Literature mining and large-scale data integration

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Computational and Systems Biology Course, Centre for Computational and Systems Biology (CoSBi), Trento, Italy, March 10-14, 2008

Technologie

Literature mining and large-scale data integration Lars Juhl Jensen EMBL Heidelberg

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

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Literature mining and large-scale data integration

1. Literature mining and large-scale data integration Lars Juhl Jensen EMBL Heidelberg

2. literature mining

3. why?

5. too much to read

6. information retrieval

7. finding the papers

8. ad hoc retrieval

9. user-specified query

10. “ yeast AND cell cycle”

11. stemming

12. yeast / yeasts

13. dynamic query expansion

14. yeast / S. cerevisiae

15. ranking

16.

17.

18.

19.

20.

21.

22.

23.

24. 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

25. no tool will find it

26. entity recognition

27. identifying the substance(s)

28. 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

29. Cdc28  yeast

30. Cdc28  cell cycle

31. good synonyms list

32. manual curation

33. orthographic variation

34. CDC28

35. Cdc28p

36. disambiguation

37. hairy

38. SDS

39. APC

40. Cdc2

41.

42.

43.

44.

45. still too much to read

46. information extraction

47. formalizing the facts

48.

49. co-mentioning

50. statistical methods

51. NLP Natural Language Processing

52.

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.

55. no new discoveries

56. text mining

57. undiscovered links

58.

59. Raynaud’s syndrome

60. fish oil

61.

62. temporal trends

63.

64. buzzwords

65.