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Biomedical literature mining (and why we really need open access)

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    Biomedical literature mining (and why we really need open access) - Presentation Transcript

    1. Biomedical literature mining (and why we really need Open Access) Lars Juhl Jensen EMBL Heidelberg
    2. why biomedicine?
    3. why literature mining?
    4. why open access?
    5. M EDLINE
    6. 17 million citations
    7. Jensen et al., Nature Reviews Genetics, 2006
    8. too much to read
    9. literature mining
    10. open access
    11. information retrieval
    12. finding the papers
    13. ad hoc retrieval
    14.  
    15. user-specified query
    16. “ yeast AND cell cycle”
    17. stemming
    18. yeast / yeasts
    19. dynamic query expansion
    20. yeast / S. cerevisiae
    21.  
    22. M EDLINE
    23. abstracts
    24. complete papers
    25. 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
    26. yeast?
    27. cell cycle?
    28. entity recognition
    29. identifying the substance(s)
    30. 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
    31. Cdc28  yeast
    32. Cdc28  cell cycle
    33. good synonyms list
    34. manual curation
    35. orthographic variation
    36. CDC28
    37. Cdc28p
    38. disambiguation
    39. hairy
    40. SDS
    41. Cdc2
    42.  
    43.  
    44. abstracts
    45. complete papers
    46. information extraction
    47. formalizing the facts
    48.  
    49. co-mentioning
    50. statistical methods
    51. NLP Natural Language Processing
      • Gene and protein names
      • Cue words for entity recognition
      • Verbs for relation extraction
      • [ nxexpr T he expression of [ nxgene the cytochrome genes [ nxpg CYC1 and CYC7 ]]] is controlled by [ nxpg HAP1 ]
    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. Jensen et al., Nature Reviews Genetics, 2006
    55. new discoveries
    56. text mining
    57.  
    58. Jensen et al., Nature Reviews Genetics, 2006
    59. abstracts
    60. complete papers
    61. temporal trends
    62. Jensen et al., Nature Reviews Genetics, 2006
    63. buzzwords
    64. Jensen et al., Nature Reviews Genetics, 2006
    65. grant applications
    66. integration of text and data
    67. Genomic neighborhood Species co-occurrence Gene fusions Database imports Experimental interaction data Microarray expression data Literature mining
    68. genotype to phenotype
    69. Korbel et al., PLoS Biology, 2005
    70. Korbel et al., PLoS Biology, 2005
    71. Korbel et al., PLoS Biology, 2005
    72. where are we now?
    73. Jensen et al., Nature Reviews Genetics, 2006
    74. abstracts
    75. complete papers
    76. restricted access
    77. open access
    78. the tools are there
    79. now we need the text!
    80. Acknowledgments
      • Jasmin Saric
      • Rossitza Ouzounova
      • Michael Kuhn
      • Jan Korbel
      • Tobias Doerks
      • Isabel Rojas
      • Miguel Andrade
      • Peer Bork

    + Lars Juhl JensenLars Juhl Jensen, 2 years ago

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