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

Page 1: 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

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structured data

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Jensen et al., Nature Reviews Genetics, 2012

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unstructured data

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central registries

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individual hospitals

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opt-out

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opt-in

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Danish registries

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civil registration system

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CPR number

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established in 1968

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Jensen et al., Nature Reviews Genetics, 2012

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national discharge registry

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14 years

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6.2 million patients

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45 million admissions

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68 million records

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119 million diagnosis

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ICD-10

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Jensen et al., Nature Reviews Genetics, 2012

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not research

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reimbursement

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diagnosis trajectories

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naïve approach

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comorbidity

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Jensen et al., Nature Reviews Genetics, 2012

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confounding factors

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“known knowns”

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gender

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age

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type of hospital encounter

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Jensen et al., Nature Communications, 2014

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“known unknowns”

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smoking

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diet

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“unknown unknowns”

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reporting biases

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matched controls

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temporal correlations

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multiple testing

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trajectories

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Jensen et al., Nature Communications, 2014

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trajectory networks

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Jensen et al., Nature Communications, 2014

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key diagnoses

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Jensen et al., Nature Communications, 2014

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direct medical implications

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electronic health records

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structured data

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Jensen et al., Nature Reviews Genetics, 2012

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unstructured data

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free text

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Danish

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busy doctors

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typos

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psychiatric patients

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text mining

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computer

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as smart as a dog

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teach it specific tricks

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comprehensive dictionary

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diseases

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drugs

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adverse drug reactions

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expansion rules

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Clozapineclozapi

n

clossapin

klozapine

chlosapin

chlosapine

chlozapin

chlozapine

klossapin

closapine

klozapinklosapi

n

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“negative modifiers”

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negations

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delusions

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pharmacovigilance

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structured data

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medication

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semi-structured data

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drug indications

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known ADRs

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unstructured data

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adverse drug reactions

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statistical correlations

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hand-crafted rules

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Eriksson et al., Drug Safety, 2014

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Eriksson et al., Drug Safety, 2014

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Eriksson et al., Drug Safety, 2014

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Eriksson et al., Drug Safety, 2014

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known ADRs

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ADR frequencies

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Eriksson et al., Drug Safety, 2014

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detect new ADRs

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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

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