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Medical data and text mining
Linking diseases, drugs, and
adverse reactions
Lars Juhl Jensen
structured data
Jensen et al., Nature Reviews Genetics, 2012
unstructured data
central registries
individual hospitals
opt-out
opt-in
Danish registries
civil registration system
CPR number
established in 1968
Jensen et al., Nature Reviews Genetics, 2012
national discharge registry
14 years
6.2 million patients
45 million admissions
68 million records
119 million diagnosis
ICD-10
Jensen et al., Nature Reviews Genetics, 2012
not research
reimbursement
diagnosis trajectories
naïve approach
comorbidity
Jensen et al., Nature Reviews Genetics, 2012
confounding factors
“known knowns”
gender
age
type of hospital encounter
Jensen et al., Nature Communications, 2014
“known unknowns”
smoking
diet
“unknown unknowns”
reporting biases
matched controls
temporal correlations
multiple testing
trajectories
Jensen et al., Nature Communications, 2014
trajectory networks
Jensen et al., Nature Communications, 2014
key diagnoses
Jensen et al., Nature Communications, 2014
direct medical implications
electronic health records
structured data
Jensen et al., Nature Reviews Genetics, 2012
unstructured data
free text
Danish
busy doctors
typos
psychiatric patients
text mining
computer
as smart as a dog
teach it specific tricks
comprehensive dictionary
diseases
drugs
adverse drug reactions
expansion rules
Clozapine
clozapi
n
clossapi
n
klozapin
e
chlosapi
n
chlosapi
ne
chlozapi
n
chlozapi
ne
klossapi
n
closapin
e
klozapi
nklo...
“negative modifiers”
negations
delusions
pharmacovigilance
structured data
medication
semi-structured data
drug indications
known ADRs
unstructured data
adverse drug reactions
statistical correlations
hand-crafted rules
Eriksson et al., Drug Safety, 2014
Drug introduction Drug discontinuationAdverse event
Adverse eventNegative modifier Indi...
Eriksson et al., Drug Safety, 2014
Drug introduction Drug discontinuationAdverse eventIdentification start
Adverse eventNe...
Eriksson et al., Drug Safety, 2014
Drug introduction Drug discontinuation
Adverse eventNegative modifier Indication Pre-ex...
Eriksson et al., Drug Safety, 2014
Drug introduction Drug discontinuation
Adverse eventNegative modifier Indication Pre-ex...
known ADRs
ADR frequencies
Eriksson et al., Drug Safety, 2014
detect new ADRs
Acknowledgments
Disease trajectories
Anders Bøck Jensen
Tudor Oprea
Pope Moseley
Søren Brunak
Adverse drug reactions
Rober...
Medical data and text mining - Linking diseases, drugs, and adverse reactions
Medical data and text mining - Linking diseases, drugs, and adverse reactions
Medical data and text mining - Linking diseases, drugs, and adverse reactions
Medical data and text mining - Linking diseases, drugs, and adverse reactions
Medical data and text mining - Linking diseases, drugs, and adverse reactions
Medical data and text mining - Linking diseases, drugs, and adverse reactions
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Medical data and text mining - Linking diseases, drugs, and adverse reactions

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Medical data and text mining - Linking diseases, drugs, and adverse reactions

