Data integration with STRING

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Data integration with STRING

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

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