Integration of biomedical literature and databases

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Nordic Conference for Scolarly Communication 2008, Scandic Star Hotel, Lund, Sweden, April 21-23, 2008

Nordic Conference for Scolarly Communication 2008, Scandic Star Hotel, Lund, Sweden, April 21-23, 2008

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  • 1. Integration of biomedical literature and databases Lars Juhl Jensen EMBL Heidelberg
  • 2. why integration?
  • 3. why biomedicine?
  • 4. why literature?
  • 5. why databases?
  • 6. open access databases
  • 7. a lot of them
  • 8. Duncan Hull, nodalpoint.org
  • 9. PubChem
  • 10.  
  • 11. 19.2 million compounds
  • 12. GenBank
  • 13.  
  • 14. 85 million sequences
  • 15. 89 billion nucleotides
  • 16. UniProt
  • 17.  
  • 18. 5.6 million sequences
  • 19. PDB
  • 20.  
  • 21. 50000 protein structures
  • 22. BIND Biomolecular Interaction Network Database
  • 23. DIP Database of Interacting Proteins
  • 24. MINT Molecular Interactions Database
  • 25. IntAct
  • 26. BioGRID
  • 27.  
  • 28. 204000 interactions
  • 29. too many
  • 30. incomplete
  • 31. literature mining
  • 32. M EDLINE
  • 33. 17.9 million citations
  • 34.  
  • 35. too much to read
  • 36. information retrieval
  • 37. finding the papers
  • 38.  
  • 39.  
  • 40. user-specified query
  • 41. “ yeast AND cell cycle”
  • 42. stemming
  • 43. yeast / yeasts
  • 44. dynamic query expansion
  • 45. yeast / S. cerevisiae
  • 46. ranking
  • 47.  
  • 48.  
  • 49. 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
  • 50. no tool will find it
  • 51. entity recognition
  • 52. identifying the substance(s)
  • 53. 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
  • 54. Cdc28  yeast
  • 55. Cdc28  cell cycle
  • 56.  
  • 57. synonyms list
  • 58. orthographic variation
  • 59. CDC28
  • 60. Cdc28p
  • 61. disambiguation
  • 62. Cdc2
  • 63. SDS
  • 64.  
  • 65. still too much to read
  • 66. information extraction
  • 67. formalizing the facts
  • 68.  
  • 69. co-mentioning
  • 70. statistical methods
  • 71. NLP Natural Language Processing
  • 72.
    • Gene and protein names
    • Cue words for entity recognition
    • Verbs for relation extraction
    • [ nxexpr T he expression of [ nxgene the cytochrome genes [ nxpg CYC1 and CYC7 ]]] is controlled by [ nxpg HAP1 ]
  • 73. 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
  • 74.  
  • 75. yet another database
  • 76. integration
  • 77. augmented browsing
  • 78.  
  • 79. semantic tagging
  • 80.  
  • 81. association networks
  • 82.  
  • 83.  
  • 84. curated knowledge
  • 85.  
  • 86. genomic context
  • 87. phylogenetic profiles
  • 88.  
  • 89. gene neighborhood
  • 90.  
  • 91. experimental data
  • 92. physical interactions
  • 93.  
  • 94. genetic interactions
  • 95.  
  • 96. literature mining
  • 97.  
  • 98. restricted access
  • 99. Bayesian framework
  • 100.  
  • 101. summary
  • 102. literature mining is good
  • 103. data integration is better
  • 104. open access
  • 105. Acknowledgments
    • STRING & STITCH
      • Christian von Mering
      • Michael Kuhn
      • Manuel Stark
      • Samuel Chaffron
      • Philippe Julien
      • Tobias Doerks
      • Jan Korbel
      • Berend Snel
      • Martijn Huynen
      • Peer Bork
    • Reflect
      • Evangelos Pafilis
      • Michael Kuhn
      • Sean O’Donoghue
      • Reinhardt Schneider
    • Natural Language Processing
      • Jasmin Saric
      • Rossitza Ouzounova
      • Isabel Rojas
      • Peer Bork
  • 106.