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Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
Data integration with STRING
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Data integration with STRING

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  • 1. Data integration with STRING Lars Juhl Jensen
  • 2. association networks
  • 3. guilt by association
  • 4. molecular networks
  • 5. proteins
  • 6. string-db.org
  • 7. small molecules
  • 8. stitch-db.org
  • 9. non-coding RNAs
  • 10. data integration
  • 11. computational predictions
  • 12. gene neighborhood
  • 13. Korbel et al., Nature Biotechnology, 2004
  • 14. experimental data
  • 15. gene expression
  • 16. curated knowledge
  • 17. pathways
  • 18. Letunic & Bork, Trends in Biochemical Sciences, 2008
  • 19. many databases
  • 20. different formats
  • 21. different identifiers
  • 22. variable quality
  • 23. not comparable
  • 24. hard work
  • 25. (Ph.D. students)
  • 26. common identifiers
  • 27. quality scores
  • 28. von Mering et al., Nucleic Acids Research, 2005
  • 29. score calibration
  • 30. von Mering et al., Nucleic Acids Research, 2005
  • 31. homology-based transfer
  • 32. Franceschini et al., Nucleic Acids Research, 2013
  • 33. missing most of the data
  • 34. text mining
  • 35. >10 km
  • 36. too much to read
  • 37. computer
  • 38. as smart as a dog
  • 39. teach it specific tricks
  • 40. named entity recognition
  • 41. comprehensive lexicon
  • 42. CDC2
  • 43. cyclin dependent kinase 1
  • 44. flexible matching
  • 45. upper- and lower-case
  • 46. CDC2
  • 47. Cdc2
  • 48. spaces and hyphens
  • 49. cyclin dependent kinase 1
  • 50. cyclin-dependent kinase 1
  • 51. name expansions
  • 52. prefixes and postfixes
  • 53. CDC2
  • 54. hCDC2
  • 55. “black list”
  • 56. SDS
  • 57. co-mentioning
  • 58. counting
  • 59. within documents
  • 60. within paragraphs
  • 61. within sentences
  • 62. external data
  • 63. payload mechanism
  • 64. extra data on nodes
  • 65. colored halos
  • 66. text in node popup
  • 67. URL in node popup
  • 68. new nodes
  • 69. ncRNAs
  • 70. new edges
  • 71. evidence type
  • 72. evidence score
  • 73. text in edge popup
  • 74. URL in edge popup
  • 75. legend
  • 76. branding with logo
  • 77. you host the data
  • 78. user accesses STRING
  • 79. STRING gets data from you
  • 80. your server must be public
  • 81. restrict access to STRING
  • 82. JSON configuration file
  • 83. TSV data files
  • 84. node data
  • 85. edge data
  • 86. extension node data
  • 87. extension edge data
  • 88. web services as alternative
  • 89. big datasets
  • 90. get only required data
  • 91. questions?

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