Text mining

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Lars Juhl Jensen

Technology Education

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

Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009

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]

Acknowledgments
NLP pipeline
– Jasmin Saric
– Rossitza Ouzounova
– Isabel Rojas
– Peer Bork
Reflect
– Heiko Horn
– Sune Frankild
– Evangelos Pafilis
– Sven Haag
– Michael Kuhn
– Peer Bork
– Reinhardt Schneider
– Sean O’Donoghue

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Text mining

1. Text mining

2. Explosion

3. exponential increase

6. some things are constant

8. “graph calculus”

9. =

10. ~45 seconds per paper

11. Information retrieval

12. find the relevant papers

13. user-specified query

14. “yeast AND cell cycle”

15.

16. stemming

17. dynamic query expansion

18. ranking

19. 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

20. no tool will find that

21. Entity recognition

22. identify the substance(s)

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. 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. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009

26. comprehensive lexicon

27. orthographic variation

28. “black list”

29. manual correction

30. still too much to read

31. Information extraction

32. formalize the facts

33. co-occurrence

34. global statistical analysis

35. NLP Natural Language Processing

36. parsing individual sentences

37. 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]

38. 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

39. store in a database

40. then the fun begins :-)

41. Acknowledgments NLP pipeline – Jasmin Saric – Rossitza Ouzounova – Isabel Rojas – Peer Bork Reflect – Heiko Horn – Sune Frankild – Evangelos Pafilis – Sven Haag – Michael Kuhn – Peer Bork – Reinhardt Schneider – Sean O’Donoghue

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