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Medical text mining
Linking diseases, drugs, and
adverse reactions
Lars Juhl Jensen
structured data
Jensen et al., Nature Reviews Genetics, 2012
statistical overview
Jensen et al., Nature Communications, 2014
comorbidity
Jensen et al., Nature Reviews Genetics, 2012
diagnosis trajectories
Jensen et al., Nature Communications, 2014
reimbursement
unstructured data
clinical narrative
free text
Danish
busy doctors
abbreviations
misspellings
unnatural language
too much to read
text mining
computer
as smart as a dog
teach it specific tricks
named entity recognition
comprehensive dictionary
synonyms
orthographic variants
drugs
ATC
misspellings
Clozapine
Clozapine
clozapi
n
clossapi
n
klozapin
e
chlosapi
n
chlosapi
ne
chlozapi
n
chlozapi
ne
klossapi
n
closapin
e
klozapi
nklosapi
n
diseases
ICD10
no synonyms
Disease Ontology
not in Danish
adverse drug reactions
MedDRA
not in Danish
“black list”
pest eller kolera
pharmacovigilance
clinical trials
spontaneous reports
underreporting
text/data mining
medication
Jensen et al., Nature Reviews Genetics, 2012
adverse events
hand-crafted rules
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
recall known ADRs
estimate frequencies
Eriksson et al., Drug Safety, 2014
discover new ADRs
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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Medical text mining: Linking diseases, drugs, and adverse reactions