Mining biomedical texts
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This document discusses mining biomedical texts to extract relevant information from the large number of papers published. It mentions that named entity recognition is used to identify concepts like small molecules, proteins, and diseases from text. Tools mentioned include Reflect.ws, a browser add-on, and STITCH, which extracts curated knowledge on drug targets and pathways. Text mining techniques like co-mentioning are also discussed to find relationships between concepts from abstracts and full texts.
Mining biomedical texts
- 1. Mining biomedical texts Lars Juhl Jensen >10 km
- 5. some things are constant
- 7. ~45 seconds per paper
- 9. find the relevant texts
- 10. still too much to read
- 11. computer
- 12. as smart as a dog
- 13. teach it specific tricks
- 19. small molecules
- 20. proteins
- 22. organisms
- 23. diseases
- 25. “ black list”
- 26. Reflect.ws
- 28. browser add-on
- 29. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009 O’Donoghue et al., Journal of Web Semantics , 2010
- 30. Firefox
- 32. Google Chrome
- 33. Safari
- 34. Utopia Documents
- 35. web services
- 36. ~150 years of publishing
- 38. dead wood
- 40. dead e-wood
- 41. added value
- 42. collaboration
- 51. STITCH
- 52. Kuhn et al., Nucleic Acids Research , 2010
- 54. drug targets
- 55. pathways
- 56. Letunic & Bork, Trends in Biochemical Sciences , 2008
- 59. Jensen & Bork, Science , 2008
- 60. text mining
- 61. co-mentioning
- 63. NLP Natural Language Processing
- 65. abstracts
- 66. full text
- 69. collaboration
- 71. a hard problem
- 72. in Danish
- 73. no lexicon
- 74. by busy doctors
- 75. acronyms
- 76. typos
- 78. delusions
- 80. F20 F200 Negation Family
- 81. diagnoses
- 83. Roque et al., PLoS Computational Biology , 2011
- 85. Roque et al., PLoS Computational Biology , 2011
- 86. medication
- 89. phenotype
- 90. genotype
- 91. Thank you! Reflect.ws Sune Frankild Heiko Horn Evangelos Pafilis Michael Kuhn Reinhardt Schneider Sean O’Donoghue SciVerse app Juan-Carlos Silla-Castro Sean O’Donoghue EPJ-mining Francisco S Roque Peter B Jensen Robert Eriksson Henriette Schmock Marlene Dalgaard Massimo Andreatta Thomas Hansen Karen Søeby Søren Bredkjær Anders Juul Thomas Werge Søren Brunak
- 92. larsjuhljensen