  1. 1. Medical data and text mining Linking diseases, drugs, and adverse reactions Lars Juhl Jensen
  2. 2. structured data
  3. 3. Jensen et al., Nature Reviews Genetics, 2012
  4. 4. unstructured data
  5. 5. central registries
  6. 6. individual hospitals
  7. 7. opt-out
  8. 8. opt-in
  9. 9. Danish registries
  10. 10. civil registration system
  11. 11. CPR number
  12. 12. established in 1968
  13. 13. Jensen et al., Nature Reviews Genetics, 2012
  14. 14. national discharge registry
  15. 15. 14 years
  16. 16. 6.2 million patients
  17. 17. 45 million admissions
  18. 18. 68 million records
  19. 19. 119 million diagnosis
  20. 20. ICD-10
  21. 21. Jensen et al., Nature Reviews Genetics, 2012
  22. 22. not research
  23. 23. reimbursement
  24. 24. diagnosis trajectories
  25. 25. naïve approach
  26. 26. comorbidity
  27. 27. Jensen et al., Nature Reviews Genetics, 2012
  28. 28. confounding factors
  29. 29. “known knowns”
  30. 30. gender
  31. 31. age
  32. 32. type of hospital encounter
  33. 33. Jensen et al., Nature Communications, 2014
  34. 34. “known unknowns”
  35. 35. smoking
  36. 36. diet
  37. 37. “unknown unknowns”
  38. 38. reporting biases
  39. 39. matched controls
  40. 40. temporal correlations
  41. 41. multiple testing
  42. 42. trajectories
  43. 43. Jensen et al., Nature Communications, 2014
  44. 44. trajectory networks
  45. 45. Jensen et al., Nature Communications, 2014
  46. 46. key diagnoses
  47. 47. Jensen et al., Nature Communications, 2014
  48. 48. direct medical implications
  49. 49. electronic health records
  50. 50. structured data
  51. 51. Jensen et al., Nature Reviews Genetics, 2012
  52. 52. unstructured data
  53. 53. free text
  54. 54. Danish
  55. 55. busy doctors
  56. 56. typos
  57. 57. psychiatric patients
  58. 58. text mining
  59. 59. computer
  60. 60. as smart as a dog
  61. 61. teach it specific tricks
  62. 62. comprehensive dictionary
  63. 63. diseases
  64. 64. drugs
  65. 65. adverse drug reactions
  66. 66. expansion rules
  67. 67. Clozapine clozapi n clossapi n klozapin e chlosapi n chlosapi ne chlozapi n chlozapi ne klossapi n closapin e klozapi nklosapi n
  68. 68. “negative modifiers”
  69. 69. negations
  70. 70. delusions
  71. 71. pharmacovigilance
  72. 72. structured data
  73. 73. medication
  74. 74. semi-structured data
  75. 75. drug indications
  76. 76. known ADRs
  77. 77. unstructured data
  78. 78. adverse drug reactions
  79. 79. statistical correlations
  80. 80. hand-crafted rules
  81. 81. Eriksson et al., Drug Safety, 2014 Drug introduction Drug discontinuationAdverse event Adverse eventNegative modifier Indication Pre-existing condition Adverse drug reaction Possible adverse drug reaction ADR of additional drug
  82. 82. Eriksson et al., Drug Safety, 2014 Drug introduction Drug discontinuationAdverse eventIdentification start Adverse eventNegative modifier Indication Pre-existing condition Adverse drug reaction Possible adverse drug reaction ADR of additional drug
  83. 83. Eriksson et al., Drug Safety, 2014 Drug introduction Drug discontinuation Adverse eventNegative modifier Indication Pre-existing condition Adverse drug reaction Possible adverse drug reaction Adverse event ADR of additional drug Identification start
  84. 84. Eriksson et al., Drug Safety, 2014 Drug introduction Drug discontinuation Adverse eventNegative modifier Indication Pre-existing condition Adverse drug reaction Possible adverse drug reaction Adverse event ADR of additional drug Identification start
  85. 85. known ADRs
  86. 86. ADR frequencies
  87. 87. Eriksson et al., Drug Safety, 2014
  88. 88. detect new ADRs
  89. 89. Acknowledgments Disease trajectories Anders Bøck Jensen Tudor Oprea Pope Moseley Søren Brunak Adverse drug reactions Robert Eriksson Thomas Werge Søren Brunak EHR text mining Peter Bjødstrup Jensen Robert Eriksson Henriette Schmock Francisco S. Roque Anders Juul Marlene Dalgaard Massimo Andreatta Sune Frankild Eva Roitmann Thomas Hansen Karen Søeby Søren Bredkjær Thomas Werge Søren Brunak

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