mining biomedical texts
TRANSCRIPT
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Lars Juhl Jensen
>10 km
Mining biomedical texts
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exponential growth
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some things are constant
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~45 seconds per paper
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information retrieval
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find the relevant texts
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still 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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identify the concepts
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comprehensive lexicon
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small molecules
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proteins
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cellular components
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organisms
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diseases
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orthographic variation
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“black list”
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Reflect.ws
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augmented browsing
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browser add-on
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009O’Donoghue et al., Journal of Web Semantics, 2010
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Firefox
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Internet Explorer
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Google Chrome
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Safari
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Utopia Documents
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web services
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~150 years of publishing
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dead wood
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dead e-wood
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added value
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collaboration
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SciVerse application
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STITCH
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Kuhn et al., Nucleic Acids Research, 2010
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curated knowledge
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drug targets
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pathways
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Letunic & Bork, Trends in Biochemical Sciences, 2008
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experimental data
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physical interactions
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Jensen & Bork, Science, 2008
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text mining
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co-mentioning
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NLPNatural Language Processing
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abstracts
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full text
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restricted access
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collaboration
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electronic patient journals
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a hard problem
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in Danish
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no lexicon
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by busy doctors
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acronyms
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typos
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about psychiatric patients
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delusions
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domain specific system
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F20
F200
Negation
Family
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diagnoses
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patient stratification
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Roque et al., PLoS Computational Biology, 2011
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disease comorbidity
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Roque et al., PLoS Computational Biology, 2011
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medication
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adverse drug events
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pharmacovigilance
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phenotype
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genotype
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Reflect.wsSune Frankild
Heiko HornEvangelos Pafilis
Michael KuhnReinhardt Schneider
Sean O’Donoghue
SciVerse appJuan-Carlos Silla-Castro
Sean O’Donoghue
EPJ-miningFrancisco S RoquePeter B JensenRobert ErikssonHenriette SchmockMarlene DalgaardMassimo AndreattaThomas HansenKaren SøebySøren BredkjærAnders JuulThomas WergeSøren Brunak
Thank you!
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larsjuhljensen