Your SlideShare is downloading. ×
Network biology: Large-scale data integration and text mining
Upcoming SlideShare
Loading in...5
×

Thanks for flagging this SlideShare!

Oops! An error has occurred.

×

Saving this for later?

Get the SlideShare app to save on your phone or tablet. Read anywhere, anytime - even offline.

Text the download link to your phone

Standard text messaging rates apply

Network biology: Large-scale data integration and text mining

288
views

Published on

Published in: Technology

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
288
On Slideshare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
1
Comments
0
Likes
0
Embeds 0
No embeds

Report content
Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
No notes for slide

Transcript

  • 1. Network biology Large-scale data integration and text mining Lars Juhl Jensen
  • 2. academic research center
  • 3. contract research
  • 4. association networks
  • 5. guilt by association
  • 6. STRING
  • 7. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
  • 8. computational predictions
  • 9. gene fusion
  • 10. Korbel et al., Nature Biotechnology, 2004
  • 11. experimental data
  • 12. physical interactions
  • 13. Jensen & Bork, Science, 2008
  • 14. curated knowledge
  • 15. metabolic pathways
  • 16. Letunic & Bork, Trends in Biochemical Sciences, 2008
  • 17. many databases
  • 18. different formats
  • 19. different identifiers
  • 20. variable quality
  • 21. not comparable
  • 22. hard work
  • 23. quality scores
  • 24. von Mering et al., Nucleic Acids Research, 2005
  • 25. calibrate vs. gold standard
  • 26. missing most of the data
  • 27. >10 km
  • 28. too much to read
  • 29. computer
  • 30. as smart as a dog
  • 31. teach it specific tricks
  • 32. named entity recognition
  • 33. comprehensive lexicon
  • 34. cyclin dependent kinase 1
  • 35. CDC2
  • 36. expansion rules
  • 37. CDC2
  • 38. hCdc2
  • 39. flexible matching
  • 40. cyclin dependent kinase 1
  • 41. cyclin-dependent kinase 1
  • 42. “black list”
  • 43. SDS
  • 44. count co-mentioning
  • 45. general approach
  • 46. species
  • 47. Pafilis et al., PLOS ONE, 2013
  • 48. environments
  • 49. small molecules
  • 50. Kuhn et al., Nucleic Acids Research, 2012
  • 51. compartments
  • 52. compartments.jensenlab.org
  • 53. tissues
  • 54. tissues.jensenlab.org
  • 55. diseases
  • 56. evidence viewers
  • 57. web services
  • 58. compartments.jensenlab.org
  • 59. download files
  • 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