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Integration of biomedical literature and databases

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2nd European Conference on Scientific Publishing in Biomedicine and Medicine, Rikshospitalet, Oslo, Norway, September 5-6, 2008

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Integration of biomedical literature and databases

  1. 1. Integration of biomedical literature and databases Lars Juhl Jensen EMBL Heidelberg
  2. 2. biomedical databases
  3. 3. DNA sequences
  4. 4. GenBank
  5. 6. protein sequences
  6. 7. UniProt
  7. 9. protein structures
  8. 10. PDB
  9. 12. expression
  10. 13. ArrayExpress
  11. 14. GEO Gene Expression Omnibus
  12. 16. modifications
  13. 17. Phospho.ELM
  14. 18. PhosphoSite
  15. 19. interactions
  16. 20. BioGRID
  17. 21. DIP Database of Interacting Proteins
  18. 22. IntAct
  19. 23. MINT Molecular Interactions Database
  20. 25. chemical compounds
  21. 26. PubChem
  22. 28. database of databases
  23. 29. Duncan Hull, nodalpoint.org
  24. 30. freely available
  25. 31. literature mining
  26. 32. PubMed
  27. 33. exponential increase
  28. 36. some things never change
  29. 38. “ graph calculus”
  30. 39. =
  31. 40. ~50 seconds per paper
  32. 41. information retrieval
  33. 42. find the relevant papers
  34. 43. ad hoc retrieval
  35. 44. user-specified query
  36. 45. “ yeast AND cell cycle”
  37. 46. stemming
  38. 47. yeast / yeasts
  39. 48. dynamic query expansion
  40. 49. yeast / S. cerevisiae
  41. 54. Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation
  42. 55. no tool will find it
  43. 56. entity recognition
  44. 57. identify the substance(s)
  45. 58. Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation
  46. 59. good synonyms list
  47. 60. orthographic variation
  48. 61. CDC28
  49. 62. Cdc28p
  50. 63. disambiguation
  51. 64. Cdc2
  52. 65. SDS
  53. 66. information extraction
  54. 67. formalize the facts
  55. 68. co-mentioning
  56. 69. NLP Natural Language Processing
  57. 70. Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation
  58. 71. integration tools
  59. 72. “ document-centric” tools
  60. 73. Reflect
  61. 75. browser add-on
  62. 76. real-time tagging service
  63. 77. any HTML document
  64. 78. augmented document
  65. 79. information from databases
  66. 81. iHOP
  67. 83. web interface
  68. 84. precomputed index
  69. 85. abstracts
  70. 86. find text about a protein
  71. 87. link proteins and text
  72. 89. experimental interactions
  73. 91. “ entity-centric” tools
  74. 92. STRING & STITCH
  75. 95. functional associations
  76. 96. heterogeneous evidence
  77. 97. information extraction
  78. 99. curated knowledge
  79. 101. interaction data
  80. 103. expression data
  81. 105. genomic context
  82. 107. quality scores
  83. 108. probabilistic framework
  84. 109. cross-species transfer
  85. 110. association networks
  86. 113. Acknowledgments <ul><li>STRING & STITCH </li></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Manuel Stark </li></ul></ul><ul><ul><li>Samuel Chaffron </li></ul></ul><ul><ul><li>Philippe Julien </li></ul></ul><ul><ul><li>Jean Muller </li></ul></ul><ul><ul><li>Tobias Doerks </li></ul></ul><ul><ul><li>Jan Korbel </li></ul></ul><ul><ul><li>Berend Snel </li></ul></ul><ul><ul><li>Martijn Huynen </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>Natural Language Processing </li></ul><ul><ul><li>Jasmin Saric </li></ul></ul><ul><ul><li>Rossitza Ouzounova </li></ul></ul><ul><ul><li>Isabel Rojas </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>Reflect </li></ul><ul><ul><li>Evangelos Pafilis </li></ul></ul><ul><ul><li>Heiko Horn </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Sean O’Donoghue </li></ul></ul><ul><ul><li>Reinhardt Schneider </li></ul></ul>
  87. 114. hands-on exercises
  88. 115. <ul><li>Exercises </li></ul><ul><li>Find literature on human CDC2 </li></ul><ul><li>Find data and literature on targets and cytochrome P450 enzymes for Aspirin, Viagra, as well as for similar compounds </li></ul><ul><li>Find information on the genes in doi:10.1371/journal.pgen.1000120 </li></ul><ul><li>Construct an interaction network of genes that cause G2/M delays in the budding yeast cell cycle </li></ul><ul><li>Tools </li></ul><ul><li>http://www.ihop-net.org </li></ul><ul><li>http://string.embl.de </li></ul><ul><li>http://stitch.embl.de </li></ul><ul><li>http://reflect.ws </li></ul>

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