pragmatic text mining: from literature to electronic health records
TRANSCRIPT
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Lars Juhl Jensen
Pragmatic text miningFrom literature to electronic health
records
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why text mining?
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data mining
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guilt by association
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structured data
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unstructured text
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biomedical literature
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>10 km
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too much to read
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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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named entity recognition
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dictionary-based approach
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identification required
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dictionary
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cyclin dependent kinase 1
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CDC2
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expansion rules
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CDC2
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hCdc2
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flexible matching
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hyphens and spaces
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“black list”
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SDS
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efficient tagger
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Pafilis et al., PLOS ONE, 2013
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the formal way
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benchmark
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manually annotated corpus
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automatic tagging
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precision
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recall
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natural language processing
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Gene and protein namesCue words for entity recognitionVerbs for relation extraction
[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]
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hard work
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the pragmatic way
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“benchmark light”
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requires fewer calories
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non-annotated corpus
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automatic tagging
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random inspection
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precision
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no recall
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relative recall
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co-mentioning
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within documents
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within paragraphs
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within sentences
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weighted score
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unifying text & data
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web resources
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text mining
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curated knowledge
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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experimental data
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von Mering et al., Nucleic Acids Research, 2005
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computational predictions
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common identifiers
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quality scores
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proteins
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Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
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small molecules
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Kuhn et al., Nucleic Acids Research, 2012
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compartments
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compartments.jensenlab.org
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tissues
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tissues.jensenlab.org
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diseases
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electronic health records
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Jensen et al., Nature Reviews Genetics, 2012
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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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clinical narrative
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Danish
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busy doctors
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psychiatric patients
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pharmacovigilance
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structured data
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medication
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text mining
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drug indications
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adverse drug events
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temporal correlation
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complex filtering
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Eriksson et al., in submitted, 2013
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Eriksson et al., submitted, 2013
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
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AcknowledgmentsProtein networksChristian von MeringDamian SzklarczykMichael KuhnManuel StarkJean MullerTobias DoerksAlexander RothMilan SimonovicBerend SnelMartijn HuynenPeer Bork
Localization and diseaseSune FrankildAlberto SantosKalliopi TsafouJanos BinderReinhard SchneiderSean O’DonoghueElectronic health recordsRobert ErikssonThomas WergeSøren Brunak