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Open access – making the most of biomedical literature mining

Open access – making the most of biomedical literature mining. Lars Juhl Jensen EMBL Heidelberg. why open access?. why biomedicine?. why literature mining?. M EDLINE.

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Open access – making the most of biomedical literature mining

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  1. Open access – making the most of biomedical literature mining Lars Juhl JensenEMBL Heidelberg

  2. why open access?

  3. why biomedicine?

  4. why literature mining?

  5. MEDLINE

  6. 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

  7. information retrieval

  8. finding the papers

  9. if you can’t find them …

  10. … they don’t exist!

  11. ad hoc retrieval

  12. users-specified query

  13. “yeast AND cell cycle”

  14. 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

  15. MEDLINE

  16. abstracts

  17. complete papers

  18. tricks

  19. stemming

  20. yeast / yeasts

  21. synonyms

  22. yeast / S. cerevisiae

  23. dynamic query expansion

  24. next logical step

  25. ontologies

  26. annotation

  27. Cdc28  yeast gene

  28. Cdc28  cell cycle

  29. 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

  30. “yeast AND cell cycle”

  31. entity recognition

  32. identifying the substance(s)

  33. 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

  34. if you can’t find them …

  35. … they don’t exist!

  36. abstracts

  37. MEDLINE

  38. tricks

  39. good synonyms list

  40. manual curation

  41. orthographic variation

  42. CDC28

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