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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 Lars Juhl Jensen
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Transcript of Medical data and text mining - Linking diseases, drugs, and adverse reactions
Medical data and text mining
Linking diseases, drugs, and adverse reactions
Lars Juhl Jensen
me
cellular network biology
proteomics data
cellular signaling
protein networks
Szklarczyk et al., Nucleic Acids Research, 2015string-db.org
text mining
>10 km
(end of commercial break)
medical data
Jensen et al., Nature Reviews Genetics, 2012
structured data
Jensen et al., Nature Reviews Genetics, 2012
unstructured data
opt-out
opt-in
(Danes say no)
diagnosis trajectories
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
naïve analysis
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
pharmacovigilance
clinical trials
spontaneous reports
underreporting
data mining
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
Clozapineclozap
in
clossapin
klozapine
chlosapin
chlosapine
chlozapin
chlozapine
klossapin
closapine
klozapinklosap
in
“black list”
pest eller kolera
hand-crafted rules
statistics
temporal correlations
drugs
adverse drug events
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
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-4Bendroflumethiazide
Apoplexy 8.5e-3Eriksson et al., Drug Safety, 2014
estimate ADR frequencies
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 DalgaardMassimo Andreatta
Sune FrankildEva RoitmannThomas HansenKaren Søeby
Søren BredkjærThomas WergeSøren Brunak
Thank you!
PS: I have an open postdoc position
