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Data and text mining of
electronic health records
Lars Juhl Jensen
structured data
Jensen et al., Nature Reviews Genetics, 2012
central registries
unstructured data
individual hospitals
opt-out
opt-in
medical registries
Danish registries
civil registration system
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
comorbidity
contingency table
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
proxy diagnoses
temporal correlations
diagnosis 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
medical records
structured data
Jensen et al., Nature Reviews Genetics, 2012
unstructured data
free text
Danish
busy doctors
typos
psychiatric patients
text mining
comprehensive dictionary
diseases
drugs
adverse drug reactions
expansion rules
Clozapine
Clozapine
clozapi
n
clossapi
n
klozapin
e
chlosapi
n
chlosapi
ne
chlozapi
n
chlozapi
ne
klossapi
n
closapin
e
klozapi
nklosapi
n
“black list”
false positives
pharmacovigilance
clinical trials
spontaneous reports
underreporting
text data mining
structured data
medication
text-mined data
adverse drug events
temporal correlations
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
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
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
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
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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Data and text mining of electronic health records