Reflect and friends - Tools and resources for mining biomedical text

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Lars Juhl Jensen

Reflect and friends
Tools and resources for mining biomedical text

>10 km

Lars Juhl Jensen

exponential growth

some things are constant

~45 seconds per paper

computer

as smart as a dog

teach it specific tricks

named entity recognition

identify the concepts

comprehensive lexicon

small molecules

proteins

cellular components

tissues

organisms

phenotypes

diseases

orthographic variation

singular vs. plural

flexible matching

spaces and hyphens

conflict resolution

“black list”

scalable implementation

>10 km
<10 hours

augmented browsing

Reflect

reflect.ws

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

browser add-on

Firefox

Google Chrome

Safari

Internet Explorer

PDF viewer

Utopia Documents

collaborate with publishers

SciVerse application

corpora

~20 mio. abstracts

1.8 mio. full-text articles

collaborate with publishers

web-centric databases

guilt by association

information extraction

co-mentioning

STRING

string-db.org

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

~2.6 million proteins

STITCH

stitch-db.org

Kuhn et al., Nucleic Acids Research, 2012

~300,000 small molecules

COMPARTMENTS

subcellular localization

compartments.jensenlab.org

search for proteins

DISEASES

>8,000 disease terms

diseases.jensenlab.org

search for diseases

search for proteins

evidence viewers

disease behavior

Thank you!
Reflect STRING and STITCH COMPARTMENT
Sune Frankild Damian Szklarczyk S
and DISEASES
Heiko Horn Andrea Franceschini
Sune Frankild
Evangelos Pafilis Michael Kuhn
Janos Binder
Janos Binder Milan Simonovic
Reinhardt Schneider Alexander Roth
Sean O’Donoghue Pablo Minguez
Tobias Doerks
Manuel Stark
Jean Muller
Peer Bork
Christian von Mering

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Reflect and friends - Tools and resources for mining biomedical text

1. Reflect and friends Tools and resources for mining biomedical text >10 km Lars Juhl Jensen

2. exponential growth

3.

4.

5. some things are constant

6.

7. ~45 seconds per paper

9. as smart as a dog

10. teach it specific tricks

11.

12.

13. named entity recognition

14. identify the concepts

15. comprehensive lexicon

16. small molecules

18. cellular components

23. orthographic variation

24. singular vs. plural

25. flexible matching

26. spaces and hyphens

27. conflict resolution

28. “black list”

29. scalable implementation

30. >10 km <10 hours

31. augmented browsing

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

35. browser add-on

37. Google Chrome

39. Internet Explorer

41. Utopia Documents

42. collaborate with publishers

43.

44. SciVerse application

45.

47. ~20 mio. abstracts

48. 1.8 mio. full-text articles

49.

50. collaborate with publishers

51. web-centric databases

52. guilt by association

53.

54. information extraction

55. co-mentioning

57. string-db.org

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

59. ~2.6 million proteins

60.

62. stitch-db.org

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

64. ~300,000 small molecules

65.

66. COMPARTMENTS

67. subcellular localization

68. compartments.jensenlab.org

69. search for proteins

70.

72. >8,000 disease terms

73. diseases.jensenlab.org

74. search for diseases

75.

76.

77.

78. search for proteins

79.

80.

81. evidence viewers

82.

83. disease behavior

84.

85. Thank you! Reflect STRING and STITCH COMPARTMENT Sune Frankild Damian Szklarczyk S and DISEASES Heiko Horn Andrea Franceschini Sune Frankild Evangelos Pafilis Michael Kuhn Janos Binder Janos Binder Milan Simonovic Reinhardt Schneider Alexander Roth Sean O’Donoghue Pablo Minguez Tobias Doerks Manuel Stark Jean Muller Peer Bork Christian von Mering