Data integration and visualization

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Data integration and visualization

  1. 1. Lars Juhl JensenData integration and visualization
  2. 2. protein networks
  3. 3. 3+ years ahead
  4. 4. STRING
  5. 5. Huynen et al., Current Opinion in Structural Biology, 2000
  6. 6. genomic context
  7. 7. experimental data
  8. 8. text mining
  9. 9. ~22 million abstracts
  10. 10. ~4 million full-text articles
  11. 11. comprehensive lexicon
  12. 12. proteins
  13. 13. small molecules
  14. 14. compartments
  15. 15. tissues
  16. 16. diseases
  17. 17. organisms
  18. 18. environments
  19. 19. orthographics variation
  20. 20. flexible matching
  21. 21. hyphens and spaces
  22. 22. expansion rules
  23. 23. singular vs. plural
  24. 24. “black list”
  25. 25. relation extraction
  26. 26. count co-mentioning
  27. 27. within documents
  28. 28. within paragraphs
  29. 29. within sentences
  30. 30. STRING
  31. 31. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
  32. 32. payload
  33. 33. compartments.jensenlab.org
  34. 34. COMPARTMENTS
  35. 35. compartments.jensenlab.org
  36. 36. TISSUES
  37. 37. tissues.jensenlab.org
  38. 38. DISEASES
  39. 39. visualization
  40. 40. de Lichtenberg, Jensen et al., Science, 2005
  41. 41. Ciccarelli, Doerks et al., Science, 2006
  42. 42. von Mering et al., Science, 2007
  43. 43. Jensen & Bork, Science, 2008

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