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STRING Large-scale data and text mining

STRING Large-scale data and text mining. Lars Juhl Jensen. association networks. guilt by association. biological systems. protein networks. STRING. 1100+ genomes. computational predictions. gene fusion. Korbel et al., Nature Biotechnology , 2004. gene neighborhood.

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STRING Large-scale data and text mining

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  1. STRINGLarge-scale data and text mining Lars Juhl Jensen

  2. association networks

  3. guilt by association

  4. biological systems

  5. protein networks

  6. STRING

  7. 1100+ genomes

  8. computational predictions

  9. gene fusion

  10. Korbel et al., Nature Biotechnology, 2004

  11. gene neighborhood

  12. Korbel et al., Nature Biotechnology, 2004

  13. phylogenetic profiles

  14. Korbel et al., Nature Biotechnology, 2004

  15. experimental data

  16. gene coexpression

  17. protein interactions

  18. Jensen & Bork, Science, 2008

  19. a real example

  20. Cell Cellulosomes Cellulose

  21. curated knowledge

  22. complexes

  23. pathways

  24. Letunic & Bork, Trends in Biochemical Sciences, 2008

  25. many databases

  26. different formats

  27. different identifiers

  28. variable quality

  29. not comparable

  30. not same species

  31. hard work

  32. (Ph.D. students)

  33. common identifiers

  34. quality scores

  35. von Mering et al., Nucleic Acids Research, 2005

  36. score calibration

  37. von Mering et al., Nucleic Acids Research, 2005

  38. homology-based transfer

  39. Franceschini et al., Nucleic Acids Research, 2013

  40. missing most of the data

  41. text mining

  42. >10 km

  43. too much to read

  44. computer

  45. comprehensive lexicon

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