alexander Peer Bork Martijn HuynenStefan Knapp Michael Yaffe Peer BorkNikolaj Blom Tony PawsonPeer BorkShawn LiGianni CesareniTony PawsonBenjamin TurkMichael YaffeSøren Brunak
  62. 62. Questions?

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