1. Lars Juhl Jensen
Text mining
>10 km

2. exponential growth

5. ~45 seconds per paper

6. corpus

7. most use abstracts

8. few use full-text articles

9. no access

11. information retrieval

12. find the relevant papers

13. ad hoc retrieval

14. user-specified query

15. “yeast AND cell cycle”

16. PubMed

18. indexing

19. fast lookup

20. stemming

21. word endings

22. dynamic query expansion

23. 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

24. no tool will find that

25. still too much to read

26. computer

27. as smart as a dog

28. teach it specific tricks

31. named entity recognition

32. identify the concepts

33. comprehensive lexicon

34. small molecules

35. proteins

36. cellular components

37. tissues

38. diseases

39. environments

40. organisms

41. orthographic expansion

42. prefixes and postfixes

43. Cdc28 vs. Cdc28p

44. singular and plural forms

45. flexible matching

46. upper- and lower-case

47. spaces and hyphens

48. “black list”

49. SDS

50. 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

51. information extraction

52. formalize the facts

53. the starting point

54. named entity recognition

55. two approaches

56. co-mentioning

57. within documents

58. within paragraphs

59. within sentences

60. weighted counts

61. NLP
Natural Language Processing

62. part-of-speech tagging

63. semantic tagging

64. sentence parsing

65. Gene and protein names
Cue words for entity recognition
Verbs for relation extraction
[nxexpr The expression of
[nxgene the cytochrome genes
[nxpg CYC1 and CYC7]]]
is controlled by
[nxpg HAP1]

66. handle negations

67. high precision

68. poor recall

69. highly domain specific

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

71. text/data integration

72. augmented browsing

73. Reflect

74. show relevant information

75. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
O’Donoghue et al., Journal of Web Semantics, 2010

76. guilt by association

78. heterogeneous evidence

79. knowledge

80. experiments

81. text mining

82. predictions

83. common identifiers

84. quality scores

85. web interface

86. STRING

87. proteins

88. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011

89. Frishman et al., Modern Genome Annotation, 2009

90. STITCH

91. small molecules

92. Kuhn et al., Nucleic Acids Research, 2012

93. COMPARTMENTS

94. subcellular localization

95. compartments.jensenlab.org

96. TISSUES

97. human tissue expression

98. tissues.jensenlab.org

99. DISEASES

100. human diseases

102. evidence viewers

104. web services

105. bulk download

106. summary

107. text mining

108. simpler

109. more useful

110. less boring

111. thank you!

112. questions?