biomedical text mining and network analysis
TRANSCRIPT
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Lars Juhl Jensen
Biomedical text miningand network analysis
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why text mining?
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data mining
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unstructured text
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too much to read
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biomedical literature
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>10 km
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electronic medical records
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in Danish
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named entity recognition
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comprehensive lexicon
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diseases
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drugs
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adverse drug reactions
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synonyms
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Clozapine
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Clozaril
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kidney failure
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renal failure
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expansion rules
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Clozapine
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Clozapineclozapi
n
clossapin
klozapine
chlosapin
chlosapine
chlozapin
chlozapine
klossapin
closapine
klozapinklosapi
n
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kidney failure
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failure of kidney
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EMR mining
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detailed phenotyping
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Roque et al., PLOS Computational Biology, 2011
3262638254947
Assigned codes
Text mined codes
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comorbidity
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Roque et al., PLOS Computational Biology, 2011
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patient stratification
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Roque et al., PLOS Computational Biology, 2011
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pharmacovigilance
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drugs
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adverse drug events
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temporal correlations
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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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molecular networks
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text mining
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data mining
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association networks
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web resources
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disease–gene associations
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diseases.jensenlab.org Frankild et al., Methods, 2015
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tissue expression
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tissues.jensenlab.org Santos et al., PeerJ, 2015
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subcellular localization
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Binder et al., Database, 2014compartments.jensenlab.org
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protein networks
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Szklarczyk et al., Nucleic Acids Research, 2015string-db.org
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chemical networks
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stitch-db.org
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questions?