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Network biology - Large-scale biomedical data and text mining
 

Network biology - Large-scale biomedical data and text mining

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    Network biology - Large-scale biomedical data and text mining Network biology - Large-scale biomedical data and text mining Presentation Transcript

    • Network biologyLarge-scale biomedical data and text mining Lars Juhl Jensen
    • three parts
    • one thing in common
    • guilt by association
    • Part 1protein networks
    • Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
    • >1100 genomes
    • genomic context
    • gene fusion
    • Korbel et al., Nature Biotechnology, 2004
    • experimental data
    • Jensen & Bork, Science, 2008
    • curated knowledge
    • Letunic & Bork, Trends in Biochemical Sciences, 2008
    • many data types
    • many databases
    • different formats
    • different identifiers
    • variable quality
    • quality scores
    • von Mering et al., Nucleic Acids Research, 2005
    • calibrate vs. gold standard
    • von Mering et al., Nucleic Acids Research, 2005
    • orthology transfer
    • Part 2literature mining
    • >10 km
    • too much to read
    • computer
    • as smart as a dog
    • teach it specific tricks
    • named entity recognition
    • identify the concepts
    • proteins
    • compartments
    • tissues
    • diseases
    • comprehensive lexicon
    • orthographic variation
    • “black list”
    • information extraction
    • co-mentioning
    • http://diseases.jensenlab.org
    • abstracts
    • restricted full-text access
    • collaborate with publishers
    • Part 3medical informatics
    • electronic health records
    • Jensen et al., Nature Reviews Genetics, 2012
    • structured data
    • Jensen et al., Nature Reviews Genetics, 2012
    • unstructured data
    • in Danish
    • by busy doctors
    • about psychiatric patients
    • comorbidity
    • Jensen et al., Nature Reviews Genetics, 2012
    • multiple testing
    • Roque et al., PLoS Computational Biology, 2011
    • patient clustering
    • Roque et al., PLoS Computational Biology, 2011
    • cluster characterization
    • Roque et al., PLoS Computational Biology, 2011
    • temporal correlation
    • medication
    • adverse drug events
    • pharmacovigilance
    • AcknowledgmentsSTRING Text mining EPR miningDamian Szklarczyk Sune Frankild Francisco S RoqueAndrea Franceschini Heiko Horn Peter B JensenMichael Kuhn Evangelos Pafilis Robert ErikssonMilan Simonovic Janos Binder Henriette SchmockAlexander Roth Reinhardt Schneider Marlene DalgaardPablo Minguez Sean O’Donoghue Massimo AndreattaTobias Doerks Thomas HansenManuel Stark Karen SøebyJean Muller Søren BredkjærPeer Bork Anders JuulChristian von Mering Thomas Werge Søren Brunak
    • larsjuhljensen
    • Thank you