the pragmatic text miner: from literature to electronic health records
TRANSCRIPT
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Lars Juhl Jensen
The pragmatic text miner
From 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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cyclin dependent kinase 1
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cyclin-dependent kinase 1
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“black list”
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SDS
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>10 km<10 hours
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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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compare
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quality metrics
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precision
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recall
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F-score
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manually annotated corpus
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use existing corpus
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not new
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make new corpus
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hard work
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natural language processing
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part-of-speech tagging
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semantic tagging
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sentence parsing
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Gene and protein names
Cue words for entity recognition
Verbs for relation extraction
[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]
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handle negations
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directionality
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high precision
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poor recall
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highly domain specific
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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 sampling
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manual inspection
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precision
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no recall
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relative recall
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compare methods
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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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benchmark
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associations good?
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tagging good enough
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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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experimental data
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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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STRING
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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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environments
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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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comorbidity
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Jensen et al., Nature Reviews Genetics, 2012
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Roque et al., PLoS Computational Biology, 2011
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in Danish
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by busy doctors
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confounding factors
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age and gender
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reporting bias
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temporal correlation
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diagnosis trajectories
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Jensen et al., in preparation, 2013
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pharmocovigilance
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adverse drug reactions
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Eriksson et al., in preparation, 2013
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ADR profiles
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Eriksson et al., in preparation, 2013
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ADR frequencies
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Eriksson et al., in preparation, 2013
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Acknowledgments
STRINGChristian von MeringDamian SzklarczykMichael KuhnManuel StarkSamuel ChaffronChris CreeveyJean MullerTobias DoerksPhilippe JulienAlexander RothMilan SimonovicJan KorbelBerend SnelMartijn HuynenPeer Bork
Text miningSune FrankildEvangelos PafilisAlberto SantosKalliopi TsafouJanos BinderLucia FaniniSarah FaulwetterChristina PavloudiJulia SchnetzerAikaterini VasileiadouHeiko HornMichael KuhnNigel BrownReinhard SchneiderSean O’Donoghue
EHR miningRobert ErikssonPeter Bjødstrup JensenAnders Boeck JensenFrancisco S. RoqueHenriette SchmockMarlene DalgaardMassimo AndreattaThomas HansenKaren SøebySøren BredkjærAnders JuulTudor OpreaPope MoseleyThomas WergeSøren Brunak
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