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Extract 2.0: Text-mining-assisted interactive annotation

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Extract 2.0: Text-mining-assisted interactive annotation

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Extract 2.0: Text-mining-assisted interactive annotation

  1. 1. Lars Juhl Jensen @larsjuhljensen Extract 2.0 Text-mining-assisted interactive annotation
  2. 2. >10 km
  3. 3. too much to read
  4. 4. text mining
  5. 5. interactive annotation
  6. 6. bookmarklet
  7. 7. identify relevant sections
  8. 8. extract normalized entities
  9. 9. Pafilis et al., Database, 2016extract.hcmr.gr
  10. 10. dictionary
  11. 11. genes / proteins
  12. 12. chemical compounds
  13. 13. organisms
  14. 14. Gene Ontology terms
  15. 15. tissues
  16. 16. diseases
  17. 17. phenotypes
  18. 18. environments
  19. 19. not comprehensive
  20. 20. expansion rules
  21. 21. plural / adjective forms
  22. 22. abbreviated forms
  23. 23. curated blacklist
  24. 24. SDS
  25. 25. software
  26. 26. C++ engine
  27. 27. flexible matching
  28. 28. 70–80% recall
  29. 29. 80–90% precision
  30. 30. >1000 abstracts / second
  31. 31. inherently thread-safe
  32. 32. Python wrapper
  33. 33. web service
  34. 34. open source
  35. 35. evaluation
  36. 36. BioCreative V IAT
  37. 37. evaluated by curators
  38. 38. positive user feedback
  39. 39. Wang et al., Database, 2016
  40. 40. BioCreative V.5 TIPS
  41. 41. perfect uptime
  42. 42. minimal response time
  43. 43. Jensen, Proceedings of BioCreative V.5, 2017tagger.jensenlab.org/BeCalm
  44. 44. Acknowledgments Evangelos Pafilis Sune Pletscher-Frankild Damian Szklarczyk Michael Kuhn Christos Arvanitidis

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