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
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
Clozapineclozapi
n
clossapin
klozapine
chlosapin
chlosapine
chlozapin
chlozapine
klossapin
closapine
klozapinklosapi
n
flexible matching
compound nouns
post-coordination rules
failure of kidney
kidney failure
“black list”
three-letter acronyms
pharmacovigilance
clinical trials
spontaneous reports
underreporting
data mining
structured data
medication
semi-structured data
drug indications
known ADRs
unstructured data
adverse drug reactions
temporal correlations
hand-crafted rules
Eriksson et al., Drug Safety, 2014
Eriksson et al., Drug Safety, 2014
Eriksson et al., Drug Safety, 2014
Eriksson et al., Drug Safety, 2014
recall known ADRs
estimate ADR frequencies
Eriksson et al., Drug Safety, 2014
discover new ADRs
Drug substance ADE p-value
Chlordiazepoxide Nystagmus 4.0e-8
Simvastatin Personality changes
8.4e-8
Dipyridamole Visual impairment
4.4e-4
Citalopram Psychosis 8.8e-4
Bendroflumethiazide
Apoplexy 8.5e-3
Eriksson et al., Drug Safety, 2014
AcknowledgmentsDisease trajectoriesAnders Bøck JensenTudor OpreaPope MoseleySøren Brunak
Adverse drug reactionsRobert ErikssonThomas WergeSøren Brunak
EHR text mining
Peter Bjødstrup Jensen
Robert ErikssonHenriette SchmockFrancisco S. Roque
Anders JuulMarlene Dalgaard
Massimo AndreattaSune FrankildEva Roitmann
Thomas HansenKaren Søeby
Søren BredkjærThomas Werge
Søren Brunak